diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 3d73ffc63ee4c719f751d19c9607e261acbabcc8..b91e58a83f43476d985fc513a98a77c943ce8789 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -16,6 +16,8 @@ src/COMPRESS/* @akohlmey src/GPU/* @ndtrung81 src/KOKKOS/* @stanmoore1 src/KIM/* @ellio167 +src/LATTE/* @cnegre +src/SPIN/* @julient31 src/USER-CGDNA/* @ohenrich src/USER-CGSDK/* @akohlmey src/USER-COLVARS/* @giacomofiorin @@ -43,3 +45,15 @@ src/USER-MISC/*_grem.* @dstelter92 # tools tools/msi2lmp/* @akohlmey +tools/emacs/* @HaoZeke + +# cmake +cmake/* @junghans @rbberger + +# python +python/* @rbberger + +# docs +doc/utils/*/* @rbberger +doc/Makefile @rbberger +doc/README @rbberger diff --git a/README b/README index a258a335e934743df088d3e36cb1bc756377096b..784b1cb13ea9abfc852cf790b1ed40c579305619 100644 --- a/README +++ b/README @@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories: README this file LICENSE the GNU General Public License (GPL) bench benchmark problems -couple code coupling examples using LAMMPS as a library +cmake CMake build system doc documentation examples simple test problems lib libraries LAMMPS can be linked with diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 4df2ddd0752bae38a0bce6d7cd797dc0c1b18fb1..f4d3cac5d2d1e67d71c48508c7349adddbd4638b 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -6,11 +6,13 @@ cmake_minimum_required(VERSION 2.8.12) project(lammps CXX) set(SOVERSION 0) -set(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src) -set(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib) -set(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib) +get_filename_component(LAMMPS_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src ABSOLUTE) +get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib ABSOLUTE) +get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) +get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE) -#To not conflict with old Makefile build system, we build everything here + +# To avoid conflicts with the conventional Makefile build system, we build everything here file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/*.cpp) file(GLOB LMP_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp) list(REMOVE_ITEM LIB_SOURCES ${LMP_SOURCES}) @@ -23,21 +25,23 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) -file(GLOB SRC_FILES ${LAMMPS_SOURCE_DIR}/*.cpp) -list(SORT SRC_FILES) -# check for files installed by make-based buildsystem -# only run this time consuming check if there are new files -if(NOT SRC_FILES STREQUAL SRC_FILES_CACHED) - file(GLOB SRC_PKG_FILES ${LAMMPS_SOURCE_DIR}/*/*.cpp) - message(STATUS "Running check for installed package (this might take a while)") - foreach(_SRC SRC_PKG_FILES) - get_filename_component(FILENAME "${_SRC}" NAME) - if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) - message(FATAL_ERROR "Found packages installed by the make-based buildsystem, please run 'make -C ${LAMMPS_SOURCE_DIR} no-all purge'") - endif() - endforeach() - set(SRC_FILES_CACHED "${SRC_FILES}" CACHE INTERNAL "List of file in LAMMPS_SOURCE_DIR" FORCE) -endif() +# check for files auto-generated by make-based buildsystem +# this is fast, so check for it all the time +message(STATUS "Running check for auto-generated files from make-based build system") +file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h) +list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h) +foreach(_SRC ${SRC_AUTOGEN_FILES}) + get_filename_component(FILENAME "${_SRC}" NAME) + if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found header file(s) generated by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${LAMMPS_SOURCE_DIR} purge\n" + "to remove\n" + "########################################################################") + endif() +endforeach() ###################################################################### # compiler tests @@ -49,13 +53,59 @@ if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict") endif() +# GNU compiler features +if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + option(ENABLE_COVERAGE "Enable code coverage" OFF) + mark_as_advanced(ENABLE_COVERAGE) + if(ENABLE_COVERAGE) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage") + endif() + option(ENABLE_SANITIZE_ADDRESS "Enable address sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_ADDRESS) + if(ENABLE_SANITIZE_ADDRESS) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address") + endif() + option(ENABLE_SANITIZE_UNDEFINED "Enable undefined behavior sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_UNDEFINED) + if(ENABLE_SANITIZE_UNDEFINED) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=undefined") + endif() + option(ENABLE_SANITIZE_THREAD "Enable thread sanitizer" OFF) + mark_as_advanced(ENABLE_SANITIZE_THREAD) + if(ENABLE_SANITIZE_THREAD) + set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=thread") + endif() +endif() + ######################################################################## # User input options # ######################################################################## -option(BUILD_SHARED_LIBS "Build shared libs" OFF) -if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg - set(CMAKE_POSITION_INDEPENDENT_CODE ON) +option(BUILD_EXE "Build lmp binary" ON) +if(BUILD_EXE) + set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically") + mark_as_advanced(LAMMPS_MACHINE) + if(LAMMPS_MACHINE) + set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") + endif() endif() + +option(BUILD_LIB "Build LAMMPS library" OFF) +if(BUILD_LIB) + option(BUILD_SHARED_LIBS "Build shared library" OFF) + if(BUILD_SHARED_LIBS) # for all pkg libs, mpi_stubs and linalg + set(CMAKE_POSITION_INDEPENDENT_CODE ON) + endif() + set(LIB_SUFFIX "" CACHE STRING "Suffix to append to liblammps and pkg-config file") + mark_as_advanced(LIB_SUFFIX) + if(LIB_SUFFIX) + set(LIB_SUFFIX "_${LIB_SUFFIX}") + endif() +endif() + +if(NOT BUILD_EXE AND NOT BUILD_LIB) + message(FATAL_ERROR "You need to at least enable one of two following options: BUILD_LIB or BUILD_EXE") +endif() + option(DEVELOPER_MODE "Enable developer mode" OFF) mark_as_advanced(DEVELOPER_MODE) option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF) @@ -88,8 +138,11 @@ set_property(CACHE LAMMPS_SIZE_LIMIT PROPERTY STRINGS LAMMPS_SMALLBIG LAMMPS_BIG add_definitions(-D${LAMMPS_SIZE_LIMIT}) set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${LAMMPS_SIZE_LIMIT}") -set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS") -add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) +# posix_memalign is not available on Windows +if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS") + add_definitions(-DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN}) +endif() option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" OFF) if(LAMMPS_EXCEPTIONS) @@ -97,12 +150,6 @@ if(LAMMPS_EXCEPTIONS) set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -DLAMMPS_EXCEPTIONS") endif() -set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary and liblammps (WON'T enable any features automatically") -mark_as_advanced(LAMMPS_MACHINE) -if(LAMMPS_MACHINE) - set(LAMMPS_MACHINE "_${LAMMPS_MACHINE}") -endif() - option(CMAKE_VERBOSE_MAKEFILE "Verbose makefile" OFF) option(ENABLE_TESTING "Enable testing" OFF) @@ -110,19 +157,17 @@ if(ENABLE_TESTING) enable_testing() endif(ENABLE_TESTING) -option(ENABLE_ALL "Build all default packages" OFF) -set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ - REAX REPLICA RIGID SHOCK SNAP SRD) -set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE - USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO - USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF - USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC +set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR + KSPACE MANYBODY MC MEAM MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP + SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS + USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE + USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) +set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) - option(PKG_${PKG} "Build ${PKG} Package" ${ENABLE_ALL}) + option(PKG_${PKG} "Build ${PKG} Package" OFF) endforeach() foreach(PKG ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) option(PKG_${PKG} "Build ${PKG} Package" OFF) @@ -134,36 +179,24 @@ macro(pkg_depends PKG1 PKG2) endif() endmacro() +# "hard" dependencies between packages resulting +# in an error instead of skipping over files pkg_depends(MPIIO MPI) -pkg_depends(QEQ MANYBODY) pkg_depends(USER-ATC MANYBODY) pkg_depends(USER-LB MPI) -pkg_depends(USER-MISC MANYBODY) pkg_depends(USER-PHONON KSPACE) -pkg_depends(CORESHELL KSPACE) ###################################################### # packages with special compiler needs or external libs ###################################################### if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE) enable_language(Fortran) - list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) endif() if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM) enable_language(C) endif() -if(PKG_MSCG) - if (CMAKE_VERSION VERSION_LESS "3.1") - message(FATAL_ERROR "For the MSCG package you need at least cmake-3.1") - endif() - # starting with CMake 3.1 this is all you have to do to enforce C++11 - set(CMAKE_CXX_STANDARD 11) # C++11... - set(CMAKE_CXX_STANDARD_REQUIRED ON) #...is required... - set(CMAKE_CXX_EXTENSIONS OFF) #...without compiler extensions like gnu++11 -endif() - find_package(OpenMP QUIET) option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL) @@ -207,7 +240,7 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE) find_package(LAPACK) if(NOT LAPACK_FOUND) enable_language(Fortran) - file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.f) + file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/*.[fF]) add_library(linalg STATIC ${LAPACK_SOURCES}) set(LAPACK_LIBRARIES linalg) endif() @@ -219,7 +252,7 @@ if(PKG_PYTHON) add_definitions(-DLMP_PYTHON) include_directories(${PYTHON_INCLUDE_DIR}) list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY}) - if(BUILD_SHARED_LIBS) + if(BUILD_LIB AND BUILD_SHARED_LIBS) if(NOT PYTHON_INSTDIR) execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))" @@ -302,8 +335,8 @@ if(PKG_LATTE) message(STATUS "LATTE not found - we will build our own") include(ExternalProject) ExternalProject_Add(latte_build - URL https://github.com/lanl/LATTE/archive/v1.1.1.tar.gz - URL_MD5 cb86f1d2473ce00aa61ff6a023154b03 + URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz + URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ) @@ -340,13 +373,10 @@ if(PKG_USER-SMD) ExternalProject_Add(Eigen3_build URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz URL_MD5 1a47e78efe365a97de0c022d127607c3 - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DEIGEN_TEST_NOQT=ON - -DCMAKE_DISABLE_FIND_PACKAGE_LAPACK=ON -DCMAKE_DISABLE_FIND_PACKAGE_Cholmod=ON -DCMAKE_DISABLE_FIND_PACKAGE_Umfpack=ON -DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=ON - -DCMAKE_DISABLE_FIND_PACKAGE_PASTIX=ON -DCMAKE_DISABLE_FIND_PACKAGE_SPQR=ON -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON -DCMAKE_DISABLE_FIND_PACKAGE_CUDA=ON - -DCMAKE_DISABLE_FIND_PACKAGE_FFTW=ON -DCMAKE_DISABLE_FIND_PACKAGE_MPFR=ON -DCMAKE_DISABLE_FIND_PACKAGE_OpenGL=ON - ) - ExternalProject_get_property(Eigen3_build INSTALL_DIR) - set(EIGEN3_INCLUDE_DIR ${INSTALL_DIR}/include/eigen3) + CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" + ) + ExternalProject_get_property(Eigen3_build SOURCE_DIR) + set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR}) list(APPEND LAMMPS_DEPS Eigen3_build) else() find_package(Eigen3) @@ -402,26 +432,36 @@ endif() if(PKG_MSCG) find_package(GSL REQUIRED) - set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mscg) - set(MSCG_TARBALL ${LAMMPS_LIB_MSCG_BIN_DIR}/MS-CG-master.zip) - set(LAMMPS_LIB_MSCG_BIN_DIR ${LAMMPS_LIB_MSCG_BIN_DIR}/MSCG-release-master/src) - if(NOT EXISTS ${LAMMPS_LIB_MSCG_BIN_DIR}) - if(NOT EXISTS ${MSCG_TARBALL}) - message(STATUS "Downloading ${MSCG_TARBALL}") - file(DOWNLOAD - https://github.com/uchicago-voth/MSCG-release/archive/master.zip - ${MSCG_TARBALL} SHOW_PROGRESS) #EXPECTED_MD5 cannot be due due to master + option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF) + if(DOWNLOAD_MSCG) + include(ExternalProject) + if(NOT LAPACK_FOUND) + set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a") + endif() + ExternalProject_Add(mscg_build + URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz + URL_MD5 8c45e269ee13f60b303edd7823866a91 + SOURCE_SUBDIR src/CMake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS} + BUILD_COMMAND make mscg INSTALL_COMMAND "" + ) + ExternalProject_get_property(mscg_build BINARY_DIR) + set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a) + ExternalProject_get_property(mscg_build SOURCE_DIR) + set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src) + list(APPEND LAMMPS_DEPS mscg_build) + if(NOT LAPACK_FOUND) + file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS}) + add_dependencies(mscg_build linalg) + endif() + else() + find_package(MSCG) + if(NOT MSCG_FOUND) + message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it") endif() - message(STATUS "Unpacking ${MSCG_TARBALL}") - execute_process(COMMAND ${CMAKE_COMMAND} -E tar xvf ${MSCG_TARBALL} - WORKING_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/mscg) endif() - file(GLOB MSCG_SOURCES ${LAMMPS_LIB_MSCG_BIN_DIR}/*.cpp) - add_library(mscg STATIC ${MSCG_SOURCES}) - list(APPEND LAMMPS_LINK_LIBS mscg) - target_compile_options(mscg PRIVATE -DDIMENSION=3 -D_exclude_gromacs=1) - target_include_directories(mscg PUBLIC ${LAMMPS_LIB_MSCG_BIN_DIR}) - target_link_libraries(mscg ${GSL_LIBRARIES} ${LAPACK_LIBRARIES}) + list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES}) + include_directories(${MSCG_INCLUDE_DIRS}) endif() if(PKG_COMPRESS) @@ -430,6 +470,11 @@ if(PKG_COMPRESS) list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES}) endif() +# the windows version of LAMMPS requires a couple extra libraries +if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows") + list(APPEND LAMMPS_LINK_LIBS -lwsock32 -lpsapi) +endif() + ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## @@ -444,6 +489,9 @@ endforeach(HEADER) set(MATH_LIBRARIES "m" CACHE STRING "math library") mark_as_advanced( MATH_LIBRARIES ) include(CheckLibraryExists) +if (CMAKE_VERSION VERSION_LESS "3.4") + enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4 +endif() foreach(FUNC sin cos) check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES}) if(NOT FOUND_${FUNC}_${MATH_LIBRARIES}) @@ -461,23 +509,14 @@ RegisterStyles(${LAMMPS_SOURCE_DIR}) ############################################## # add sources of enabled packages ############################################ -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) +foreach(PKG ${DEFAULT_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) - # ignore PKG files which were manually installed in src folder - # headers are ignored during RegisterStyles file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) - foreach(PKG_FILE in ${${PKG}_SOURCES}) - get_filename_component(FNAME ${PKG_FILE} NAME) - list(REMOVE_ITEM LIB_SOURCES ${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() - - foreach(PKG_FILE in ${${PKG}_HEADERS}) - get_filename_component(FNAME ${PKG_FILE} NAME) - DetectAndRemovePackageHeader(${LAMMPS_SOURCE_DIR}/${FNAME}) - endforeach() + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) if(PKG_${PKG}) # detects styles in package and adds them to global list @@ -488,6 +527,17 @@ foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES}) endif() endforeach() +# dedicated check for entire contents of accelerator packages +foreach(PKG ${ACCEL_PACKAGES}) + set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) + + file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/*.cpp) + file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/*.h) + + # check for package files in src directory due to old make system + DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS}) +endforeach() + ############################################## # add lib sources of (simple) enabled packages ############################################ @@ -533,6 +583,41 @@ endif() # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### +if(PKG_CORESHELL) + set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL) + set(CORESHELL_SOURCES) + set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}") + + # detects styles which have a CORESHELL version + RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES) + + get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES) + + list(APPEND LIB_SOURCES ${CORESHELL_SOURCES}) + include_directories(${CORESHELL_SOURCES_DIR}) +endif() + +# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed +if(PKG_QEQ) + set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ) + file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h) + file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp) + + if(NOT PKG_MANYBODY) + list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h) + list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp) + endif() + set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}") + + foreach(MY_HEADER ${QEQ_HEADERS}) + AddStyleHeader(${MY_HEADER} FIX) + endforeach() + + get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES) + list(APPEND LIB_SOURCES ${QEQ_SOURCES}) + include_directories(${QEQ_SOURCES_DIR}) +endif() + if(PKG_USER-OMP) set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP) set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp @@ -544,8 +629,31 @@ if(PKG_USER-OMP) # detects styles which have USER-OMP version RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES) + get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES) + # manually add package dependent source files from USER-OMP that do not provide styles + + if(PKG_ASPHERE) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp) + endif() + + if(PKG_RIGID) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp) + endif() + + if(PKG_USER-REAXC) + list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp + ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp) + endif() + list(APPEND LIB_SOURCES ${USER-OMP_SOURCES}) include_directories(${USER-OMP_SOURCES_DIR}) endif() @@ -622,6 +730,10 @@ if(PKG_USER-INTEL) message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") endif() endif() + option(INJECT_KNL_FLAG "Inject flags for KNL build" OFF) + if(INJECT_KNL_FLAG) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xMIC-AVX512") + endif() option(INJECT_INTEL_FLAG "Inject OMG fast flags for USER-INTEL" ON) if(INJECT_INTEL_FLAG AND CMAKE_CXX_COMPILER_ID STREQUAL "Intel") if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) @@ -686,8 +798,7 @@ if(PKG_GPU) endif() option(CUDPP_OPT "Enable CUDPP_OPT" ON) - set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture") - set_property(CACHE GPU_ARCH PROPERTY STRINGS sm_10 sm_20 sm_30 sm_60) + set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)") file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) @@ -796,36 +907,173 @@ GenerateStyleHeaders(${LAMMPS_STYLE_HEADERS_DIR}) include_directories(${LAMMPS_SOURCE_DIR}) include_directories(${LAMMPS_STYLE_HEADERS_DIR}) +###################################### +# Generate lmpinstalledpkgs.h +###################################### +set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n") +set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n") +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) + if(PKG_${PKG}) + set(temp "${temp} \"${PKG}\",\n") + endif() +endforeach() +set(temp "${temp} NULL\n};\n#endif\n\n") +message(STATUS "Generating lmpinstalledpkgs.h...") +file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h") + ########################################### # Actually add executable and lib to build ############################################ -add_library(lammps ${LIB_SOURCES}) +get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) +list (FIND LANGUAGES "Fortran" _index) +if (${_index} GREATER -1) + list(APPEND LAMMPS_LINK_LIBS ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}) +endif() list(REMOVE_DUPLICATES LAMMPS_LINK_LIBS) -target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) -if(LAMMPS_DEPS) - add_dependencies(lammps ${LAMMPS_DEPS}) +if(BUILD_LIB) + add_library(lammps ${LIB_SOURCES}) + target_link_libraries(lammps ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lammps ${LAMMPS_DEPS}) + endif() + set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LIB_SUFFIX}) + if(BUILD_SHARED_LIBS) + set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) + install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) + configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc @ONLY) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + endif() +else() + list(APPEND LMP_SOURCES ${LIB_SOURCES}) endif() -set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE}) -if(BUILD_SHARED_LIBS) - set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION}) - install(TARGETS lammps LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) - install(FILES ${LAMMPS_SOURCE_DIR}/library.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps) - configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY) - install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) + +if(BUILD_EXE) + add_executable(lmp ${LMP_SOURCES}) + if(BUILD_LIB) + target_link_libraries(lmp lammps) + else() + target_link_libraries(lmp ${LAMMPS_LINK_LIBS}) + if(LAMMPS_DEPS) + add_dependencies(lmp ${LAMMPS_DEPS}) + endif() + endif() + + set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) + install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) + if(ENABLE_TESTING) + add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) + endif() endif() -add_executable(lmp ${LMP_SOURCES}) -target_link_libraries(lmp lammps) -set_target_properties(lmp PROPERTIES OUTPUT_NAME lmp${LAMMPS_MACHINE}) -install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) -if(ENABLE_TESTING) - add_test(ShowHelp lmp${LAMMPS_MACHINE} -help) +############################################################################### +# Build documentation +############################################################################### +option(BUILD_DOC "Build LAMMPS documentation" OFF) +if(BUILD_DOC) + include(ProcessorCount) + ProcessorCount(NPROCS) + find_package(PythonInterp 3 REQUIRED) + + set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv) + + file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/*.txt) + file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt) + list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES}) + + add_custom_command( + OUTPUT docenv + COMMAND ${VIRTUALENV} docenv + ) + + set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin) + + add_custom_command( + OUTPUT requirements.txt + DEPENDS docenv + COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt + COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade + COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters + ) + + set(RST_FILES "") + set(RST_DIR ${CMAKE_BINARY_DIR}/rst) + file(MAKE_DIRECTORY ${RST_DIR}) + foreach(TXT_FILE ${DOC_SOURCES}) + get_filename_component(FILENAME ${TXT_FILE} NAME_WE) + set(RST_FILE ${RST_DIR}/${FILENAME}.rst) + list(APPEND RST_FILES ${RST_FILE}) + add_custom_command( + OUTPUT ${RST_FILE} + DEPENDS requirements.txt docenv ${TXT_FILE} + COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE} + ) + endforeach() + + add_custom_command( + OUTPUT html + DEPENDS ${RST_FILES} + COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR} + COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html + ) + + add_custom_target( + doc ALL + DEPENDS html + SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES} + ) + + install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR}) endif() -################################## +############################################################################### +# Install potential files in data directory +############################################################################### +set(LAMMPS_POTENTIALS_DIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps/potentials) +install(DIRECTORY ${LAMMPS_SOURCE_DIR}/../potentials DESTINATION ${CMAKE_INSTALL_DATADIR}/lammps/potentials) + +configure_file(etc/profile.d/lammps.sh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh @ONLY) +configure_file(etc/profile.d/lammps.csh.in ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh @ONLY) +install( + FILES ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.sh + ${CMAKE_BINARY_DIR}/etc/profile.d/lammps.csh + DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d +) + +############################################################################### +# Testing +# +# Requires latest gcovr (for GCC 8.1 support):# +# pip install git+https://github.com/gcovr/gcovr.git +############################################################################### +if(ENABLE_COVERAGE) + find_program(GCOVR_BINARY gcovr) + find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY) + + if(GCOVR_FOUND) + get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE) + + add_custom_target( + gen_coverage_xml + COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Generating XML Coverage Report..." + ) + + add_custom_target( + gen_coverage_html + COMMAND ${GCOVR_BINARY} -s --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} + COMMENT "Generating HTML Coverage Report..." + ) + endif() +endif() + +############################################################################### # Print package summary -################################## -foreach(PKG ${DEFAULT_PACKAGES} ${OTHER_PACKAGES} ${ACCEL_PACKAGES}) +############################################################################### +foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES}) if(PKG_${PKG}) message(STATUS "Building package: ${PKG}") endif() @@ -834,7 +1082,7 @@ endforeach() string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS) include(FeatureSummary) -feature_summary(INCLUDE_QUIET_PACKAGES WHAT ALL) +feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> Build type ${CMAKE_BUILD_TYPE} Install path ${CMAKE_INSTALL_PREFIX} @@ -872,13 +1120,17 @@ message(STATUS "Link libraries: ${LAMMPS_LINK_LIBS}") if(BUILD_MPI) message(STATUS "Using mpi with headers in ${MPI_CXX_INCLUDE_PATH} and ${MPI_CXX_LIBRARIES}") endif() -if(ENABLED_GPU) +if(PKG_GPU) message(STATUS "GPU Api: ${GPU_API}") if(GPU_API STREQUAL "CUDA") message(STATUS "GPU Arch: ${GPU_ARCH}") elseif(GPU_API STREQUAL "OpenCL") message(STATUS "OCL Tune: ${OCL_TUNE}") endif() + message(STATUS "GPU Precision: ${GPU_PREC}") +endif() +if(PKG_KOKKOS) + message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}") endif() if(PKG_KSPACE) message(STATUS "Using ${FFT} as FFT") diff --git a/cmake/Modules/FindMSCG.cmake b/cmake/Modules/FindMSCG.cmake new file mode 100644 index 0000000000000000000000000000000000000000..311ff7803836aa43c2c48bd4040a60686b1803db --- /dev/null +++ b/cmake/Modules/FindMSCG.cmake @@ -0,0 +1,22 @@ +# - Find mscg +# Find the native MSCG headers and libraries. +# +# MSCG_INCLUDE_DIRS - where to find mscg.h, etc. +# MSCG_LIBRARIES - List of libraries when using mscg. +# MSCG_FOUND - True if mscg found. +# + +find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg) + +find_library(MSCG_LIBRARY NAMES mscg) + +set(MSCG_LIBRARIES ${MSCG_LIBRARY}) +set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR}) + +include(FindPackageHandleStandardArgs) +# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE +# if all listed variables are TRUE + +find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR) + +mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY ) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index c6f580f4632d92fabc4fe6d2b95464b18a5c9487..29ea3725972ce2e1166ef70297c3d6067e90c769 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -45,14 +45,10 @@ function(FindStyleHeadersExt path style_class extension headers sources) endfunction(FindStyleHeadersExt) function(CreateStyleHeader path filename) - math(EXPR N "${ARGC}-2") - set(temp "") - if(N GREATER 0) - math(EXPR ARG_END "${ARGC}-1") - - foreach(IDX RANGE 2 ${ARG_END}) - list(GET ARGV ${IDX} FNAME) + if(ARGC GREATER 2) + list(REMOVE_AT ARGV 0 1) + foreach(FNAME ${ARGV}) get_filename_component(FNAME ${FNAME} NAME) set(temp "${temp}#include \"${FNAME}\"\n") endforeach() @@ -107,35 +103,6 @@ function(RegisterStyles search_path) FindStyleHeaders(${search_path} REGION_CLASS region_ REGION ) # region ) # domain endfunction(RegisterStyles) -function(RemovePackageHeader headers pkg_header) - get_property(hlist GLOBAL PROPERTY ${headers}) - list(REMOVE_ITEM hlist ${pkg_header}) - set_property(GLOBAL PROPERTY ${headers} "${hlist}") -endfunction(RemovePackageHeader) - -function(DetectAndRemovePackageHeader fname) - RemovePackageHeader(ANGLE ${fname}) - RemovePackageHeader(ATOM_VEC ${fname}) - RemovePackageHeader(BODY ${fname}) - RemovePackageHeader(BOND ${fname}) - RemovePackageHeader(COMMAND ${fname}) - RemovePackageHeader(COMPUTE ${fname}) - RemovePackageHeader(DIHEDRAL ${fname}) - RemovePackageHeader(DUMP ${fname}) - RemovePackageHeader(FIX ${fname}) - RemovePackageHeader(IMPROPER ${fname}) - RemovePackageHeader(INTEGRATE ${fname}) - RemovePackageHeader(KSPACE ${fname}) - RemovePackageHeader(MINIMIZE ${fname}) - RemovePackageHeader(NBIN ${fname}) - RemovePackageHeader(NPAIR ${fname}) - RemovePackageHeader(NSTENCIL ${fname}) - RemovePackageHeader(NTOPO ${fname}) - RemovePackageHeader(PAIR ${fname}) - RemovePackageHeader(READER ${fname}) - RemovePackageHeader(REGION ${fname}) -endfunction(DetectAndRemovePackageHeader) - function(RegisterStylesExt search_path extension sources) FindStyleHeadersExt(${search_path} ANGLE_CLASS ${extension} ANGLE ${sources}) FindStyleHeadersExt(${search_path} ATOM_CLASS ${extension} ATOM_VEC ${sources}) @@ -181,3 +148,21 @@ function(GenerateStyleHeaders output_path) GenerateStyleHeader(${output_path} READER reader ) # read_dump GenerateStyleHeader(${output_path} REGION region ) # domain endfunction(GenerateStyleHeaders) + +function(DetectBuildSystemConflict lammps_src_dir) + if(ARGC GREATER 1) + list(REMOVE_AT ARGV 0) + foreach(SRC_FILE ${ARGV}) + get_filename_component(FILENAME ${SRC_FILE} NAME) + if(EXISTS ${lammps_src_dir}/${FILENAME}) + message(FATAL_ERROR "\n########################################################################\n" + "Found package(s) installed by the make-based build system\n" + "\n" + "Please run\n" + "make -C ${lammps_src_dir} no-all purge\n" + "to uninstall\n" + "########################################################################") + endif() + endforeach() + endif() +endfunction(DetectBuildSystemConflict) diff --git a/cmake/README.md b/cmake/README.md index cc67cceb52ec7b40327af88b52709eda7a6c1416..b6644ffda959c45faec16e89e0a6a3275725c796 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -1,19 +1,1663 @@ -cmake-buildsystem ------------------ +# Building LAMMPS using CMake -To use the cmake build system instead of the make-driven one, do: +LAMMPS recently acquired support for building with CMake thanks to the efforts +of Christoph Junghans (LANL) and Richard Berger (Temple U). One of the key +strengths of CMake is that it can generate the necessary build system files of +your own personal preference. It also enables using common development IDEs such +as Eclipse, Visual Studio, QtCreator, Xcode and many more for LAMMPS +development. + +CMake can both be used as a command-line (CLI) utility `cmake` or through one of +its GUIs. `ccmake` is a text-based ui to configure and build CMake projects. +`cmake-gui` is a graphical frontend for running CMake operations that works on +Linux desktop environments, Windows and MacOS X. + +The following is a tutorial-style introduction in using the CMake system. It +should give you the necessary foundation to understand how to do the most common +tasks, act as a reference and provide examples of typical use cases. + +## Table of Contents + + * [Quick Start for the Impatient](#quick-start-for-the-impatient) + * [Building LAMMPS using cmake](#building-lammps-using-cmake-1) + * [Prerequisites](#prerequisites) + * [Build directory vs. Source Directory](#build-directory-vs-source-directory) + * [Defining and using presets](#defining-and-using-presets) + * [Reference](#reference) + * [Common CMAKE Configuration Options](#common-cmake-configuration-options) + * [LAMMPS Configuration Options](#lammps-configuration-options) + * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages) + * [Default Packages](#default-packages) + * [Other Packages](#other-packages) + * [User Packages](#user-packages) + * [Package-Specific Configuration Options](#package-specific-configuration-options) + * [KSPACE Package](#kspace-package) + * [MKL](#mkl) + * [FFTW2](#fftw2) + * [FFTW3](#fftw3) + * [LAPACK](#lapack) + * [PYTHON Package](#python-package) + * [GPU Package](#gpu-package) + * [VORONOI Package](#voronoi-package) + * [USER-SMD Package](#user-smd-package) + * [Optional Features](#optional-features) + * [zlib support](#zlib-support) + * [JPEG support](#jpeg-support) + * [PNG support](#png-support) + * [GZIP support](#gzip-support) + * [FFMPEG support](#ffmpeg-support) + * [Compilers](#compilers) + * [Building with GNU Compilers](#building-with-gnu-compilers) + * [Building with Intel Compilers](#building-with-intel-compilers) + * [Building with LLVM/Clang Compilers](#building-with-llvmclang-compilers) + * [Examples](#examples) + + +## Quick Start for the Impatient +If you want to skip ahead and just run the compilation using `cmake`, please +find a minimal example below. Together with the options reference below, this +should get you started. + +```bash +git clone https://github.com/lammps/lammps.git +mkdir lammps/build +cd lammps/build +cmake ../cmake [-DOPTION_A=VALUE_A -DOPTION_B=VALUE_B ...] +make +``` + +# Building LAMMPS using `cmake` + +## Prerequisites +This tutorial assumes you are running in a command-line environment using a +shell like Bash. + +* Linux: any terminal window will work +* MacOS X: launch the Terminal app +* Windows 10: install and run "Bash on Windows" (aka Ubuntu on Windows) + +Before we start, please download the latest and greatest version of LAMMPS from +GitHub. You can either download it as a tarball or ZIP file, or via git. When +you start with a fresh lammps directory, the contents should look like this: + +```bash +$ ls +bench doc lib potentials README tools +cmake examples LICENSE python src +``` + +## Build directory vs. Source Directory + +By using CMake we separate building LAMMPS into multiple phases: + +1. **Configuration**: define which features we want to enable/disable and how it should be compiled +2. **Compilation**: compile each source file and generate binaries and libraries based on the configuration +3. **Installation** (Optional): finally we can install the generated binaries on our system + +In the GNU Make based build system of LAMMPS, configuration occurs by running +special make targets like `make yes-MOLECULAR`. These targets modify the +**source directory** (`src/`) directory by copying package files and patching +Makefile. In some cases you are force to manually edit Makefiles to add compiler +options and/or correct include directory and library paths. + +These edits and copy operations are no longer necessary when compiling with +CMake. The source directory stays untouched, so you compile LAMMPS in many +different variants using the same source code checkout. It enables true +**out-of-source** builds. + +When using Cmake, you can compile in **any** folder outside of the source +directory. Any working directory you choose becomes a so-called **build +directory**. All configuration files and compilation results are stored in this +folder. We recommend calling it something like `build/`. + +Let's have a look a quick example, where we get the greatest and latest version +of LAMMPS from GitHub via git: +```bash +git clone https://github.com/lammps/lammps.git +``` + +We then create a new `build` folder and make it our current working directory: +``` +mkdir lammps/build +cd lammps/build +``` + +To configure LAMMPS we run `cmake` inside of this folder. However it requires at +least one argument. `cmake` needs to read the LAMMPS `CMakeLists.txt` file to +know what to do. This file is located in the `cmake/` subdirectory of the +lammps checkout. To run `cmake` add the relative or absolute path to the `cmake/` +directory as first argument. + +E.g., if the current working directory is `lammps/build` you can specify the +relative path to `lammps/cmake` as follows: ``` -cmake /path/to/lammps/source/cmake +cmake ../cmake ``` -(please note the cmake directory as the very end) -To enable package, e.g. GPU do +You could also specify the absolute path: ``` -cmake /path/to/lammps/source/cmake -DENABLE_GPU=ON +cmake /path/to/my/lammps/folder/cmake ``` -cmake has many many options, do get an overview use the curses-based cmake interface, ccmake: +Please note: **This does NOT compile the code!** Running cmake only configures +the next build. It generates the necessary files to compile the code. On +Unix/Linux it defaults to generating Makefiles. You can also choose other output +formats to generate files for Eclipse, Xcode or Visual Studio which are +supported on other platorms. + +To compile LAMMPS once the Makefiles are generated, simply type `make` in the +build directory. + ``` -ccmake /path/to/lammps/source/cmake +make ``` -(Don't forget to press "g" for generate once you are done with configuring) +# Defining and using presets + +The CMake build exposes a lot of different options. In the old build system +some of the package selections were possible by using special make target like +`make yes-std` or `make no-lib`. Achieving the same result with cmake requires +specifying all options manually. This can quickly become a very long command +line that is hard to handle. While these could be stored in a simple script +file, there is another way of defining "presets" to compile LAMMPS in a certain +way. + +A preset is a regular CMake script file that can use constructs such as +variables, lists and for-loops to manipulate configuration options and create +an [*initial cache*](https://cmake.org/cmake/help/v3.12/manual/cmake.1.html). +Options must be set with the `CACHE` and `FORCE` flag to ensure they are +considered even during a second cmake run. + +Such a file can then be passed to cmake via the `-C` flag. Several examples of +presets can be found in the `cmake/presets` folder. + +```bash +# build LAMMPS with all "standard" packages which don't use libraries and enable GPU package +mkdir build +cd build +cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on +``` + +# Reference + +## Common CMAKE Configuration Options + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
CMAKE_INSTALL_PREFIXInstall location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do. +
CMAKE_BUILD_TYPEControls if debugging symbols are added to the generated binaries +
+
Release (default)
+
Debug
+
+
+ + +## LAMMPS Configuration Options + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
LAMMPS_SIZE_LIMITControls the integer sizes used by LAMMPS internally +
+
LAMMPS_SMALLBIG (default)
+
32bit , 64bit
+
LAMMPS_SMALLSMALL
+
32bit , 32bit
+
LAMMPS_BIGBIG
+
64bit , 64bit
+
+
LAMMPS_MEMALIGNcontrols the alignment of blocks of memory allocated by LAMMPS +
+
64 (default)
+
+
LAMMPS_EXCEPTIONScontrols whether LAMMPS dies after an error or throws a C++ exception. This is particularly useful when running through the C library interface, since an error + in LAMMPS then doesn't kill the parent process +
+
off (default)
+
on
+
+
LAMMPS_MACHINEallows appending a machine suffix to the generate LAMMPS binary +
+
*none* (default)
+
+
BUILD_SHARED_LIBScontrol whether to build LAMMPS as a shared-library +
+
off (default)
+
on
+
+
BUILD_DOCcontrol whether to build LAMMPS documentation +
+
off (default)
+
on
+
+
LAMMPS_LONGLONG_TO_LONGWorkaround if your system or MPI version does not recognize long long data types +
+
off (default)
+
on
+
+
+ +## Parallelization and Accelerator Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
BUILD_MPIcontrol whether to build LAMMPS with MPI support. This will look for + `mpicxx` in your path and use this MPI implementation. +
+
off (default)
+
on
+
+
BUILD_OMPcontrol whether to build LAMMPS with OpenMP support. +
+
off (default)
+
on
+
+
PKG_OPT + A handful of pair styles which are optimized for improved CPU performance on + single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. + +
+
off (default)
+
on
+
+
PKG_USER-OMP + Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace + styles which are altered to enable threading on many-core CPUs via OpenMP + directives. + +
+
off (default)
+
on
+
+
PKG_USER-INTEL + Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which + are optimized for Intel CPUs and KNLs (Knights Landing). + +
+
off (default)
+
on
+
+
PKG_GPU + Dozens of pair styles and a version of the PPPM long-range Coulombic solver + optimized for GPUs. All such styles have a “gpu” as a suffix in their style + name. The GPU code can be compiled with either CUDA or OpenCL, however the + OpenCL variants are no longer actively maintained and only the CUDA versions + are regularly tested. + +
+
off (default)
+
on
+
+
PKG_KOKKOSDozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. +
+
off (default)
+
on
+
+
+ +## Default Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PKG_ASPHEREComputes, time-integration fixes, and pair styles for aspherical particle models including ellipsoids, 2d lines, and 3d triangles. +
+
off (default)
+
on
+
+
PKG_BODYBody-style particles with internal structure. Computes, time-integration fixes, pair styles, as well as the body styles themselves. +
+
off (default)
+
on
+
+
PKG_CLASS2Bond, angle, dihedral, improper, and pair styles for the COMPASS CLASS2 molecular force field. +
+
off (default)
+
on
+
+
PKG_COLLOIDCoarse-grained finite-size colloidal particles. Pair styles and fix wall styles for colloidal interactions. Includes the Fast Lubrication Dynamics (FLD) method for hydrodynamic interactions, which is a simplified approximation to Stokesian dynamics. +
+
off (default)
+
on
+
+
PKG_COMPRESSCompressed output of dump files via the zlib compression library, using dump styles with a “gz” in their style name. +
+
off (default)
+
on
+
+
PKG_CORESHELLCompute and pair styles that implement the adiabatic core/shell model for polarizability. The pair styles augment Born, Buckingham, and Lennard-Jones styles with core/shell capabilities. The compute temp/cs command calculates the temperature of a system with core/shell particles. +
+
off (default)
+
on
+
+
PKG_DIPOLEAn atom style and several pair styles for point dipole models with short-range or long-range interactions. +
+
off (default)
+
on
+
+
PKG_GRANULARPair styles and fixes for finite-size granular particles, which interact with each other and boundaries via frictional and dissipative potentials. +
+
off (default)
+
on
+
+
PKG_KSPACEA variety of long-range Coulombic solvers, as well as pair styles which compute the corresponding short-range pairwise Coulombic interactions. These include Ewald, particle-particle particle-mesh (PPPM), and multilevel summation method (MSM) solvers. +
+
off (default)
+
on
+
+
PKG_MANYBODY + A variety of manybody and bond-order potentials. These include (AI)REBO, BOP, + EAM, EIM, Stillinger-Weber, and Tersoff potentials. + +
+
off (default)
+
on
+
+
PKG_MC + Several fixes and a pair style that have Monte Carlo (MC) or MC-like + attributes. These include fixes for creating, breaking, and swapping bonds, + for performing atomic swaps, and performing grand-canonical MC (GCMC) in + conjuction with dynamics. + +
+
off (default)
+
on
+
+
PKG_MEAM +

A pair style for the modified embedded atom (MEAM) potential.

+ +

Please note that the MEAM package has been superseded by the USER-MEAMC package, +which is a direct translation of the MEAM package to C++. USER-MEAMC contains +additional optimizations making it run faster than MEAM on most machines, while +providing the identical features and USER interface.

+
+
+
off (default)
+
on
+
+
PKG_MISC + A variety of compute, fix, pair, dump styles with specialized capabilities that + don’t align with other packages. + +
+
off (default)
+
on
+
+
PKG_MOLECULE + A large number of atom, pair, bond, angle, dihedral, improper styles that are + used to model molecular systems with fixed covalent bonds. The pair styles + include the Dreiding (hydrogen-bonding) and CHARMM force fields, and a TIP4P + water model. + +
+
off (default)
+
on
+
+
PKG_PERI + An atom style, several pair styles which implement different Peridynamics + materials models, and several computes which calculate diagnostics. + Peridynamics is a a particle-based meshless continuum model. + +
+
off (default)
+
on
+
+
PKG_QEQ + Several fixes for performing charge equilibration (QEq) via different + algorithms. These can be used with pair styles that perform QEq as part of + their formulation. + +
+
off (default)
+
on
+
+
PKG_REAX + A pair style which wraps a Fortran library which implements the ReaxFF + potential, which is a universal reactive force field. See the USER-REAXC + package for an alternate implementation in C/C++. Also a fix reax/bonds + command for monitoring molecules as bonds are created and destroyed. + +
+
off (default)
+
on
+
+
PKG_REPLICA + A collection of multi-replica methods which can be used when running multiple + LAMMPS simulations (replicas). See Section 6.5 for an overview of how to run + multi-replica simulations in LAMMPS. Methods in the package include nudged + elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated + dynamics (TAD), parallel tempering, and a verlet/split algorithm for + performing long-range Coulombics on one set of processors, and the remainder + of the force field calcalation on another set. + +
+
off (default)
+
on
+
+
PKG_RIGID + Fixes which enforce rigid constraints on collections of atoms or particles. + This includes SHAKE and RATTLE, as well as varous rigid-body integrators for a + few large bodies or many small bodies. Also several computes which calculate + properties of rigid bodies. + +
+
off (default)
+
on
+
+
PKG_SHOCK + Fixes for running impact simulations where a shock-wave passes through a + material. + +
+
off (default)
+
on
+
+
PKG_SNAP + A pair style for the spectral neighbor analysis potential (SNAP). SNAP is + methodology for deriving a highly accurate classical potential fit to a large + archive of quantum mechanical (DFT) data. Also several computes which analyze + attributes of the potential. + +
+
off (default)
+
on
+
+
PKG_SRD + A pair of fixes which implement the Stochastic Rotation Dynamics (SRD) method + for coarse-graining of a solvent, typically around large colloidal particles. + +
+
off (default)
+
on
+
+
+ +## Other Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PKG_KIMA pair_style kim command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, enabling any of them to be used in LAMMPS simulations. +
+
off (default)
+
on
+
+
PKG_PYTHONEnable support for Python scripting inside of LAMMPS. +
+
off (default)
+
on
+
+
PKG_MSCG + A fix mscg command which can parameterize a Multi-Scale Coarse-Graining (MSCG) + model using the open-source MS-CG library. + +
+
off (default)
+
on
+
+
PKG_MPIIO + Support for parallel output/input of dump and restart files via the MPIIO library. + +
+
off (default)
+
on
+
+
PKG_POEMS + A fix that wraps the Parallelizable Open source Efficient Multibody Software + (POEMS) library, which is able to simulate the dynamics of articulated body + systems. These are systems with multiple rigid bodies (collections of + particles) whose motion is coupled by connections at hinge points. + +
+
off (default)
+
on
+
+
PKG_LATTE + A fix command which wraps the LATTE DFTB code, so that molecular dynamics can + be run with LAMMPS using density-functional tight-binding quantum forces + calculated by LATTE. + +
+
off (default)
+
on
+
+
+ +## User Packages + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PKG_USER-ATC + ATC stands for atoms-to-continuum. This package implements a fix atc command + to either couple molecular dynamics with continuum finite element equations or + perform on-the-fly conversion of atomic information to continuum fields. + +
+
off (default)
+
on
+
+
PKG_USER-AWPMD + AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics. This package + implements an atom, pair, and fix style which allows electrons to be treated + as explicit particles in a classical molecular dynamics model. + +
+
off (default)
+
on
+
+
PKG_USER-CGDNA + Several pair styles, a bond style, and integration fixes for coarse-grained + models of single- and double-stranded DNA based on the oxDNA model of Doye, + Louis and Ouldridge at the University of Oxford. This includes Langevin-type + rigid-body integrators with improved stability. + +
+
off (default)
+
on
+
+
PKG_USER-CGSDK + Several pair styles and an angle style which implement the coarse-grained SDK + model of Shinoda, DeVane, and Klein which enables simulation of ionic liquids, + electrolytes, lipids and charged amino acids. + +
+
off (default)
+
on
+
+
PKG_USER-COLVARS + COLVARS stands for collective variables, which can be used to implement + various enhanced sampling methods, including Adaptive Biasing Force, + Metadynamics, Steered MD, Umbrella Sampling and Restraints. A fix colvars + command is implemented which wraps a COLVARS library, which implements these + methods. simulations. + +
+
off (default)
+
on
+
+
PKG_USER-DIFFRACTION + Two computes and a fix for calculating x-ray and electron diffraction + intensities based on kinematic diffraction theory. + +
+
off (default)
+
on
+
+
PKG_USER-DPD + DPD stands for dissipative particle dynamics. This package implements + coarse-grained DPD-based models for energetic, reactive molecular crystalline + materials. It includes many pair styles specific to these systems, including + for reactive DPD, where each particle has internal state for multiple species + and a coupled set of chemical reaction ODEs are integrated each timestep. + Highly accurate time integrators for isothermal, isoenergetic, isobaric and + isenthalpic conditions are included. These enable long timesteps via the + Shardlow splitting algorithm. + +
+
off (default)
+
on
+
+
PKG_USER-DRUDE + Fixes, pair styles, and a compute to simulate thermalized Drude oscillators as + a model of polarization. + +
+
off (default)
+
on
+
+
PKG_USER-EFF + EFF stands for electron force field which allows a classical MD code to model + electrons as particles of variable radius. This package contains atom, pair, + fix and compute styles which implement the eFF as described in A. + Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, 2010. The eFF + potential was first introduced by Su and Goddard, in 2007. + +
+
off (default)
+
on
+
+
PKG_USER-FEP + FEP stands for free energy perturbation. This package provides methods for + performing FEP simulations by using a fix adapt/fep command with soft-core + pair potentials, which have a “soft” in their style name. + +
+
off (default)
+
on
+
+
PKG_USER-H5MD + H5MD stands for HDF5 for MD. HDF5 is a portable, binary, self-describing file + format, used by many scientific simulations. H5MD is a format for molecular + simulations, built on top of HDF5. This package implements a dump h5md command + to output LAMMPS snapshots in this format. + +
+
off (default)
+
on
+
+
PKG_USER-LB + Fixes which implement a background Lattice-Boltzmann (LB) fluid, which can be + used to model MD particles influenced by hydrodynamic forces. + +
+
off (default)
+
on
+
+
PKG_USER-MANIFOLD + Several fixes and a “manifold” class which enable simulations of particles + constrained to a manifold (a 2D surface within the 3D simulation box). This is + done by applying the RATTLE constraint algorithm to formulate single-particle + constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of + the manifold) n = grad(g). + +
+
off (default)
+
on
+
+
PKG_USER-MEAMC + A pair style for the modified embedded atom (MEAM) potential translated from + the Fortran version in the MEAM package to plain C++. In contrast to the MEAM + package, no library needs to be compiled and the pair style can be + instantiated multiple times. + +
+
off (default)
+
on
+
+
PKG_USER-MESO + Several extensions of the the dissipative particle dynamics (DPD) method. + Specifically, energy-conserving DPD (eDPD) that can model non-isothermal + processes, many-body DPD (mDPD) for simulating vapor-liquid coexistence, and + transport DPD (tDPD) for modeling advection-diffusion-reaction systems. The + equations of motion of these DPD extensions are integrated through a modified + velocity-Verlet (MVV) algorithm. + +
+
off (default)
+
on
+
+
PKG_USER-MGPT + A pair style which provides a fast implementation of the quantum-based MGPT + multi-ion potentials. The MGPT or model GPT method derives from + first-principles DFT-based generalized pseudopotential theory (GPT) through a + series of systematic approximations valid for mid-period transition metals + with nearly half-filled d bands. The MGPT method was originally developed by + John Moriarty at LLNL. The pair style in this package calculates forces and + energies using an optimized matrix-MGPT algorithm due to Tomas Oppelstrup at + LLNL. + +
+
off (default)
+
on
+
+
PKG_USER-MISC + A potpourri of (mostly) unrelated features contributed to LAMMPS by users. + Each feature is a single fix, compute, pair, bond, angle, dihedral, improper, + or command style. + +
+
off (default)
+
on
+
+
PKG_USER-MOFFF + Pair, angle and improper styles needed to employ the MOF-FF force field by + Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force + field with the primary aim to simulate MOFs and related porous framework + materials, using spherical Gaussian charges. It is described in S. Bureekaew + et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. For the usage of MOF-FF see + the example in the example directory as well as the MOF+ website. + +
+
off (default)
+
on
+
+
PKG_USER-MOLFILE + A dump molfile command which uses molfile plugins that are bundled with the + VMD molecular visualization and analysis program, to enable LAMMPS to dump + snapshots in formats compatible with various molecular simulation tools. + +
+
off (default)
+
on
+
+
PKG_USER-NETCDF + Dump styles for writing NetCDF formatted dump files. NetCDF is a portable, + binary, self-describing file format developed on top of HDF5. The file + contents follow the AMBER NetCDF trajectory conventions + (http://ambermd.org/netcdf/nctraj.xhtml), but include extensions. + +
+
off (default)
+
on
+
+
PKG_USER-PHONON + A fix phonon command that calculates dynamical matrices, which can then be + used to compute phonon dispersion relations, directly from molecular dynamics + simulations. + +
+
off (default)
+
on
+
+
PKG_USER-QTB + Two fixes which provide a self-consistent quantum treatment of vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero point energy into the system, altering the energy power spectrum and the heat capacity to account for their quantum nature. This is useful when modeling systems at temperatures lower than their classical limits or when temperatures ramp across the classical limits in a simulation. + +
+
off (default)
+
on
+
+
PKG_USER-QUIP + A pair_style quip command which wraps the QUIP libAtoms library, which + includes a variety of interatomic potentials, including Gaussian Approximation + Potential (GAP) models developed by the Cambridge University group. + +
+
off (default)
+
on
+
+
PKG_USER-QMMM + A fix qmmm command which allows LAMMPS to be used in a QM/MM simulation, + currently only in combination with the Quantum ESPRESSO package. + +
+
off (default)
+
on
+
+
PKG_USER-REAXC + A pair style which implements the ReaxFF potential in C/C++ (in contrast to + the REAX package and its Fortran library). ReaxFF is universal reactive force + field. See the src/USER-REAXC/README file for more info on differences between + the two packages. Also two fixes for monitoring molecules as bonds are created + and destroyed. + +
+
off (default)
+
on
+
+
PKG_USER-SMD + An atom style, fixes, computes, and several pair styles which implements + smoothed Mach dynamics (SMD) for solids, which is a model related to smoothed + particle hydrodynamics (SPH) for liquids (see the USER-SPH package). + +
+
off (default)
+
on
+
+
PKG_USER-SMTBQ + A pair style which implements a Second Moment Tight Binding model with QEq + charge equilibration (SMTBQ) potential for the description of ionocovalent + bonds in oxides. + +
+
off (default)
+
on
+
+
PKG_USER-SPH + An atom style, fixes, computes, and several pair styles which implements + smoothed particle hydrodynamics (SPH) for liquids. See the related USER-SMD + package package for smooth Mach dynamics (SMD) for solids. + +
+
off (default)
+
on
+
+
PKG_USER-TALLY + Several compute styles that can be called when pairwise interactions are + calculated to tally information (forces, heat flux, energy, stress, etc) about + individual interactions. + +
+
off (default)
+
on
+
+
PKG_USER-UEF + A fix style for the integration of the equations of motion under extensional + flow with proper boundary conditions, as well as several supporting compute + styles and an output option. + +
+
off (default)
+
on
+
+
PKG_USER-VTK + A dump vtk command which outputs snapshot info in the VTK format, enabling + visualization by Paraview or other visualization packages. + +
+
off (default)
+
on
+
+
+ +## Package-Specific Configuration Options + +### KSPACE Package + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFT +

FFT library for KSPACE package

+

If either MKL or FFTW is selected cmake will try to locate these libraries automatically. To control which one should be used please see the options below for each FFT library.

+
+
+
KISSFFT
+
FFTW3
+
FFTW2
+
MKL
+
+
PACK_ARRAYOptimization for FFT +
+
PACK_ARRAY
+
PACK_POINTER
+
PACK_MEMCPY
+
+
+ +### MKL + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
MKL_INCLUDE_DIRS +
MKL_LIBRARIES +
+ +TODO static vs dynamic linking + +### FFTW2 + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFTW2_INCLUDE_DIRS +
FFTW2_LIBRARIES +
+ +### FFTW3 + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFTW3_INCLUDE_DIRS +
FFTW3_LIBRARIES +
+ +### LAPACK +TODO + +### PYTHON Package + + +### GPU Package +The GPU package builds a support library which can either use OpenCL or CUDA as +target API. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
GPU_APIAPI used by GPU package +
+
OpenCL (default)
+
CUDA
+
+
GPU_PRECPrecision size used by GPU package kernels +
+
SINGLE_DOUBLE
+
SINGLE_SINGLE
+
DOUBLE_DOUBLE
+
+
OCL_TUNE (OpenCL only)Tuning target for OpenCL driver code +
+
GENERIC (default)
+
INTEL (Intel CPU)
+
PHI (Intel Xeon Phi)
+
FERMI (NVIDIA)
+
KEPLER (NVIDIA)
+
CYPRESS (AMD)
+
+
GPU_ARCH (CUDA only)CUDA SM architecture targeted by GPU package +
+
sm_20 (Fermi)
+
sm_30 (Kepler)
+
sm_50 (Maxwell)
+
sm_60 (Pascal)
+
sm_70 (Volta)
+
+
CUDPP_OPT (CUDA only)Enable CUDA Performance Primitives Optimizations +
+
on (default)
+
off
+
+
+ +### VORONOI Package + +TODO + +### USER-SMD Package + +Requires a Eigen3 installation + + + + + + + + + + + + + + + + +
OptionDescriptionValues
EIGEN3_INCLUDE_DIR +
+ +## Optional Features + +### zlib support + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
ZLIB_INCLUDE_DIR +
ZLIB_LIBRARIES +
+ +### JPEG support + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
JPEG_INCLUDE_DIR +
JPEG_LIBRARIES +
+ +### PNG support +(requires zlib support) + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionValues
PNG_INCLUDE_DIR +
PNG_LIBRARIES +
+ +### GZIP support + +requires `gzip` to be in your `PATH` + + + + + + + + + + + + + + + + +
OptionDescriptionValues
GZIP_EXECUTABLE +
+ +### FFMPEG support + +requires `ffmpeg` to be in your `PATH` + + + + + + + + + + + + + + + + +
OptionDescriptionValues
FFMPEG_EXECUTABLE +
+ + +## Compilers + +By default, `cmake` will use your environment C/C++/Fortran compilers for a build. It uses the `CC`, `CXX` and `FC` environment variables to detect which compilers should be used. However, these values +will be cached after the first run of `cmake`. Subsequent runs of `cmake` will ignore changes in these environment variables. To ensure the correct values are used you avoid the cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, `CMAKE_Fortran_COMPILER` options directly. + + + + + + + + + + + + + + + + + + + + + + + + + + +
OptionDescriptionDefault
CMAKE_C_COMPILERC Compiler which should be used by CMakevalue of `CC` environment variable at first `cmake` run
CMAKE_CXX_COMPILERC++ compiler which should be used by CMake + value of `CXX` environment variable at first `cmake` run +
CMAKE_Fortran_COMPILERC++ compiler which should be used by CMake + value of `FC` environment variable at first `cmake` run +
+ +### Building with GNU Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran +``` + +### Building with Intel Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort +``` + + +### Building with LLVM/Clang Compilers + +```bash +cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang +``` + + +## Examples diff --git a/cmake/etc/profile.d/lammps.csh.in b/cmake/etc/profile.d/lammps.csh.in new file mode 100644 index 0000000000000000000000000000000000000000..def49bf75c0112503f7286dbb68843a258e993f3 --- /dev/null +++ b/cmake/etc/profile.d/lammps.csh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@ diff --git a/cmake/etc/profile.d/lammps.sh.in b/cmake/etc/profile.d/lammps.sh.in new file mode 100644 index 0000000000000000000000000000000000000000..acd75fa0cff7bae7013d8c32d8453e2083dc217d --- /dev/null +++ b/cmake/etc/profile.d/lammps.sh.in @@ -0,0 +1,2 @@ +# set environment for LAMMPS executables to find potential files +export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@} diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index c5e17017825c01bb59ec02597dd5a43957a69bba..400b7593cff4034539df766111dd53d6fbbeaac9 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -13,6 +13,6 @@ Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library URL: http://lammps.sandia.gov Version: Requires: -Libs: -L${libdir} -llammps@LAMMPS_MACHINE@ +Libs: -L${libdir} -llammps@LIB_SUFFIX@@ Libs.private: -lm Cflags: -I${includedir} @LAMMPS_API_DEFINES@ diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake new file mode 100644 index 0000000000000000000000000000000000000000..f7e90ddbb44153f12af59cf4f51f64afe0c3317a --- /dev/null +++ b/cmake/presets/all_off.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake new file mode 100644 index 0000000000000000000000000000000000000000..2c6f67904e6d50ff785ccb67664a4136fb737470 --- /dev/null +++ b/cmake/presets/all_on.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${ALL_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake new file mode 100644 index 0000000000000000000000000000000000000000..6c03d983f6e9989e50883d974973fd08323acb8e --- /dev/null +++ b/cmake/presets/manual_selection.cmake @@ -0,0 +1,69 @@ +set(PKG_ASPHERE OFF CACHE BOOL "" FORCE) +set(PKG_BODY OFF CACHE BOOL "" FORCE) +set(PKG_CLASS2 OFF CACHE BOOL "" FORCE) +set(PKG_COLLOID OFF CACHE BOOL "" FORCE) +set(PKG_COMPRESS OFF CACHE BOOL "" FORCE) +set(PKG_CORESHELL OFF CACHE BOOL "" FORCE) +set(PKG_DIPOLE OFF CACHE BOOL "" FORCE) +set(PKG_GPU OFF CACHE BOOL "" FORCE) +set(PKG_GRANULAR OFF CACHE BOOL "" FORCE) +set(PKG_KIM OFF CACHE BOOL "" FORCE) +set(PKG_KOKKOS OFF CACHE BOOL "" FORCE) +set(PKG_KSPACE OFF CACHE BOOL "" FORCE) +set(PKG_LATTE OFF CACHE BOOL "" FORCE) +set(PKG_LIB OFF CACHE BOOL "" FORCE) +set(PKG_MANYBODY OFF CACHE BOOL "" FORCE) +set(PKG_MC OFF CACHE BOOL "" FORCE) +set(PKG_MEAM OFF CACHE BOOL "" FORCE) +set(PKG_MISC OFF CACHE BOOL "" FORCE) +set(PKG_MOLECULE OFF CACHE BOOL "" FORCE) +set(PKG_MPIIO OFF CACHE BOOL "" FORCE) +set(PKG_MSCG OFF CACHE BOOL "" FORCE) +set(PKG_OPT OFF CACHE BOOL "" FORCE) +set(PKG_PERI OFF CACHE BOOL "" FORCE) +set(PKG_POEMS OFF CACHE BOOL "" FORCE) +set(PKG_PYTHOFF OFF CACHE BOOL "" FORCE) +set(PKG_QEQ OFF CACHE BOOL "" FORCE) +set(PKG_REAX OFF CACHE BOOL "" FORCE) +set(PKG_REPLICA OFF CACHE BOOL "" FORCE) +set(PKG_RIGID OFF CACHE BOOL "" FORCE) +set(PKG_SHOCK OFF CACHE BOOL "" FORCE) +set(PKG_SNAP OFF CACHE BOOL "" FORCE) +set(PKG_SRD OFF CACHE BOOL "" FORCE) +set(PKG_VOROFFOI OFF CACHE BOOL "" FORCE) + +set(PKG_USER OFF CACHE BOOL "" FORCE) +set(PKG_USER-ATC OFF CACHE BOOL "" FORCE) +set(PKG_USER-AWPMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-BOCS OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGDNA OFF CACHE BOOL "" FORCE) +set(PKG_USER-CGSDK OFF CACHE BOOL "" FORCE) +set(PKG_USER-COLVARS OFF CACHE BOOL "" FORCE) +set(PKG_USER-DIFFRACTIOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-DPD OFF CACHE BOOL "" FORCE) +set(PKG_USER-DRUDE OFF CACHE BOOL "" FORCE) +set(PKG_USER-EFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-FEP OFF CACHE BOOL "" FORCE) +set(PKG_USER-H5MD OFF CACHE BOOL "" FORCE) +set(PKG_USER-INTEL OFF CACHE BOOL "" FORCE) +set(PKG_USER-LB OFF CACHE BOOL "" FORCE) +set(PKG_USER-MANIFOLD OFF CACHE BOOL "" FORCE) +set(PKG_USER-MEAMC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MESO OFF CACHE BOOL "" FORCE) +set(PKG_USER-MGPT OFF CACHE BOOL "" FORCE) +set(PKG_USER-MISC OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE) +set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE) +set(PKG_USER-OMP OFF CACHE BOOL "" FORCE) +set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE) +set(PKG_USER-QTB OFF CACHE BOOL "" FORCE) +set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE) +set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMD OFF CACHE BOOL "" FORCE) +set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE) +set(PKG_USER-SPH OFF CACHE BOOL "" FORCE) +set(PKG_USER-TALLY OFF CACHE BOOL "" FORCE) +set(PKG_USER-UEF OFF CACHE BOOL "" FORCE) +set(PKG_USER-VTK OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake new file mode 100644 index 0000000000000000000000000000000000000000..cd603aa80450f29a6da3906188d711f8ae755404 --- /dev/null +++ b/cmake/presets/nolib.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake new file mode 100644 index 0000000000000000000000000000000000000000..36da89795756de1890c2a7b19e39cab56ea2daea --- /dev/null +++ b/cmake/presets/std.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/std_nolib.cmake b/cmake/presets/std_nolib.cmake new file mode 100644 index 0000000000000000000000000000000000000000..9bffefcbe00f205aa5aaa3d3724f958147fda38d --- /dev/null +++ b/cmake/presets/std_nolib.cmake @@ -0,0 +1,26 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${STANDARD_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() + +foreach(PKG ${PACKAGES_WITH_LIB}) + set(PKG_${PKG} OFF CACHE BOOL "" FORCE) +endforeach() diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake new file mode 100644 index 0000000000000000000000000000000000000000..cb81b6755836871025e5438c978e0eb8b673d8c4 --- /dev/null +++ b/cmake/presets/user.cmake @@ -0,0 +1,22 @@ +set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU + GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MEAM MISC + MOLECULE MPIIO MSCG OPT PERI POEMS + PYTHON QEQ REAX REPLICA RIGID SHOCK SNAP SRD VORONOI) + +set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS + USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD + USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO + USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE + USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB + USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-UEF USER-VTK) + +set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI + USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE + USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + +set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) + +foreach(PKG ${USER_PACKAGES}) + set(PKG_${PKG} ON CACHE BOOL "" FORCE) +endforeach() diff --git a/doc/Makefile b/doc/Makefile index 0a5dbe1e7d64be21628f6e85e0e72a7468752d57..81f362349950be2123d2da4bd14255e7f9f27739 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -9,6 +9,7 @@ TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/doc_anchor_check PYTHON = $(shell which python3) +VIRTUALENV = virtualenv HAS_PYTHON3 = NO HAS_VIRTUALENV = NO @@ -16,7 +17,13 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0) HAS_PYTHON3 = YES endif +ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0) +VIRTUALENV = virtualenv-3 +HAS_VIRTUALENV = YES +endif + ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0) +VIRTUALENV = virtualenv HAS_VIRTUALENV = YES endif @@ -42,11 +49,11 @@ help: # ------------------------------------------ -clean-all: +clean-all: clean rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe clean: - rm -rf $(RSTDIR) html + rm -rf $(RSTDIR) html old epub rm -rf spelling clean-spelling: @@ -150,7 +157,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST) @(\ mkdir -p $(RSTDIR) ; \ . $(VENV)/bin/activate ;\ - txt2rst $< > $@ ;\ + txt2rst -v $< > $@ ;\ deactivate ;\ ) @@ -158,7 +165,7 @@ $(VENV): @if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi @( \ - virtualenv -p $(PYTHON) $(VENV); \ + $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ pip install Sphinx; \ pip install sphinxcontrib-images; \ diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt new file mode 100644 index 0000000000000000000000000000000000000000..30e3343bd21c1203b8182f5f42dbab92a15c723b --- /dev/null +++ b/doc/src/Commands.txt @@ -0,0 +1,51 @@ +"Previous Section"_Run.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Packages.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html#comm) + +:line + +Commands :h2 + +These pages describe how a LAMMPS input script is formatted and the +commands in it are used to define a LAMMPS simulation. + + + + + +"LAMMPS input scripts"_Commands_input.html +"Parsing rules for input scripts"_Commands_parse.html +"Input script structure"_Commands_structure.html +"Commands by category"_Commands_category.html :all(b) + +"All commands"_Commands_all.html +"Fix commands"_Commands_fix.html +"Compute commands"_Commands_compute.html +"Pair commands"_Commands_pair.html +"Bond, angle, dihedral, improper commands"_Commands_bond.html +"KSpace solvers"_Commands_kspace.html :all(b) + + + diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt new file mode 100644 index 0000000000000000000000000000000000000000..13db1272b928e558ceda0853df22162945e6c6e5 --- /dev/null +++ b/doc/src/Commands_all.txt @@ -0,0 +1,128 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +All commands :h3 + +An alphabetic list of all LAMMPS commmands. + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"clear"_clear.html, +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"create_box"_create_box.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"dimension"_dimension.html, +"displace_atoms"_displace_atoms.html, +"dump"_dump.html, +"dump image"_dump_image.html, +"dump_modify"_dump_modify.html, +"dump movie"_dump_image.html, +"dump netcdf"_dump_netcdf.html, +"dump netcdf/mpiio"_dump_netcdf.html, +"dump vtk"_dump_vtk.html, +"echo"_echo.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"group"_group.html, +"group2ndx"_group2ndx.html, +"if"_if.html, +"info"_info.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"include"_include.html, +"jump"_jump.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"label"_label.html, +"lattice"_lattice.html, +"log"_log.html, +"mass"_mass.html, +"minimize"_minimize.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"molecule"_molecule.html, +"ndx2group"_group2ndx.html, +"neb"_neb.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"newton"_newton.html, +"next"_next.html, +"package"_package.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"partition"_partition.html, +"prd"_prd.html, +"print"_print.html, +"processors"_processors.html, +"python"_python.html, +"quit"_quit.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"region"_region.html, +"replicate"_replicate.html, +"rerun"_rerun.html, +"reset_ids"_reset_ids.html, +"reset_timestep"_reset_timestep.html, +"restart"_restart.html, +"run"_run.html, +"run_style"_run_style.html, +"set"_set.html, +"shell"_shell.html, +"special_bonds"_special_bonds.html, +"suffix"_suffix.html, +"tad"_tad.html, +"temper"_temper.html, +"temper/grem"_temper_grem.html, +"temper/npt"_temper_npt.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"timer"_timer.html, +"timestep"_timestep.html, +"uncompute"_uncompute.html, +"undump"_undump.html, +"unfix"_unfix.html, +"units"_units.html, +"variable"_variable.html, +"velocity"_velocity.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt new file mode 100644 index 0000000000000000000000000000000000000000..314260cb14bc582a5791912ac055ec50260878f1 --- /dev/null +++ b/doc/src/Commands_bond.txt @@ -0,0 +1,124 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Bond, angle, dihedral, and improper commands :h3 + +:line + +Bond_style potentials :h3,link(bond) + +All LAMMPS "bond_style"_bond_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_bond_none.html, +"zero"_bond_zero.html, +"hybrid"_bond_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_bond_class2.html, +"fene (iko)"_bond_fene.html, +"fene/expand (o)"_bond_fene_expand.html, +"gromos (o)"_bond_gromos.html, +"harmonic (ko)"_bond_harmonic.html, +"harmonic/shift (o)"_bond_harmonic_shift.html, +"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, +"morse (o)"_bond_morse.html, +"nonlinear (o)"_bond_nonlinear.html, +"oxdna/fene"_bond_oxdna.html, +"oxdna2/fene"_bond_oxdna.html, +"quartic (o)"_bond_quartic.html, +"table (o)"_bond_table.html :tb(c=4,ea=c) + +:line + +Angle_style potentials :h3,link(angle) + +All LAMMPS "angle_style"_angle_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_angle_none.html, +"zero"_angle_zero.html, +"hybrid"_angle_hybrid.html :tb(c=3,ea=c) + +"charmm (ko)"_angle_charmm.html, +"class2 (ko)"_angle_class2.html, +"cosine (o)"_angle_cosine.html, +"cosine/delta (o)"_angle_cosine_delta.html, +"cosine/periodic (o)"_angle_cosine_periodic.html, +"cosine/shift (o)"_angle_cosine_shift.html, +"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, +"cosine/squared (o)"_angle_cosine_squared.html, +"dipole (o)"_angle_dipole.html, +"fourier (o)"_angle_fourier.html, +"fourier/simple (o)"_angle_fourier_simple.html, +"harmonic (iko)"_angle_harmonic.html, +"quartic (o)"_angle_quartic.html, +"sdk"_angle_sdk.html, +"table (o)"_angle_table.html :tb(c=4,ea=c) + +:line + +Dihedral_style potentials :h3,link(dihedral) + +All LAMMPS "dihedral_style"_dihedral_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_dihedral_none.html, +"zero"_dihedral_zero.html, +"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c) + +"charmm (iko)"_dihedral_charmm.html, +"charmmfsw"_dihedral_charmm.html, +"class2 (ko)"_dihedral_class2.html, +"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, +"fourier (io)"_dihedral_fourier.html, +"harmonic (io)"_dihedral_harmonic.html, +"helix (o)"_dihedral_helix.html, +"multi/harmonic (o)"_dihedral_multi_harmonic.html, +"nharmonic (o)"_dihedral_nharmonic.html, +"opls (iko)"_dihedral_opls.htm;, +"quadratic (o)"_dihedral_quadratic.html, +"spherical (o)"_dihedral_spherical.html, +"table (o)"_dihedral_table.html, +"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) + +:line + +Improper_style potentials :h3,link(improper) + +All LAMMPS "improper_style"_improper_style.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_improper_none.html, +"zero"_improper_zero.html, +"hybrid"_improper_hybrid.html :tb(c=3,ea=c) + +"class2 (ko)"_improper_class2.html, +"cossq (o)"_improper_cossq.html, +"cvff (io)"_improper_cvff.html, +"distance"_improper_distance.html, +"fourier (o)"_improper_fourier.html, +"harmonic (iko)"_improper_harmonic.html, +"ring (o)"_improper_ring.html, +"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt new file mode 100644 index 0000000000000000000000000000000000000000..5d047c67272ef0e8bedb1d2d9e52260ee4be0b2e --- /dev/null +++ b/doc/src/Commands_category.txt @@ -0,0 +1,141 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Commands by category :h3 + +This page lists most of the LAMMPS commands, grouped by category. The +"Commands all"_Commands_all.html doc page lists all commands +alphabetically. It also includes long lists of style options for +entries that appear in the following categories as a single command +(fix, compute, pair, etc). + +Initialization: + +"newton"_newton.html, +"package"_package.html, +"processors"_processors.html, +"suffix"_suffix.html, +"units"_units.html :ul + +Setup simulation box: + +"boundary"_boundary.html, +"box"_box.html, +"change_box"_change_box.html, +"create_box"_create_box.html, +"dimension"_dimension.html, +"lattice"_lattice.html, +"region"_region.html :ul + +Setup atoms: + +"atom_modify"_atom_modify.html, +"atom_style"_atom_style.html, +"balance"_balance.html, +"create_atoms"_create_atoms.html, +"create_bonds"_create_bonds.html, +"delete_atoms"_delete_atoms.html, +"delete_bonds"_delete_bonds.html, +"displace_atoms"_displace_atoms.html, +"group"_group.html, +"mass"_mass.html, +"molecule"_molecule.html, +"read_data"_read_data.html, +"read_dump"_read_dump.html, +"read_restart"_read_restart.html, +"replicate"_replicate.html, +"set"_set.html, +"velocity"_velocity.html :ul + +Force fields: + +"angle_coeff"_angle_coeff.html, +"angle_style"_angle_style.html, +"bond_coeff"_bond_coeff.html, +"bond_style"_bond_style.html, +"bond_write"_bond_write.html, +"dielectric"_dielectric.html, +"dihedral_coeff"_dihedral_coeff.html, +"dihedral_style"_dihedral_style.html, +"improper_coeff"_improper_coeff.html, +"improper_style"_improper_style.html, +"kspace_modify"_kspace_modify.html, +"kspace_style"_kspace_style.html, +"pair_coeff"_pair_coeff.html, +"pair_modify"_pair_modify.html, +"pair_style"_pair_style.html, +"pair_write"_pair_write.html, +"special_bonds"_special_bonds.html :ul + +Settings: + +"comm_modify"_comm_modify.html, +"comm_style"_comm_style.html, +"info"_info.html, +"min_modify"_min_modify.html, +"min_style"_min_style.html, +"neigh_modify"_neigh_modify.html, +"neighbor"_neighbor.html, +"partition"_partition.html, +"reset_timestep"_reset_timestep.html, +"run_style"_run_style.html, +"timer"_timer.html, +"timestep"_timestep.html :ul + +Operations within timestepping (fixes) and diagnostics (computes): + +"compute"_compute.html, +"compute_modify"_compute_modify.html, +"fix"_fix.html, +"fix_modify"_fix_modify.html, +"uncompute"_uncompute.html, +"unfix"_unfix.html :ul + +Output: + +"dump image"_dump_image.html, +"dump movie"_dump_image.html, +"dump"_dump.html, +"dump_modify"_dump_modify.html, +"restart"_restart.html, +"thermo"_thermo.html, +"thermo_modify"_thermo_modify.html, +"thermo_style"_thermo_style.html, +"undump"_undump.html, +"write_coeff"_write_coeff.html, +"write_data"_write_data.html, +"write_dump"_write_dump.html, +"write_restart"_write_restart.html :ul + +Actions: + +"minimize"_minimize.html, +"neb"_neb.html, +"prd"_prd.html, +"rerun"_rerun.html, +"run"_run.html, +"tad"_tad.html, +"temper"_temper.html :ul + +Input script control: + +"clear"_clear.html, +"echo"_echo.html, +"if"_if.html, +"include"_include.html, +"jump"_jump.html, +"label"_label.html, +"log"_log.html, +"next"_next.html, +"print"_print.html, +"python"_python.html, +"quit"_quit.html, +"shell"_shell.html, +"variable"_variable.html :ul + diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt new file mode 100644 index 0000000000000000000000000000000000000000..028e274c9be4a80555dfcab5a417d738b763bfda --- /dev/null +++ b/doc/src/Commands_compute.txt @@ -0,0 +1,153 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Compute commands :h3 + +An alphabetic list of all LAMMPS "compute"_compute.html commands. +Some styles have accelerated versions. This is indicated by +additional letters in parenthesis: g = GPU, i = USER-INTEL, k = +KOKKOS, o = USER-OMP, t = OPT. + +"ackland/atom"_compute_ackland_atom.html, +"aggregate/atom"_compute_cluster_atom.html, +"angle"_compute_angle.html, +"angle/local"_compute_angle_local.html, +"angmom/chunk"_compute_angmom_chunk.html, +"basal/atom"_compute_basal_atom.html, +"body/local"_compute_body_local.html, +"bond"_compute_bond.html, +"bond/local"_compute_bond_local.html, +"centro/atom"_compute_centro_atom.html, +"chunk/atom"_compute_chunk_atom.html, +"cluster/atom"_compute_cluster_atom.html, +"cna/atom"_compute_cna_atom.html, +"cnp/atom"_compute_cnp_atom.html, +"com"_compute_com.html, +"com/chunk"_compute_com_chunk.html, +"contact/atom"_compute_contact_atom.html, +"coord/atom"_compute_coord_atom.html, +"damage/atom"_compute_damage_atom.html, +"dihedral"_compute_dihedral.html, +"dihedral/local"_compute_dihedral_local.html, +"dilatation/atom"_compute_dilatation_atom.html, +"dipole/chunk"_compute_dipole_chunk.html, +"displace/atom"_compute_displace_atom.html, +"dpd"_compute_dpd.html, +"dpd/atom"_compute_dpd_atom.html, +"edpd/temp/atom"_compute_edpd_temp_atom.html, +"entropy/atom"_compute_entropy_atom.html, +"erotate/asphere"_compute_erotate_asphere.html, +"erotate/rigid"_compute_erotate_rigid.html, +"erotate/sphere"_compute_erotate_sphere.html, +"erotate/sphere/atom"_compute_erotate_sphere_atom.html, +"event/displace"_compute_event_displace.html, +"fep"_compute_fep.html, +"force/tally"_compute_tally.html, +"fragment/atom"_compute_cluster_atom.html, +"global/atom"_compute_global_atom.html, +"group/group"_compute_group_group.html, +"gyration"_compute_gyration.html, +"gyration/chunk"_compute_gyration_chunk.html, +"heat/flux"_compute_heat_flux.html, +"heat/flux/tally"_compute_tally.html, +"hexorder/atom"_compute_hexorder_atom.html, +"improper"_compute_improper.html, +"improper/local"_compute_improper_local.html, +"inertia/chunk"_compute_inertia_chunk.html, +"ke"_compute_ke.html, +"ke/atom"_compute_ke_atom.html, +"ke/atom/eff"_compute_ke_atom_eff.html, +"ke/eff"_compute_ke_eff.html, +"ke/rigid"_compute_ke_rigid.html, +"meso/e/atom"_compute_meso_e_atom.html, +"meso/rho/atom"_compute_meso_rho_atom.html, +"meso/t/atom"_compute_meso_t_atom.html, +"msd"_compute_msd.html, +"msd/chunk"_compute_msd_chunk.html, +"msd/nongauss"_compute_msd_nongauss.html, +"omega/chunk"_compute_omega_chunk.html, +"orientorder/atom"_compute_orientorder_atom.html, +"pair"_compute_pair.html, +"pair/local"_compute_pair_local.html, +"pe"_compute_pe.html, +"pe/atom"_compute_pe_atom.html, +"pe/mol/tally"_compute_tally.html, +"pe/tally"_compute_tally.html, +"plasticity/atom"_compute_plasticity_atom.html, +"pressure"_compute_pressure.html, +"pressure/uef"_compute_pressure_uef.html, +"property/atom"_compute_property_atom.html, +"property/chunk"_compute_property_chunk.html, +"property/local"_compute_property_local.html, +"rdf"_compute_rdf.html, +"reduce"_compute_reduce.html, +"reduce/region"_compute_reduce.html, +"rigid/local"_compute_rigid_local.html, +"saed"_compute_saed.html, +"slice"_compute_slice.html, +"smd/contact/radius"_compute_smd_contact_radius.html, +"smd/damage"_compute_smd_damage.html, +"smd/hourglass/error"_compute_smd_hourglass_error.html, +"smd/internal/energy"_compute_smd_internal_energy.html, +"smd/plastic/strain"_compute_smd_plastic_strain.html, +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, +"smd/rho"_compute_smd_rho.html, +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, +"smd/tlsph/dt"_compute_smd_tlsph_dt.html, +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, +"smd/tlsph/shape"_compute_smd_tlsph_shape.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/stress"_compute_smd_tlsph_stress.html, +"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, +"smd/ulsph/strain"_compute_smd_ulsph_strain.html, +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, +"smd/ulsph/stress"_compute_smd_ulsph_stress.html, +"smd/vol"_compute_smd_vol.html, +"sna/atom"_compute_sna_atom.html, +"snad/atom"_compute_sna_atom.html, +"snav/atom"_compute_sna_atom.html, +"spin"_compute_spin.html, +"stress/atom"_compute_stress_atom.html, +"stress/tally"_compute_tally.html, +"tdpd/cc/atom"_compute_tdpd_cc_atom.html, +"temp (k)"_compute_temp.html, +"temp/asphere"_compute_temp_asphere.html, +"temp/body"_compute_temp_body.html, +"temp/chunk"_compute_temp_chunk.html, +"temp/com"_compute_temp_com.html, +"temp/deform"_compute_temp_deform.html, +"temp/deform/eff"_compute_temp_deform_eff.html, +"temp/drude"_compute_temp_drude.html, +"temp/eff"_compute_temp_eff.html, +"temp/partial"_compute_temp_partial.html, +"temp/profile"_compute_temp_profile.html, +"temp/ramp"_compute_temp_ramp.html, +"temp/region"_compute_temp_region.html, +"temp/region/eff"_compute_temp_region_eff.html, +"temp/rotate"_compute_temp_rotate.html, +"temp/sphere"_compute_temp_sphere.html, +"temp/uef"_compute_temp_uef.html, +"ti"_compute_ti.html, +"torque/chunk"_compute_torque_chunk.html, +"vacf"_compute_vacf.html, +"vcm/chunk"_compute_vcm_chunk.html, +"voronoi/atom"_compute_voronoi_atom.html, +"xrd"_compute_xrd.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt new file mode 100644 index 0000000000000000000000000000000000000000..e002c117701110fc6dd33e83865386f52d2bae3e --- /dev/null +++ b/doc/src/Commands_fix.txt @@ -0,0 +1,229 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Fix commands :h3 + +An alphabetic list of all LAMMPS "fix"_fix.html commands. Some styles +have accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"adapt"_fix_adapt.html, +"adapt/fep"_fix_adapt_fep.html, +"addforce"_fix_addforce.html, +"addtorque"_fix_addtorque.html, +"append/atoms"_fix_append_atoms.html, +"atc"_fix_atc.html, +"atom/swap"_fix_atom_swap.html, +"ave/atom"_fix_ave_atom.html, +"ave/chunk"_fix_ave_chunk.html, +"ave/correlate"_fix_ave_correlate.html, +"ave/correlate/long"_fix_ave_correlate_long.html, +"ave/histo"_fix_ave_histo.html, +"ave/histo/weight"_fix_ave_histo.html, +"ave/time"_fix_ave_time.html, +"aveforce"_fix_aveforce.html, +"balance"_fix_balance.html, +"bond/break"_fix_bond_break.html, +"bond/create"_fix_bond_create.html, +"bond/react"_fix_bond_react.html, +"bond/swap"_fix_bond_swap.html, +"box/relax"_fix_box_relax.html, +"cmap"_fix_cmap.html, +"colvars"_fix_colvars.html, +"controller"_fix_controller.html, +"deform (k)"_fix_deform.html, +"deposit"_fix_deposit.html, +"dpd/energy (k)"_fix_dpd_energy.html, +"drag"_fix_drag.html, +"drude"_fix_drude.html, +"drude/transform/direct"_fix_drude_transform.html, +"drude/transform/reverse"_fix_drude_transform.html, +"dt/reset"_fix_dt_reset.html, +"edpd/source"_fix_dpd_source.html, +"efield"_fix_efield.html, +"ehex"_fix_ehex.html, +"enforce2d (k)"_fix_enforce2d.html, +"eos/cv"_fix_eos_cv.html, +"eos/table"_fix_eos_table.html, +"eos/table/rx (k)"_fix_eos_table_rx.html, +"evaporate"_fix_evaporate.html, +"external"_fix_external.html, +"filter/corotate"_fix_filter_corotate.html, +"flow/gauss"_fix_flow_gauss.html, +"freeze"_fix_freeze.html, +"gcmc"_fix_gcmc.html, +"gld"_fix_gld.html, +"gle"_fix_gle.html, +"gravity (o)"_fix_gravity.html, +"grem"_fix_grem.html, +"halt"_fix_halt.html, +"heat"_fix_heat.html, +"imd"_fix_imd.html, +"indent"_fix_indent.html, +"ipi"_fix_ipi.html, +"langevin (k)"_fix_langevin.html, +"langevin/drude"_fix_langevin_drude.html, +"langevin/eff"_fix_langevin_eff.html, +"langevin/spin"_fix_langevin_spin.html, +"latte"_fix_latte.html, +"lb/fluid"_fix_lb_fluid.html, +"lb/momentum"_fix_lb_momentum.html, +"lb/pc"_fix_lb_pc.html, +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, +"lb/viscous"_fix_lb_viscous.html, +"lineforce"_fix_lineforce.html, +"manifoldforce"_fix_manifoldforce.html, +"meso"_fix_meso.html, +"meso/stationary"_fix_meso_stationary.html, +"momentum (k)"_fix_momentum.html, +"move"_fix_move.html, +"mscg"_fix_mscg.html, +"msst"_fix_msst.html, +"mvv/dpd"_fix_mvv_dpd.html, +"mvv/edpd"_fix_mvv_dpd.html, +"mvv/tdpd"_fix_mvv_dpd.html, +"neb"_fix_neb.html, +"nph (ko)"_fix_nh.html, +"nph/asphere (o)"_fix_nph_asphere.html, +"nph/body"_fix_nph_body.html, +"nph/eff"_fix_nh_eff.html, +"nph/sphere (o)"_fix_nph_sphere.html, +"nphug (o)"_fix_nphug.html, +"npt (kio)"_fix_nh.html, +"npt/asphere (o)"_fix_npt_asphere.html, +"npt/body"_fix_npt_body.html, +"npt/eff"_fix_nh_eff.html, +"npt/sphere (o)"_fix_npt_sphere.html, +"npt/uef"_fix_nh_uef.html, +"nve (kio)"_fix_nve.html, +"nve/asphere (i)"_fix_nve_asphere.html, +"nve/asphere/noforce"_fix_nve_asphere_noforce.html, +"nve/body"_fix_nve_body.html, +"nve/dot"_fix_nve_dot.html, +"nve/dotc/langevin"_fix_nve_dotc_langevin.html, +"nve/eff"_fix_nve_eff.html, +"nve/limit"_fix_nve_limit.html, +"nve/line"_fix_nve_line.html, +"nve/manifold/rattle"_fix_nve_manifold_rattle.html, +"nve/noforce"_fix_nve_noforce.html, +"nve/sphere (o)"_fix_nve_sphere.html, +"nve/spin"_fix_nve_spin.html, +"nve/tri"_fix_nve_tri.html, +"nvk"_fix_nvk.html, +"nvt (iko)"_fix_nh.html, +"nvt/asphere (o)"_fix_nvt_asphere.html, +"nvt/body"_fix_nvt_body.html, +"nvt/eff"_fix_nh_eff.html, +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, +"nvt/sllod (io)"_fix_nvt_sllod.html, +"nvt/sllod/eff"_fix_nvt_sllod_eff.html, +"nvt/sphere (o)"_fix_nvt_sphere.html, +"nvt/uef"_fix_nh_uef.html, +"oneway"_fix_oneway.html, +"orient/bcc"_fix_orient.html, +"orient/fcc"_fix_orient.html, +"phonon"_fix_phonon.html, +"pimd"_fix_pimd.html, +"planeforce"_fix_planeforce.html, +"poems"_fix_poems.html, +"pour"_fix_pour.html, +"precession/spin"_fix_precession_spin.html, +"press/berendsen"_fix_press_berendsen.html, +"print"_fix_print.html, +"property/atom (k)"_fix_property_atom.html, +"python/invoke"_fix_python_invoke.html, +"python/move"_fix_python_move.html, +"qbmsst"_fix_qbmsst.html, +"qeq/comb (o)"_fix_qeq_comb.html, +"qeq/dynamic"_fix_qeq.html, +"qeq/fire"_fix_qeq.html, +"qeq/point"_fix_qeq.html, +"qeq/reax (ko)"_fix_qeq_reax.html, +"qeq/shielded"_fix_qeq.html, +"qeq/slater"_fix_qeq.html, +"qmmm"_fix_qmmm.html, +"qtb"_fix_qtb.html, +"rattle"_fix_shake.html, +"reax/bonds"_fix_reax_bonds.html, +"reax/c/bonds (k)"_fix_reax_bonds.html, +"reax/c/species (k)"_fix_reaxc_species.html, +"recenter"_fix_recenter.html, +"restrain"_fix_restrain.html, +"rhok"_fix_rhok.html, +"rigid (o)"_fix_rigid.html, +"rigid/nph (o)"_fix_rigid.html, +"rigid/npt (o)"_fix_rigid.html, +"rigid/nve (o)"_fix_rigid.html, +"rigid/nvt (o)"_fix_rigid.html, +"rigid/small (o)"_fix_rigid.html, +"rigid/small/nph"_fix_rigid.html, +"rigid/small/npt"_fix_rigid.html, +"rigid/small/nve"_fix_rigid.html, +"rigid/small/nvt"_fix_rigid.html, +"rx (k)"_fix_rx.html, +"saed/vtk"_fix_saed_vtk.html, +"setforce (k)"_fix_setforce.html, +"shake"_fix_shake.html, +"shardlow (k)"_fix_shardlow.html, +"smd"_fix_smd.html, +"smd/adjust/dt"_fix_smd_adjust_dt.html, +"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, +"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, +"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, +"smd/setvel"_fix_smd_setvel.html, +"smd/wall/surface"_fix_smd_wall_surface.html, +"spring"_fix_spring.html, +"spring/chunk"_fix_spring_chunk.html, +"spring/rg"_fix_spring_rg.html, +"spring/self"_fix_spring_self.html, +"srd"_fix_srd.html, +"store/force"_fix_store_force.html, +"store/state"_fix_store_state.html, +"tdpd/source"_fix_dpd_source.html, +"temp/berendsen"_fix_temp_berendsen.html, +"temp/csld"_fix_temp_csvr.html, +"temp/csvr"_fix_temp_csvr.html, +"temp/rescale"_fix_temp_rescale.html, +"temp/rescale/eff"_fix_temp_rescale_eff.html, +"tfmc"_fix_tfmc.html, +"thermal/conductivity"_fix_thermal_conductivity.html, +"ti/spring"_fix_ti_spring.html, +"tmd"_fix_tmd.html, +"ttm"_fix_ttm.html, +"ttm/mod"_fix_ttm.html, +"tune/kspace"_fix_tune_kspace.html, +"vector"_fix_vector.html, +"viscosity"_fix_viscosity.html, +"viscous"_fix_viscous.html, +"wall/body/polygon"_fix_wall_body_polygon.html, +"wall/body/polyhedron"_fix_wall_body_polyhedron.html, +"wall/colloid"_fix_wall.html, +"wall/ees"_fix_wall_ees.html, +"wall/gran"_fix_wall_gran.html, +"wall/gran/region"_fix_wall_gran_region.html, +"wall/harmonic"_fix_wall.html, +"wall/lj1043"_fix_wall.html, +"wall/lj126"_fix_wall.html, +"wall/lj93 (k)"_fix_wall.html, +"wall/piston"_fix_wall_piston.html, +"wall/reflect (k)"_fix_wall_reflect.html, +"wall/region"_fix_wall_region.html, +"wall/region/ees"_fix_wall_ees.html, +"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) diff --git a/doc/src/Commands_input.txt b/doc/src/Commands_input.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b3dda741b42dd03bcca359e654ef0ab1ae6a043 --- /dev/null +++ b/doc/src/Commands_input.txt @@ -0,0 +1,60 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS input scripts :h3 + +LAMMPS executes by reading commands from a input script (text file), +one line at a time. When the input script ends, LAMMPS exits. Each +command causes LAMMPS to take some action. It may set an internal +variable, read in a file, or run a simulation. Most commands have +default settings, which means you only need to use the command if you +wish to change the default. + +In many cases, the ordering of commands in an input script is not +important. However the following rules apply: + +(1) LAMMPS does not read your entire input script and then perform a +simulation with all the settings. Rather, the input script is read +one line at a time and each command takes effect when it is read. +Thus this sequence of commands: + +timestep 0.5 +run 100 +run 100 :pre + +does something different than this sequence: + +run 100 +timestep 0.5 +run 100 :pre + +In the first case, the specified timestep (0.5 fs) is used for two +simulations of 100 timesteps each. In the 2nd case, the default +timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs +timestep is used for the 2nd one. + +(2) Some commands are only valid when they follow other commands. For +example you cannot set the temperature of a group of atoms until atoms +have been defined and a group command is used to define which atoms +belong to the group. + +(3) Sometimes command B will use values that can be set by command A. +This means command A must precede command B in the input script if it +is to have the desired effect. For example, the +"read_data"_read_data.html command initializes the system by setting +up the simulation box and assigning atoms to processors. If default +values are not desired, the "processors"_processors.html and +"boundary"_boundary.html commands need to be used before read_data to +tell LAMMPS how to map processors to the simulation box. + +Many input script errors are detected by LAMMPS and an ERROR or +WARNING message is printed. The "Errors"_Errors.html doc page gives +more information on what errors mean. The documentation for each +command lists restrictions on how the command can be used. + diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1263445050bda692218aa311831d3565d22155c --- /dev/null +++ b/doc/src/Commands_kspace.txt @@ -0,0 +1,36 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +KSpace solvers :h3 + +All LAMMPS "kspace_style"_kspace_style.html solvers. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"ewald (o)"_kspace_style.html, +"ewald/disp"_kspace_style.html, +"msm (o)"_kspace_style.html, +"msm/cg (o)"_kspace_style.html, +"pppm (gok)"_kspace_style.html, +"pppm/cg (o)"_kspace_style.html, +"pppm/disp (i)"_kspace_style.html, +"pppm/disp/tip4p"_kspace_style.html, +"pppm/stagger"_kspace_style.html, +"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt new file mode 100644 index 0000000000000000000000000000000000000000..eaf272061347931f1fda5dedf9776170ca8eb41a --- /dev/null +++ b/doc/src/Commands_pair.txt @@ -0,0 +1,231 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +"All commands"_Commands_all.html, +"Fix styles"_Commands_fix.html, +"Compute styles"_Commands_compute.html, +"Pair styles"_Commands_pair.html, +"Bond styles"_Commands_bond.html, +"Angle styles"_Commands_bond.html#angle, +"Dihedral styles"_Commands_bond.html#dihedral, +"Improper styles"_Commands_bond.html#improper, +"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) + +Pair_style potentials :h3 + +All LAMMPS "pair_style"_pair_style.html commands. Some styles have +accelerated versions. This is indicated by additional letters in +parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = +OPT. + +"none"_pair_none.html, +"zero"_pair_zero.html, +"hybrid"_pair_hybrid.html, +"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c) + +"adp (o)"_pair_adp.html, +"agni (o)"_pair_agni.html, +"airebo (oi)"_pair_airebo.html, +"airebo/morse (oi)"_pair_airebo.html, +"awpmd/cut"_pair_awpmd.html, +"beck (go)"_pair_beck.html, +"body/nparticle"_pair_body_nparticle.html, +"body/rounded/polygon"_pair_body_rounded_polygon.html, +"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html, +"bop"_pair_bop.html, +"born (go)"_pair_born.html, +"born/coul/dsf"_pair_born.html, +"born/coul/dsf/cs"_pair_born.html, +"born/coul/long (go)"_pair_born.html, +"born/coul/long/cs"_pair_born.html, +"born/coul/msm (o)"_pair_born.html, +"born/coul/wolf (go)"_pair_born.html, +"born/coul/wolf/cs"_pair_born.html, +"brownian (o)"_pair_brownian.html, +"brownian/poly (o)"_pair_brownian.html, +"buck (giko)"_pair_buck.html, +"buck/coul/cut (giko)"_pair_buck.html, +"buck/coul/long (giko)"_pair_buck.html, +"buck/coul/long/cs"_pair_buck.html, +"buck/coul/msm (o)"_pair_buck.html, +"buck/long/coul/long (o)"_pair_buck_long.html, +"buck/mdf"_pair_mdf.html, +"colloid (go)"_pair_colloid.html, +"comb (o)"_pair_comb.html, +"comb3"_pair_comb.html, +"coul/cut (gko)"_pair_coul.html, +"coul/cut/soft (o)"_pair_lj_soft.html, +"coul/debye (gko)"_pair_coul.html, +"coul/diel (o)"_pair_coul_diel.html, +"coul/dsf (gko)"_pair_coul.html, +"coul/long (gko)"_pair_coul.html, +"coul/long/cs"_pair_coul.html, +"coul/long/soft (o)"_pair_lj_soft.html, +"coul/msm"_pair_coul.html, +"coul/shield"_pair_coul_shield.html, +"coul/streitz"_pair_coul.html, +"coul/wolf (ko)"_pair_coul.html, +"coul/wolf/cs"_pair_coul.html, +"dpd (gio)"_pair_dpd.html, +"dpd/fdt"_pair_dpd_fdt.html, +"dpd/fdt/energy (k)"_pair_dpd_fdt.html, +"dpd/tstat (go)"_pair_dpd.html, +"dsmc"_pair_dsmc.html, +"eam (gikot)"_pair_eam.html, +"eam/alloy (gikot)"_pair_eam.html, +"eam/cd (o)"_pair_eam.html, +"eam/fs (gikot)"_pair_eam.html, +"edip (o)"_pair_edip.html, +"edip/multi"_pair_edip.html, +"edpd"_pair_meso.html, +"eff/cut"_pair_eff.html, +"eim (o)"_pair_eim.html, +"exp6/rx (k)"_pair_exp6_rx.html, +"extep"_pair_extep.html, +"gauss (go)"_pair_gauss.html, +"gauss/cut"_pair_gauss.html, +"gayberne (gio)"_pair_gayberne.html, +"gran/hertz/history (o)"_pair_gran.html, +"gran/hooke (o)"_pair_gran.html, +"gran/hooke/history (o)"_pair_gran.html, +"gw"_pair_gw.html, +"gw/zbl"_pair_gw.html, +"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, +"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, +"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, +"kim"_pair_kim.html, +"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, +"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"lcbop"_pair_lcbop.html, +"lennard/mdf"_pair_mdf.html, +"line/lj"_pair_line_lj.html, +"list"_pair_list.html, +"lj/charmm/coul/charmm (iko)"_pair_charmm.html, +"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, +"lj/charmm/coul/long (giko)"_pair_charmm.html, +"lj/charmm/coul/long/soft (o)"_pair_charmm.html, +"lj/charmm/coul/msm"_pair_charmm.html, +"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, +"lj/charmmfsw/coul/long"_pair_charmm.html, +"lj/class2 (gko)"_pair_class2.html, +"lj/class2/coul/cut (ko)"_pair_class2.html, +"lj/class2/coul/long (gko)"_pair_class2.html, +"lj/cubic (go)"_pair_lj_cubic.html, +"lj/cut (gikot)"_pair_lj.html, +"lj/cut/coul/cut (gko)"_pair_lj.html, +"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/debye (gko)"_pair_lj.html, +"lj/cut/coul/dsf (gko)"_pair_lj.html, +"lj/cut/coul/long (gikot)"_pair_lj.html, +"lj/cut/coul/long/cs"_pair_lj.html, +"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/msm (go)"_pair_lj.html, +"lj/cut/coul/wolf (o)"_pair_lj.html, +"lj/cut/dipole/cut (go)"_pair_dipole.html, +"lj/cut/dipole/long"_pair_dipole.html, +"lj/cut/dipole/sf (go)"_pair_dipole.html, +"lj/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/thole/long (o)"_pair_thole.html, +"lj/cut/tip4p/cut (o)"_pair_lj.html, +"lj/cut/tip4p/long (ot)"_pair_lj.html, +"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, +"lj/expand (gko)"_pair_lj_expand.html, +"lj/gromacs (gko)"_pair_gromacs.html, +"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, +"lj/long/coul/long (io)"_pair_lj_long.html, +"lj/long/dipole/long"_pair_dipole.html, +"lj/long/tip4p/long"_pair_lj_long.html, +"lj/mdf"_pair_mdf.html, +"lj/sdk (gko)"_pair_sdk.html, +"lj/sdk/coul/long (go)"_pair_sdk.html, +"lj/sdk/coul/msm (o)"_pair_sdk.html, +"lj/smooth (o)"_pair_lj_smooth.html, +"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, +"lj96/cut (go)"_pair_lj96.html, +"lubricate (o)"_pair_lubricate.html, +"lubricate/poly (o)"_pair_lubricate.html, +"lubricateU"_pair_lubricateU.html, +"lubricateU/poly"_pair_lubricateU.html, +"mdpd"_pair_meso.html, +"mdpd/rhosum"_pair_meso.html, +"meam"_pair_meam.html, +"meam/c"_pair_meam.html, +"meam/spline (o)"_pair_meam_spline.html, +"meam/sw/spline"_pair_meam_sw_spline.html, +"mgpt"_pair_mgpt.html, +"mie/cut (o)"_pair_mie.html, +"momb"_pair_momb.html, +"morse (gkot)"_pair_morse.html, +"morse/smooth/linear"_pair_morse.html, +"morse/soft"_pair_morse.html, +"multi/lucy"_pair_multi_lucy.html, +"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, +"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, +"nm/cut (o)"_pair_nm.html, +"nm/cut/coul/cut (o)"_pair_nm.html, +"nm/cut/coul/long (o)"_pair_nm.html, +"oxdna/coaxstk"_pair_oxdna.html, +"oxdna/excv"_pair_oxdna.html, +"oxdna/hbond"_pair_oxdna.html, +"oxdna/stk"_pair_oxdna.html, +"oxdna/xstk"_pair_oxdna.html, +"oxdna2/coaxstk"_pair_oxdna2.html, +"oxdna2/dh"_pair_oxdna2.html, +"oxdna2/excv"_pair_oxdna2.html, +"oxdna2/stk"_pair_oxdna2.html, +"peri/eps"_pair_peri.html, +"peri/lps (o)"_pair_peri.html, +"peri/pmb (o)"_pair_peri.html, +"peri/ves"_pair_peri.html, +"polymorphic"_pair_polymorphic.html, +"python"_pair_python.html, +"quip"_pair_quip.html, +"reax"_pair_reax.html, +"reax/c (ko)"_pair_reaxc.html, +"rebo (oi)"_pair_airebo.html, +"resquared (go)"_pair_resquared.html, +"smd/hertz"_pair_smd_hertz.html, +"smd/tlsph"_pair_smd_tlsph.html, +"smd/triangulated/surface"_pair_smd_triangulated_surface.html, +"smd/ulsph"_pair_smd_ulsph.html, +"smtbq"_pair_smtbq.html, +"snap (k)"_pair_snap.html, +"snap (k)"_pair_snap.html, +"soft (go)"_pair_soft.html, +"sph/heatconduction"_pair_sph_heatconduction.html, +"sph/idealgas"_pair_sph_idealgas.html, +"sph/lj"_pair_sph_lj.html, +"sph/rhosum"_pair_sph_rhosum.html, +"sph/taitwater"_pair_sph_taitwater.html, +"sph/taitwater/morris"_pair_sph_taitwater_morris.html, +"spin/dmi"_pair_spin_dmi.html, +"spin/exchange"_pair_spin_exchange.html, +"spin/magelec"_pair_spin_magelec.html, +"spin/neel"_pair_spin_neel.html, +"srp"_pair_srp.html, +"sw (giko)"_pair_sw.html, +"table (gko)"_pair_table.html, +"table/rx (k)"_pair_table_rx.html, +"tdpd"_pair_meso.html, +"tersoff (giko)"_pair_tersoff.html, +"tersoff/mod (gko)"_pair_tersoff_mod.html, +"tersoff/mod/c (o)"_pair_tersoff_mod.html, +"tersoff/table (o)"_pair_tersoff.html, +"tersoff/zbl (gko)"_pair_tersoff_zbl.html, +"thole"_pair_thole.html, +"tip4p/cut (o)"_pair_coul.html, +"tip4p/long (o)"_pair_coul.html, +"tip4p/long/soft (o)"_pair_lj_soft.html, +"tri/lj"_pair_tri_lj.html, +"ufm (got)"_pair_ufm.html, +"vashishta (ko)"_pair_vashishta.html, +"vashishta/table (o)"_pair_vashishta.html, +"yukawa (gok)"_pair_yukawa.html, +"yukawa/colloid (go)"_pair_yukawa_colloid.html, +"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt new file mode 100644 index 0000000000000000000000000000000000000000..cbe2261986bb8f8f96089dac3dff3a03dc39dd42 --- /dev/null +++ b/doc/src/Commands_parse.txt @@ -0,0 +1,136 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Parsing rules for input scripts :h3 + +Each non-blank line in the input script is treated as a command. +LAMMPS commands are case sensitive. Command names are lower-case, as +are specified command arguments. Upper case letters may be used in +file names or user-chosen ID strings. + +Here are 6 rulse for how each line in the input script is parsed by +LAMMPS: + +(1) If the last printable character on the line is a "&" character, +the command is assumed to continue on the next line. The next line is +concatenated to the previous line by removing the "&" character and +line break. This allows long commands to be continued across two or +more lines. See the discussion of triple quotes in (6) for how to +continue a command across multiple line without using "&" characters. + +(2) All characters from the first "#" character onward are treated as +comment and discarded. See an exception in (6). Note that a +comment after a trailing "&" character will prevent the command from +continuing on the next line. Also note that for multi-line commands a +single leading "#" will comment out the entire command. + +(3) The line is searched repeatedly for $ characters, which indicate +variables that are replaced with a text string. See an exception in +(6). + +If the $ is followed by curly brackets, then the variable name is the +text inside the curly brackets. If no curly brackets follow the $, +then the variable name is the single character immediately following +the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and +"x". + +How the variable is converted to a text string depends on what style +of variable it is; see the "variable"_variable.html doc page for details. +It can be a variable that stores multiple text strings, and return one +of them. The returned text string can be multiple "words" (space +separated) which will then be interpreted as multiple arguments in the +input command. The variable can also store a numeric formula which +will be evaluated and its numeric result returned as a string. + +As a special case, if the $ is followed by parenthesis, then the text +inside the parenthesis is treated as an "immediate" variable and +evaluated as an "equal-style variable"_variable.html. This is a way +to use numeric formulas in an input script without having to assign +them to variable names. For example, these 3 input script lines: + +variable X equal (xlo+xhi)/2+sqrt(v_area) +region 1 block $X 2 INF INF EDGE EDGE +variable X delete :pre + +can be replaced by + +region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre + +so that you do not have to define (or discard) a temporary variable X. + +Additionally, the "immediate" variable expression may be followed by a +colon, followed by a C-style format string, e.g. ":%f" or ":%.10g". +The format string must be appropriate for a double-precision +floating-point value. The format string is used to output the result +of the variable expression evaluation. If a format string is not +specified a high-precision "%.20g" is used as the default. + +This can be useful for formatting print output to a desired precion: + +print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre + +Note that neither the curly-bracket or immediate form of variables can +contain nested $ characters for other variables to substitute for. +Thus you cannot do this: + +variable a equal 2 +variable b2 equal 4 +print "B2 = $\{b$a\}" :pre + +Nor can you specify this $($x-1.0) for an immediate variable, but +you could use $(v_x-1.0), since the latter is valid syntax for an +"equal-style variable"_variable.html. + +See the "variable"_variable.html command for more details of how +strings are assigned to variables and evaluated, and how they can be +used in input script commands. + +(4) The line is broken into "words" separated by whitespace (tabs, +spaces). Note that words can thus contain letters, digits, +underscores, or punctuation characters. + +(5) The first word is the command name. All successive words in the +line are arguments. + +(6) If you want text with spaces to be treated as a single argument, +it can be enclosed in either single or double or triple quotes. A +long single argument enclosed in single or double quotes can span +multiple lines if the "&" character is used, as described above. When +the lines are concatenated together (and the "&" characters and line +breaks removed), the text will become a single line. If you want +multiple lines of an argument to retain their line breaks, the text +can be enclosed in triple quotes, in which case "&" characters are not +needed. For example: + +print "Volume = $v" +print 'Volume = $v' +if "$\{steps\} > 1000" then quit +variable a string "red green blue & + purple orange cyan" +print """ +System volume = $v +System temperature = $t +""" :pre + +In each case, the single, double, or triple quotes are removed when +the single argument they enclose is stored internally. + +See the "dump modify format"_dump_modify.html, "print"_print.html, +"if"_if.html, and "python"_python.html commands for examples. + +A "#" or "$" character that is between quotes will not be treated as a +comment indicator in (2) or substituted for as a variable in (3). + +NOTE: If the argument is itself a command that requires a quoted +argument (e.g. using a "print"_print.html command as part of an +"if"_if.html or "run every"_run.html command), then single, double, or +triple quotes can be nested in the usual manner. See the doc pages +for those commands for examples. Only one of level of nesting is +allowed, but that should be sufficient for most use cases. + diff --git a/doc/src/Commands_structure.txt b/doc/src/Commands_structure.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5d2c7b07b1f8b4afdb2d255f4953cfbba0e330b --- /dev/null +++ b/doc/src/Commands_structure.txt @@ -0,0 +1,95 @@ +"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Input script structure :h3 + +This page describes the structure of a typical LAMMPS input script. +The examples directory in the LAMMPS distribution contains many sample +input scripts; it is discussed on the "Examples"_Examples.html doc +page. + +A LAMMPS input script typically has 4 parts: + +Initialization +Atom definition +Settings +Run a simulation :ol + +The last 2 parts can be repeated as many times as desired. I.e. run a +simulation, change some settings, run some more, etc. Each of the 4 +parts is now described in more detail. Remember that almost all +commands need only be used if a non-default value is desired. + +(1) Initialization + +Set parameters that need to be defined before atoms are created or +read-in from a file. + +The relevant commands are "units"_units.html, +"dimension"_dimension.html, "newton"_newton.html, +"processors"_processors.html, "boundary"_boundary.html, +"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. + +If force-field parameters appear in the files that will be read, these +commands tell LAMMPS what kinds of force fields are being used: +"pair_style"_pair_style.html, "bond_style"_bond_style.html, +"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, +"improper_style"_improper_style.html. + +(2) Atom definition + +There are 3 ways to define atoms in LAMMPS. Read them in from a data +or restart file via the "read_data"_read_data.html or +"read_restart"_read_restart.html commands. These files can contain +molecular topology information. Or create atoms on a lattice (with no +molecular topology), using these commands: "lattice"_lattice.html, +"region"_region.html, "create_box"_create_box.html, +"create_atoms"_create_atoms.html. The entire set of atoms can be +duplicated to make a larger simulation using the +"replicate"_replicate.html command. + +(3) Settings + +Once atoms and molecular topology are defined, a variety of settings +can be specified: force field coefficients, simulation parameters, +output options, etc. + +Force field coefficients are set by these commands (they can also be +set in the read-in files): "pair_coeff"_pair_coeff.html, +"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, +"dihedral_coeff"_dihedral_coeff.html, +"improper_coeff"_improper_coeff.html, +"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, +"special_bonds"_special_bonds.html. + +Various simulation parameters are set by these commands: +"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, +"group"_group.html, "timestep"_timestep.html, +"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, +"min_style"_min_style.html, "min_modify"_min_modify.html. + +Fixes impose a variety of boundary conditions, time integration, and +diagnostic options. The "fix"_fix.html command comes in many flavors. + +Various computations can be specified for execution during a +simulation using the "compute"_compute.html, +"compute_modify"_compute_modify.html, and "variable"_variable.html +commands. + +Output options are set by the "thermo"_thermo.html, "dump"_dump.html, +and "restart"_restart.html commands. + +(4) Run a simulation + +A molecular dynamics simulation is run using the "run"_run.html +command. Energy minimization (molecular statics) is performed using +the "minimize"_minimize.html command. A parallel tempering +(replica-exchange) simulation can be run using the +"temper"_temper.html command. + diff --git a/doc/src/Developer/developer.tex b/doc/src/Developer/developer.tex index 9d9a93a53d7cd83aa6518e6d7fcce6da0c7880f5..8852f441680eb4921a010fe5399f21b865e29585 100644 --- a/doc/src/Developer/developer.tex +++ b/doc/src/Developer/developer.tex @@ -476,7 +476,7 @@ is the name of the class. This code allows LAMMPS to find your fix when it parses input script. In addition, your fix header must be included in the file "style\_fix.h". In case if you use LAMMPS make, this file is generated automatically - all files starting with prefix -fix\_ are included, so call your header the same way. Otherwise, dont +fix\_ are included, so call your header the same way. Otherwise, don't forget to add your include into "style\_fix.h". Let's write a simple fix which will print average velocity at the end diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9cd8214b4c2be66334502ddb3fa8d2cc607b02c9 Binary files /dev/null and b/doc/src/Eqs/fix_integration_spin_stdecomposition.jpg differ diff --git a/doc/src/Eqs/fix_integration_spin_stdecomposition.tex b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex new file mode 100644 index 0000000000000000000000000000000000000000..8c7baf296d1773a8e5371133c5a35a92615424da --- /dev/null +++ b/doc/src/Eqs/fix_integration_spin_stdecomposition.tex @@ -0,0 +1,40 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm,tikz} +\usetikzlibrary{automata,arrows,shapes,snakes} +\begin{document} +\begin{varwidth}{50in} +\begin{tikzpicture} + +%Global +\node (v1) at (0,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; +\node (s1) at (0,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (r) at (0,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{r} \leftarrow \bm{r}+L_r.\Delta t$ }; +\node (s2) at (0,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{s} \leftarrow \bm{s}+L_s.\Delta t/2$ }; +\node (v2) at (0,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] { $\bm{v} \leftarrow \bm{v}+L_v.\Delta t/2$ }; + +\draw[line width=2pt, ->] (v1) -- (s1); +\draw[line width=2pt, ->] (s1) -- (r); +\draw[line width=2pt, ->] (r) -- (s2); +\draw[line width=2pt, ->] (s2) -- (v2); + +%Spin +\node (s01) at (6,6.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; +\node (sN1) at (6,4.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (sN) at (6,3.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N} \leftarrow \bm{s}_{\rm N}+L_{s_{\rm N}}.\Delta t/2$ }; +\node (sN2) at (6,1.5) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_{\rm N-1}\leftarrow\bm{s}_{\rm N-1}+L_{s_{\rm N-1}}.\Delta t/4$}; +\node (s02) at (6,0.0) [draw,thick,minimum width=0.2cm,minimum height=0.2cm] {$\bm{s}_0 \leftarrow \bm{s}_0+L_{s_0}.\Delta t/4$ }; + +\draw[line width=2pt,dashed, ->] (s01) -- (sN1); +\draw[line width=2pt, ->] (sN1) -- (sN); +\draw[line width=2pt, ->] (sN) -- (sN2); +\draw[line width=2pt,dashed, ->] (sN2) -- (s02); + +%from Global to Spin +\draw[line width=2pt, dashed, ->] (s1) -- (s01.west); +\draw[line width=2pt, dashed, ->] (s1) -- (s02.west); + +\end{tikzpicture} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.jpg b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg new file mode 100644 index 0000000000000000000000000000000000000000..f83aadd9eb1f61a70f34ab91ca89bfb32a9d7930 Binary files /dev/null and b/doc/src/Eqs/fix_langevin_spin_sLLG.jpg differ diff --git a/doc/src/Eqs/fix_langevin_spin_sLLG.tex b/doc/src/Eqs/fix_langevin_spin_sLLG.tex new file mode 100644 index 0000000000000000000000000000000000000000..346dde9cec587b7d409ac42fb062d253b04e9b99 --- /dev/null +++ b/doc/src/Eqs/fix_langevin_spin_sLLG.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \frac{d \vec{s}_{i}}{dt} = \frac{1}{\left(1+\lambda^2 \right)} \left( \left( + \vec{\omega}_{i} +\vec{\eta} \right) \times \vec{s}_{i} + \lambda\, \vec{s}_{i} + \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) \right), \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_aniso.jpg b/doc/src/Eqs/force_spin_aniso.jpg new file mode 100644 index 0000000000000000000000000000000000000000..8bc9d7421c23853dcce1601df6b8ffc459a37605 Binary files /dev/null and b/doc/src/Eqs/force_spin_aniso.jpg differ diff --git a/doc/src/Eqs/force_spin_aniso.tex b/doc/src/Eqs/force_spin_aniso.tex new file mode 100644 index 0000000000000000000000000000000000000000..d6abfd580d1d848dad55515ad037ac32cb5b4ce0 --- /dev/null +++ b/doc/src/Eqs/force_spin_aniso.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{aniso} = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/force_spin_zeeman.jpg b/doc/src/Eqs/force_spin_zeeman.jpg new file mode 100644 index 0000000000000000000000000000000000000000..14fb5500cf3328480bd30dc352de699575201bf8 Binary files /dev/null and b/doc/src/Eqs/force_spin_zeeman.jpg differ diff --git a/doc/src/Eqs/force_spin_zeeman.tex b/doc/src/Eqs/force_spin_zeeman.tex new file mode 100644 index 0000000000000000000000000000000000000000..d623ef85ae32cbb4dab12d51c2370ca41820e335 --- /dev/null +++ b/doc/src/Eqs/force_spin_zeeman.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_body_rounded.jpg b/doc/src/Eqs/pair_body_rounded.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e7136ddd20c2acea0e89fa8412497333f15cb541 Binary files /dev/null and b/doc/src/Eqs/pair_body_rounded.jpg differ diff --git a/doc/src/Eqs/pair_body_rounded.tex b/doc/src/Eqs/pair_body_rounded.tex new file mode 100644 index 0000000000000000000000000000000000000000..54e095340f1ab3ae13d672d35797a56faeee927a --- /dev/null +++ b/doc/src/Eqs/pair_body_rounded.tex @@ -0,0 +1,13 @@ +\documentstyle[12pt]{article} + +\begin{document} + +\begin{eqnarray*} + F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\ + &=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\ + F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\ + &=& 0 \qquad \qquad \qquad \qquad \delta_n > 0 +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_entropy.jpg b/doc/src/Eqs/pair_entropy.jpg new file mode 100644 index 0000000000000000000000000000000000000000..44161e6aa0e74a05544f8f29aab3ca942ef305a5 Binary files /dev/null and b/doc/src/Eqs/pair_entropy.jpg differ diff --git a/doc/src/Eqs/pair_entropy.tex b/doc/src/Eqs/pair_entropy.tex new file mode 100644 index 0000000000000000000000000000000000000000..304c9d6138500061a55df40a6d8fb9b7863b45d7 --- /dev/null +++ b/doc/src/Eqs/pair_entropy.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy2.jpg b/doc/src/Eqs/pair_entropy2.jpg new file mode 100644 index 0000000000000000000000000000000000000000..db3dcb0ca75f444a6640e704c61326d7c8c598a9 Binary files /dev/null and b/doc/src/Eqs/pair_entropy2.jpg differ diff --git a/doc/src/Eqs/pair_entropy2.tex b/doc/src/Eqs/pair_entropy2.tex new file mode 100644 index 0000000000000000000000000000000000000000..c91004840fee1a3998702a2ce61cd14c85048b71 --- /dev/null +++ b/doc/src/Eqs/pair_entropy2.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_entropy3.jpg b/doc/src/Eqs/pair_entropy3.jpg new file mode 100644 index 0000000000000000000000000000000000000000..0d5e0025b7200f9ca4255c48bd2bbabb291553a2 Binary files /dev/null and b/doc/src/Eqs/pair_entropy3.jpg differ diff --git a/doc/src/Eqs/pair_entropy3.tex b/doc/src/Eqs/pair_entropy3.tex new file mode 100644 index 0000000000000000000000000000000000000000..b0b3c763585dc98de3a66cde754a2bcd90db91f3 --- /dev/null +++ b/doc/src/Eqs/pair_entropy3.tex @@ -0,0 +1,10 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +$$ + \bar{s}_S^i = \frac{\sum_j s_S^j + s_S^i}{N + 1} , +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_forces.jpg b/doc/src/Eqs/pair_spin_dmi_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..fba6a91cbf6fdb6ee6736073a114d08c907d6d3c Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_forces.tex b/doc/src/Eqs/pair_spin_dmi_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..1c0c246db4c70852212f86c9a7ab7e6b518c323c --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_forces.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) + ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) + , \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.jpg b/doc/src/Eqs/pair_spin_dmi_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..3eb24c67e3b26f97c362fd05982ead5fb0f5c150 Binary files /dev/null and b/doc/src/Eqs/pair_spin_dmi_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_dmi_interaction.tex b/doc/src/Eqs/pair_spin_dmi_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..79f63a333a6c823258f5d9012fa40561e00fb9cb --- /dev/null +++ b/doc/src/Eqs/pair_spin_dmi_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} + \left( \vec{e}_{ij} \times \vec{D} \right) + \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), + \nonumber + \end{equation} +\end{varwidth} +\end{document} + \vec{D}\left(r_{ij}\right) + {\rm ~and~} \vec{D}\left(r_{ij}\right) = \vec{e}_{ij} \times \vec{D} diff --git a/doc/src/Eqs/pair_spin_exchange_forces.jpg b/doc/src/Eqs/pair_spin_exchange_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b312a9ccdaaf44b7647f2c444c7d79a740cea88c Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_forces.tex b/doc/src/Eqs/pair_spin_exchange_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..ac5ef682f3ca9d9532ff6d258cb1012529058636 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_forces.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} + \left(r_{ij} \right)\,\vec{s}_{j} + ~~{\rm and}~~ + \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{ + \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij} + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_function.jpg b/doc/src/Eqs/pair_spin_exchange_function.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d9a7ed3ce0ba64ef054f9ca7c2115ab971d003e5 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_function.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_function.tex b/doc/src/Eqs/pair_spin_exchange_function.tex new file mode 100644 index 0000000000000000000000000000000000000000..054c6992f0136c814dbdafdd88cb2934681ece21 --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_function.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + {J}\left( r_{ij} \right) = 4 a \left( \frac{r_{ij}}{d} \right)^2 \left( 1 - b \left( \frac{r_{ij}}{d} \right)^2 \right) e^{-\left( \frac{r_{ij}}{d} + \right)^2 }\Theta (R_c - r_{ij}) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.jpg b/doc/src/Eqs/pair_spin_exchange_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c70d8a6554003e37472d648c1944a13ee9d3f859 Binary files /dev/null and b/doc/src/Eqs/pair_spin_exchange_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_exchange_interaction.tex b/doc/src/Eqs/pair_spin_exchange_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..f20b3e5740ce2db9cb86a70910ca2b80f263fe4f --- /dev/null +++ b/doc/src/Eqs/pair_spin_exchange_interaction.tex @@ -0,0 +1,11 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_forces.jpg b/doc/src/Eqs/pair_spin_me_forces.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d9ae440fb577c5f33d23029ff187175ba7163ac4 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_forces.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_forces.tex b/doc/src/Eqs/pair_spin_me_forces.tex new file mode 100644 index 0000000000000000000000000000000000000000..f9462fc3d50480294787f063048b9a7acba118b8 --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_forces.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{F}^{i} = -\sum_{j}^{Neighbor} \left( \vec{s}_{i}\times \vec{s}_{j} \right) + \times \vec{E} ~~{\rm and}~~ \vec{\omega}^{i} = -\frac{1}{\hbar} + \sum_{j}^{Neighbor} \vec{s}_j \times \left(\vec{E}\times r_{ij} \right),\nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_me_interaction.jpg b/doc/src/Eqs/pair_spin_me_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..8ecddc959226c0e94fa533f36ad84f3afced6ba6 Binary files /dev/null and b/doc/src/Eqs/pair_spin_me_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_me_interaction.tex b/doc/src/Eqs/pair_spin_me_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..64501e9c2fa44243c2859c7ca096003d0b22653b --- /dev/null +++ b/doc/src/Eqs/pair_spin_me_interaction.tex @@ -0,0 +1,12 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times\vec{D}(r_{ij}) ~~{\rm and}~~ + \vec{F}_i = -\sum_{j}^{Neighb} \frac{\partial D(r_{ij})}{\partial r_{ij}} \left(\vec{s}_{i}\times \vec{s}_{j} \right) \cdot \vec{r}_{ij}, \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_functions.jpg b/doc/src/Eqs/pair_spin_neel_functions.jpg new file mode 100644 index 0000000000000000000000000000000000000000..57023634bf9de762613994e44174702f83c630d0 Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_functions.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_functions.tex b/doc/src/Eqs/pair_spin_neel_functions.tex new file mode 100644 index 0000000000000000000000000000000000000000..ead5a2b87a2fc879c1b3739b627f74b90f05dddf --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_functions.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{eqnarray} + g_1(r_{ij}) &=& g(r_{ij}) + \frac{12}{35} q(r_{ij}) \nonumber \\ + q_1(r_{ij}) &=& \frac{9}{5} q(r_{ij}) \nonumber \\ + q_2(r_{ij}) &=& - \frac{2}{5} q(r_{ij}) \nonumber + \end{eqnarray} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_spin_neel_interaction.jpg b/doc/src/Eqs/pair_spin_neel_interaction.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c30600d840e56bd04d994a0d16d73c80ddf760dd Binary files /dev/null and b/doc/src/Eqs/pair_spin_neel_interaction.jpg differ diff --git a/doc/src/Eqs/pair_spin_neel_interaction.tex b/doc/src/Eqs/pair_spin_neel_interaction.tex new file mode 100644 index 0000000000000000000000000000000000000000..8b4ac33e732cccf30e83e56269617dac780e7cac --- /dev/null +++ b/doc/src/Eqs/pair_spin_neel_interaction.tex @@ -0,0 +1,16 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath,amssymb,amsthm,bm} +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \mathcal{H}_{N\acute{e}el}=-\sum_{{ i,j=1,i\neq j}}^N g_1(r_{ij})\left(({\bm e}_{ij}\cdot {\bm s}_{i})({\bm e}_{ij} + \cdot {\bm s}_{j})-\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + +q_1(r_{ij})\left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3}\right) + \left( ({\bm e}_{ij}\cdot {\bm s}_{i})^2 -\frac{{\bm s}_{i}\cdot{\bm s}_{j}}{3} \right) + + q_2(r_{ij}) \Big( ({\bm e}_{ij}\cdot {\bm s}_{i}) ({\bm e}_{ij}\cdot {\bm s}_{j})^3 + ({\bm e}_{ij}\cdot + {\bm s}_{j}) ({\bm e}_{ij}\cdot {\bm s}_{i})^3\Big) \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b6206c780e7a8e02ea5303ad09889dd070e44a0 --- /dev/null +++ b/doc/src/Errors.txt @@ -0,0 +1,37 @@ +"Previous Section"_Python.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Manual.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Errors :h2 + +These doc pages describe the errors you can encounter when using +LAMMPS. The common problems include conceptual issues. The messages +and warnings doc pages give complete lists of all the messages the +code may generate (except those generated by USER packages), with +additional details for many of them. + + + + + +"Common problems"_Errors_common.html +"Reporting bugs"_Errors_bugs.html +"Error messages"_Errors_messages.html +"Warning messages"_Errors_warnings.html :all(b) + + diff --git a/doc/src/Errors_bugs.txt b/doc/src/Errors_bugs.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a8e62e77546206de35b1132a3484d731db61af3 --- /dev/null +++ b/doc/src/Errors_bugs.txt @@ -0,0 +1,35 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Reporting bugs :h3 + +If you are confident that you have found a bug in LAMMPS, follow these +steps. + +Check the "New features and bug +fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW +site"_lws to see if the bug has already been reported or fixed or the +"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is +pending. + +Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if +it has been discussed before. + +If not, send an email to the mailing list describing the problem with +any ideas you have as to what is causing it or where in the code the +problem might be. The developers will ask for more info if needed, +such as an input script or data files. + +The most useful thing you can do to help us fix the bug is to isolate +the problem. Run it on the smallest number of atoms and fewest number +of processors and with the simplest input script that reproduces the +bug and try to identify what command or combination of commands is +causing the problem. + +NOTE: this page needs to have GitHub issues info added diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt new file mode 100644 index 0000000000000000000000000000000000000000..43d1a85a7bd0ff2772c5dfeb690073d93d50bb10 --- /dev/null +++ b/doc/src/Errors_common.txt @@ -0,0 +1,123 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Common problems :h3 + +If two LAMMPS runs do not produce the exact same answer on different +machines or different numbers of processors, this is typically not a +bug. In theory you should get identical answers on any number of +processors and on any machine. In practice, numerical round-off can +cause slight differences and eventual divergence of molecular dynamics +phase space trajectories within a few 100s or few 1000s of timesteps. +However, the statistical properties of the two runs (e.g. average +energy or temperature) should still be the same. + +If the "velocity"_velocity.html command is used to set initial atom +velocities, a particular atom can be assigned a different velocity +when the problem is run on a different number of processors or on +different machines. If this happens, the phase space trajectories of +the two simulations will rapidly diverge. See the discussion of the +{loop} option in the "velocity"_velocity.html command for details and +options that avoid this issue. + +Similarly, the "create_atoms"_create_atoms.html command generates a +lattice of atoms. For the same physical system, the ordering and +numbering of atoms by atom ID may be different depending on the number +of processors. + +Some commands use random number generators which may be setup to +produce different random number streams on each processor and hence +will produce different effects when run on different numbers of +processors. A commonly-used example is the "fix +langevin"_fix_langevin.html command for thermostatting. + +A LAMMPS simulation typically has two stages, setup and run. Most +LAMMPS errors are detected at setup time; others like a bond +stretching too far may not occur until the middle of a run. + +LAMMPS tries to flag errors and print informative error messages so +you can fix the problem. For most errors it will also print the last +input script command that it was processing. Of course, LAMMPS cannot +figure out your physics or numerical mistakes, like choosing too big a +timestep, specifying erroneous force field coefficients, or putting 2 +atoms on top of each other! If you run into errors that LAMMPS +doesn't catch that you think it should flag, please send an email to +the "developers"_http://lammps.sandia.gov/authors.html. + +If you get an error message about an invalid command in your input +script, you can determine what command is causing the problem by +looking in the log.lammps file or using the "echo command"_echo.html +to see it on the screen. If you get an error like "Invalid ... +style", with ... being fix, compute, pair, etc, it means that you +mistyped the style name or that the command is part of an optional +package which was not compiled into your executable. The list of +available styles in your executable can be listed by using "the -h +command-line argument"_Section_start.html#start_6. The installation +and compilation of optional packages is explained in the "installation +instructions"_Section_start.html#start_3. + +For a given command, LAMMPS expects certain arguments in a specified +order. If you mess this up, LAMMPS will often flag the error, but it +may also simply read a bogus argument and assign a value that is +valid, but not what you wanted. E.g. trying to read the string "abc" +as an integer value of 0. Careful reading of the associated doc page +for the command should allow you to fix these problems. In most cases, +where LAMMPS expects to read a number, either integer or floating point, +it performs a stringent test on whether the provided input actually +is an integer or floating-point number, respectively, and reject the +input with an error message (for instance, when an integer is required, +but a floating-point number 1.0 is provided): + +ERROR: Expected integer parameter in input script or data file :pre + +Some commands allow for using variable references in place of numeric +constants so that the value can be evaluated and may change over the +course of a run. This is typically done with the syntax {v_name} for a +parameter, where name is the name of the variable. On the other hand, +immediate variable expansion with the syntax ${name} is performed while +reading the input and before parsing commands, + +NOTE: Using a variable reference (i.e. {v_name}) is only allowed if +the documentation of the corresponding command explicitly says it is. + +Generally, LAMMPS will print a message to the screen and logfile and +exit gracefully when it encounters a fatal error. Sometimes it will +print a WARNING to the screen and logfile and continue on; you can +decide if the WARNING is important or not. A WARNING message that is +generated in the middle of a run is only printed to the screen, not to +the logfile, to avoid cluttering up thermodynamic output. If LAMMPS +crashes or hangs without spitting out an error message first then it +could be a bug (see "this section"_#err_2) or one of the following +cases: + +LAMMPS runs in the available memory a processor allows to be +allocated. Most reasonable MD runs are compute limited, not memory +limited, so this shouldn't be a bottleneck on most platforms. Almost +all large memory allocations in the code are done via C-style malloc's +which will generate an error message if you run out of memory. +Smaller chunks of memory are allocated via C++ "new" statements. If +you are unlucky you could run out of memory just when one of these +small requests is made, in which case the code will crash or hang (in +parallel), since LAMMPS doesn't trap on those errors. + +Illegal arithmetic can cause LAMMPS to run slow or crash. This is +typically due to invalid physics and numerics that your simulation is +computing. If you see wild thermodynamic values or NaN values in your +LAMMPS output, something is wrong with your simulation. If you +suspect this is happening, it is a good idea to print out +thermodynamic info frequently (e.g. every timestep) via the +"thermo"_thermo.html so you can monitor what is happening. +Visualizing the atom movement is also a good idea to insure your model +is behaving as you expect. + +In parallel, one way LAMMPS can hang is due to how different MPI +implementations handle buffering of messages. If the code hangs +without an error message, it may be that you need to specify an MPI +setting or two (usually via an environment variable) to enable +buffering or boost the sizes of messages that can be buffered. diff --git a/doc/src/Section_errors.txt b/doc/src/Errors_messages.txt similarity index 87% rename from doc/src/Section_errors.txt rename to doc/src/Errors_messages.txt index 2821f1ff5d046d9b6ef94d8dc4a1e3eb8cb70b58..03fc25b5618c3b6803c719cdbb5473edad5cbf6a 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Errors_messages.txt @@ -1,192 +1,33 @@ -"Previous Section"_Section_python.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_history.html :c +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -12. Errors :h2 +Error messages :h3 -This section describes the errors you can encounter when using LAMMPS, -either conceptually, or as printed out by the program. +This is an alphabetic list of the ERROR messages LAMMPS prints out and +the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Error messages also +list the source file and line number where the error was generated. +For example, a message like this: -12.1 "Common problems"_#err_1 -12.2 "Reporting bugs"_#err_2 -12.3 "Error & warning messages"_#err_3 :all(b) - -:line -:line - -12.1 Common problems :link(err_1),h4 - -If two LAMMPS runs do not produce the exact same answer on different -machines or different numbers of processors, this is typically not a -bug. In theory you should get identical answers on any number of -processors and on any machine. In practice, numerical round-off can -cause slight differences and eventual divergence of molecular dynamics -phase space trajectories within a few 100s or few 1000s of timesteps. -However, the statistical properties of the two runs (e.g. average -energy or temperature) should still be the same. - -If the "velocity"_velocity.html command is used to set initial atom -velocities, a particular atom can be assigned a different velocity -when the problem is run on a different number of processors or on -different machines. If this happens, the phase space trajectories of -the two simulations will rapidly diverge. See the discussion of the -{loop} option in the "velocity"_velocity.html command for details and -options that avoid this issue. - -Similarly, the "create_atoms"_create_atoms.html command generates a -lattice of atoms. For the same physical system, the ordering and -numbering of atoms by atom ID may be different depending on the number -of processors. - -Some commands use random number generators which may be setup to -produce different random number streams on each processor and hence -will produce different effects when run on different numbers of -processors. A commonly-used example is the "fix -langevin"_fix_langevin.html command for thermostatting. - -A LAMMPS simulation typically has two stages, setup and run. Most -LAMMPS errors are detected at setup time; others like a bond -stretching too far may not occur until the middle of a run. - -LAMMPS tries to flag errors and print informative error messages so -you can fix the problem. For most errors it will also print the last -input script command that it was processing. Of course, LAMMPS cannot -figure out your physics or numerical mistakes, like choosing too big a -timestep, specifying erroneous force field coefficients, or putting 2 -atoms on top of each other! If you run into errors that LAMMPS -doesn't catch that you think it should flag, please send an email to -the "developers"_http://lammps.sandia.gov/authors.html. - -If you get an error message about an invalid command in your input -script, you can determine what command is causing the problem by -looking in the log.lammps file or using the "echo command"_echo.html -to see it on the screen. If you get an error like "Invalid ... -style", with ... being fix, compute, pair, etc, it means that you -mistyped the style name or that the command is part of an optional -package which was not compiled into your executable. The list of -available styles in your executable can be listed by using "the -h -command-line argument"_Section_start.html#start_6. The installation -and compilation of optional packages is explained in the "installation -instructions"_Section_start.html#start_3. - -For a given command, LAMMPS expects certain arguments in a specified -order. If you mess this up, LAMMPS will often flag the error, but it -may also simply read a bogus argument and assign a value that is -valid, but not what you wanted. E.g. trying to read the string "abc" -as an integer value of 0. Careful reading of the associated doc page -for the command should allow you to fix these problems. In most cases, -where LAMMPS expects to read a number, either integer or floating point, -it performs a stringent test on whether the provided input actually -is an integer or floating-point number, respectively, and reject the -input with an error message (for instance, when an integer is required, -but a floating-point number 1.0 is provided): - -ERROR: Expected integer parameter in input script or data file :pre - -Some commands allow for using variable references in place of numeric -constants so that the value can be evaluated and may change over the -course of a run. This is typically done with the syntax {v_name} for a -parameter, where name is the name of the variable. On the other hand, -immediate variable expansion with the syntax ${name} is performed while -reading the input and before parsing commands, - -NOTE: Using a variable reference (i.e. {v_name}) is only allowed if -the documentation of the corresponding command explicitly says it is. - -Generally, LAMMPS will print a message to the screen and logfile and -exit gracefully when it encounters a fatal error. Sometimes it will -print a WARNING to the screen and logfile and continue on; you can -decide if the WARNING is important or not. A WARNING message that is -generated in the middle of a run is only printed to the screen, not to -the logfile, to avoid cluttering up thermodynamic output. If LAMMPS -crashes or hangs without spitting out an error message first then it -could be a bug (see "this section"_#err_2) or one of the following -cases: - -LAMMPS runs in the available memory a processor allows to be -allocated. Most reasonable MD runs are compute limited, not memory -limited, so this shouldn't be a bottleneck on most platforms. Almost -all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. -Smaller chunks of memory are allocated via C++ "new" statements. If -you are unlucky you could run out of memory just when one of these -small requests is made, in which case the code will crash or hang (in -parallel), since LAMMPS doesn't trap on those errors. - -Illegal arithmetic can cause LAMMPS to run slow or crash. This is -typically due to invalid physics and numerics that your simulation is -computing. If you see wild thermodynamic values or NaN values in your -LAMMPS output, something is wrong with your simulation. If you -suspect this is happening, it is a good idea to print out -thermodynamic info frequently (e.g. every timestep) via the -"thermo"_thermo.html so you can monitor what is happening. -Visualizing the atom movement is also a good idea to insure your model -is behaving as you expect. - -In parallel, one way LAMMPS can hang is due to how different MPI -implementations handle buffering of messages. If the code hangs -without an error message, it may be that you need to specify an MPI -setting or two (usually via an environment variable) to enable -buffering or boost the sizes of messages that can be buffered. - -:line - -12.2 Reporting bugs :link(err_2),h4 - -If you are confident that you have found a bug in LAMMPS, follow these -steps. - -Check the "New features and bug -fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW -site"_lws to see if the bug has already been reported or fixed or the -"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is -pending. - -Check the "mailing list"_http://lammps.sandia.gov/mail.html -to see if it has been discussed before. - -If not, send an email to the mailing list describing the problem with -any ideas you have as to what is causing it or where in the code the -problem might be. The developers will ask for more info if needed, -such as an input script or data files. - -The most useful thing you can do to help us fix the bug is to isolate -the problem. Run it on the smallest number of atoms and fewest number -of processors and with the simplest input script that reproduces the -bug and try to identify what command or combination of commands is -causing the problem. - -As a last resort, you can send an email directly to the -"developers"_http://lammps.sandia.gov/authors.html. - -:line - -12.3 Error & warning messages :h3,link(err_3) - -These are two alphabetic lists of the "ERROR"_#error and -"WARNING"_#warn messages LAMMPS prints out and the reason why. If the -explanation here is not sufficient, the documentation for the -offending command may help. -Error and warning messages also list the source file and line number -where the error was generated. For example, this message - -ERROR: Illegal velocity command (velocity.cpp:78) +ERROR: Illegal velocity command (velocity.cpp:78) :pre means that line #78 in the file src/velocity.cpp generated the error. Looking in the source code may help you figure out what went wrong. Note that error messages from "user-contributed -packages"_Section_start.html#start_3 are not listed here. If such an -error occurs and is not self-explanatory, you'll need to look in the -source code or contact the author of the package. +packages"_Packages_user.html are not listed here. If such an error +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. -Errors: :h3,link(error) +Doc page with "WARNING messages"_Errors_warnings.html + +:line :dlb @@ -10996,904 +10837,3 @@ Self-explanatory. :dd Self-explanatory. :dd :dle - -Warnings: :h3,link(warn) - -:dlb - -{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt - -The adjust/cutoff command is turned on and the Coulombic cutoff has been -adjusted to match the user-specified accuracy. :dd - -{Angle atoms missing at step %ld} :dt - -One or more of 3 atoms needed to compute a particular angle are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the angle has blown apart and an atom is -too far away. :dd - -{Angle style in data file differs from currently defined angle style} :dt - -Self-explanatory. :dd - -{Atom style in data file differs from currently defined atom style} :dt - -Self-explanatory. :dd - -{Bond atom missing in box size check} :dt - -The 2nd atoms needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond atom missing in image check} :dt - -The 2nd atom in a particular bond is missing on this processor. -Typically this is because the pairwise cutoff is set too short or the -bond has blown apart and an atom is too far away. :dd - -{Bond atoms missing at step %ld} :dt - -The 2nd atom needed to compute a particular bond is missing on this -processor. Typically this is because the pairwise cutoff is set too -short or the bond has blown apart and an atom is too far away. :dd - -{Bond style in data file differs from currently defined bond style} :dt - -Self-explanatory. :dd - -{Bond/angle/dihedral extent > half of periodic box length} :dt - -This is a restriction because LAMMPS can be confused about which image -of an atom in the bonded interaction is the correct one to use. -"Extent" in this context means the maximum end-to-end length of the -bond/angle/dihedral. LAMMPS computes this by taking the maximum bond -length, multiplying by the number of bonds in the interaction (e.g. 3 -for a dihedral) and adding a small amount of stretch. :dd - -{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt - -Self-explanatory. :dd - -{Calling write_dump before a full system init.} :dt - -The write_dump command is used before the system has been fully -initialized as part of a 'run' or 'minimize' command. Not all dump -styles and features are fully supported at this point and thus the -command may fail or produce incomplete or incorrect output. Insert -a "run 0" command, if a full system init is required. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt - -This means the temperature associated with the rigid bodies may be -incorrect on this timestep. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt - -Self-explanatory. :dd - -{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt - -Self-explanatory. :dd - -{Charges are set, but coulombic solver is not used} :dt - -Self-explanatory. :dd - -{Charges did not converge at step %ld: %lg} :dt - -Self-explanatory. :dd - -{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt - -Self-explanatory. :dd - -{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt - -The neighbor cutoff used may not encompass enough ghost atoms -to perform this operation correctly. :dd - -{Computing temperature of portions of rigid bodies} :dt - -The group defined by the temperature compute does not encompass all -the atoms in one or more rigid bodies, so the change in -degrees-of-freedom for the atoms in those partial rigid bodies will -not be accounted for. :dd - -{Create_bonds max distance > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus no bond can be created between them. :dd - -{Delete_atoms cutoff > minimum neighbor cutoff} :dt - -This means atom pairs for some atom types may not be in the neighbor -list and thus an atom in that pair cannot be deleted. :dd - -{Dihedral atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular dihedral are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the dihedral has blown apart and an atom is -too far away. :dd - -{Dihedral problem} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Dihedral style in data file differs from currently defined dihedral style} :dt - -Self-explanatory. :dd - -{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt - -If the fix changes the timestep, the dump dcd file will not -reflect the change. :dd - -{Energy due to X extra global DOFs will be included in minimizer energies} :dt - -When using fixes like box/relax, the potential energy used by the minimizer -is augmented by an additional energy provided by the fix. Thus the printed -converged energy may be different from the total potential energy. :dd - -{Energy tally does not account for 'zero yes'} :dt - -The energy removed by using the 'zero yes' flag is not accounted -for in the energy tally and thus energy conservation cannot be -monitored in this case. :dd - -{Estimated error in splitting of dispersion coeffs is %g} :dt - -Error is greater than 0.0001 percent. :dd - -{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt - -Self-explanatory. Choosing a different cutoff value may help. :dd - -{FENE bond too long} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %d %d %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{FENE bond too long: %ld %g} :dt - -A FENE bond has stretched dangerously far. It's interaction strength -will be truncated to attempt to prevent the bond from blowing up. :dd - -{Fix SRD walls overlap but fix srd overlap not set} :dt - -You likely want to set this in your input script. :dd - -{Fix bond/swap will ignore defined angles} :dt - -See the doc page for fix bond/swap for more info on this -restriction. :dd - -{Fix deposit near setting < possible overlap separation %g} :dt - -This test is performed for finite size particles with a diameter, not -for point particles. The near setting is smaller than the particle -diameter which can lead to overlaps. :dd - -{Fix evaporate may delete atom with non-zero molecule ID} :dt - -This is probably an error, since you should not delete only one atom -of a molecule. :dd - -{Fix gcmc using full_energy option} :dt - -Fix gcmc has automatically turned on the full_energy option since it -is required for systems like the one specified by the user. User input -included one or more of the following: kspace, triclinic, a hybrid -pair style, an eam pair style, or no "single" function for the pair -style. :dd - -{Fix property/atom mol or charge w/out ghost communication} :dt - -A model typically needs these properties defined for ghost atoms. :dd - -{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt - -Self-explanatory. :dd - -{Fix qeq has non-zero lower Taper radius cutoff} :dt - -Absolute value must be <= 0.01. :dd - -{Fix qeq has very low Taper radius cutoff} :dt - -Value should typically be >= 5.0. :dd - -{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt - -Self-explanatory. :dd - -{Fix qeq/fire tolerance may be too small for damped fires} :dt - -Self-explanatory. :dd - -{Fix rattle should come after all other integration fixes} :dt - -This fix is designed to work after all other integration fixes change -atom positions. Thus it should be the last integration fix specified. -If not, it will not satisfy the desired constraints as well as it -otherwise would. :dd - -{Fix recenter should come after all other integration fixes} :dt - -Other fixes may change the position of the center-of-mass, so -fix recenter should come last. :dd - -{Fix srd SRD moves may trigger frequent reneighboring} :dt - -This is because the SRD particles may move long distances. :dd - -{Fix srd grid size > 1/4 of big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd particle moved outside valid domain} :dt - -This may indicate a problem with your simulation parameters. :dd - -{Fix srd particles may move > big particle diameter} :dt - -This may cause accuracy problems. :dd - -{Fix srd viscosity < 0.0 due to low SRD density} :dt - -This may cause accuracy problems. :dd - -{Fix thermal/conductivity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that fix -thermal/conductivity comes first. If you are using fix ave/spatial to -measure the temperature profile induced by fix viscosity, then this -may cause a glitch in the profile since you are averaging immediately -after swaps have occurred. Flipping the order of the 2 fixes -typically helps. :dd - -{Fix viscosity comes before fix ave/spatial} :dt - -The order of these 2 fixes in your input script is such that -fix viscosity comes first. If you are using fix ave/spatial -to measure the velocity profile induced by fix viscosity, then -this may cause a glitch in the profile since you are averaging -immediately after swaps have occurred. Flipping the order -of the 2 fixes typically helps. :dd - -{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt - -This is current restriction with Kokkos. :dd - -{For better accuracy use 'pair_modify table 0'} :dt - -The user-specified force accuracy cannot be achieved unless the table -feature is disabled by using 'pair_modify table 0'. :dd - -{Geometric mixing assumed for 1/r^6 coefficients} :dt - -Self-explanatory. :dd - -{Group for fix_modify temp != fix group} :dt - -The fix_modify command is specifying a temperature computation that -computes a temperature on a different group of atoms than the fix -itself operates on. This is probably not what you want to do. :dd - -{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt - -This is the size of the matrix. :dd - -{Ignoring unknown or incorrect info command flag} :dt - -Self-explanatory. An unknown argument was given to the info command. -Compare your input with the documentation. :dd - -{Improper atoms missing at step %ld} :dt - -One or more of 4 atoms needed to compute a particular improper are -missing on this processor. Typically this is because the pairwise -cutoff is set too short or the improper has blown apart and an atom is -too far away. :dd - -{Improper problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed improper atoms is extreme; you may want -to check your simulation geometry. :dd - -{Improper style in data file differs from currently defined improper style} :dt - -Self-explanatory. :dd - -{Inconsistent image flags} :dt - -The image flags for a pair on bonded atoms appear to be inconsistent. -Inconsistent means that when the coordinates of the two atoms are -unwrapped using the image flags, the two atoms are far apart. -Specifically they are further apart than half a periodic box length. -Or they are more than a box length apart in a non-periodic dimension. -This is usually due to the initial data file not having correct image -flags for the 2 atoms in a bond that straddles a periodic boundary. -They should be different by 1 in that case. This is a warning because -inconsistent image flags will not cause problems for dynamics or most -LAMMPS simulations. However they can cause problems when such atoms -are used with the fix rigid or replicate commands. Note that if you -have an infinite periodic crystal with bonds then it is impossible to -have fully consistent image flags, since some bonds will cross -periodic boundaries and connect two atoms with the same image -flag. :dd - -{KIM Model does not provide 'energy'; Potential energy will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'forces'; Forces will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt - -Self-explanatory. :dd - -{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt - -Self-explanatory. :dd - -{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt - -The kspace_modify slab parameter should be larger to insure periodic -grids padded with empty space do not overlap. :dd - -{Less insertions than requested} :dt - -The fix pour command was unsuccessful at finding open space -for as many particles as it tried to insert. :dd - -{Library error in lammps_gather_atoms} :dt - -This library function cannot be used if atom IDs are not defined -or are not consecutively numbered. :dd - -{Library error in lammps_scatter_atoms} :dt - -This library function cannot be used if atom IDs are not defined or -are not consecutively numbered, or if no atom map is defined. See the -atom_modify command for details about atom maps. :dd - -{Lost atoms via change_box: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms via displace_atoms: original %ld current %ld} :dt - -The command options you have used caused atoms to be lost. :dd - -{Lost atoms: original %ld current %ld} :dt - -Lost atoms are checked for each time thermo output is done. See the -thermo_modify lost command for options. Lost atoms usually indicate -bad dynamics, e.g. atoms have been blown far out of the simulation -box, or moved further than one processor's sub-domain away before -reneighboring. :dd - -{MSM mesh too small, increasing to 2 points in each direction} :dt - -Self-explanatory. :dd - -{Mismatch between velocity and compute groups} :dt - -The temperature computation used by the velocity command will not be -on the same group of atoms that velocities are being set for. :dd - -{Mixing forced for lj coefficients} :dt - -Self-explanatory. :dd - -{Molecule attributes do not match system attributes} :dt - -An attribute is specified (e.g. diameter, charge) that is -not defined for the specified atom style. :dd - -{Molecule has bond topology but no special bond settings} :dt - -This means the bonded atoms will not be excluded in pair-wise -interactions. :dd - -{Molecule template for create_atoms has multiple molecules} :dt - -The create_atoms command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix gcmc has multiple molecules} :dt - -The fix gcmc command will only create molecules of a single type, -i.e. the first molecule in the template. :dd - -{Molecule template for fix shake has multiple molecules} :dt - -The fix shake command will only recognize molecules of a single -type, i.e. the first molecule in the template. :dd - -{More than one compute centro/atom} :dt - -It is not efficient to use compute centro/atom more than once. :dd - -{More than one compute cluster/atom} :dt - -It is not efficient to use compute cluster/atom more than once. :dd - -{More than one compute cna/atom defined} :dt - -It is not efficient to use compute cna/atom more than once. :dd - -{More than one compute contact/atom} :dt - -It is not efficient to use compute contact/atom more than once. :dd - -{More than one compute coord/atom} :dt - -It is not efficient to use compute coord/atom more than once. :dd - -{More than one compute damage/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute dilatation/atom} :dt - -Self-explanatory. :dd - -{More than one compute erotate/sphere/atom} :dt - -It is not efficient to use compute erorate/sphere/atom more than once. :dd - -{More than one compute hexorder/atom} :dt - -It is not efficient to use compute hexorder/atom more than once. :dd - -{More than one compute ke/atom} :dt - -It is not efficient to use compute ke/atom more than once. :dd - -{More than one compute orientorder/atom} :dt - -It is not efficient to use compute orientorder/atom more than once. :dd - -{More than one compute plasticity/atom} :dt - -Self-explanatory. :dd - -{More than one compute sna/atom} :dt - -Self-explanatory. :dd - -{More than one compute snad/atom} :dt - -Self-explanatory. :dd - -{More than one compute snav/atom} :dt - -Self-explanatory. :dd - -{More than one fix poems} :dt - -It is not efficient to use fix poems more than once. :dd - -{More than one fix rigid} :dt - -It is not efficient to use fix rigid more than once. :dd - -{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt - -This is because excluding specific pair interactions also excludes -them from long-range interactions which may not be the desired effect. -The special_bonds command handles this consistently by insuring -excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated -consistently by both the short-range pair style and the long-range -solver. This is not done for exclusions of charged atom pairs via the -neigh_modify exclude command. :dd - -{New thermo_style command, previous thermo_modify settings will be lost} :dt - -If a thermo_style command is used after a thermo_modify command, the -settings changed by the thermo_modify command will be reset to their -default values. This is because the thermo_modify command acts on -the currently defined thermo style, and a thermo_style command creates -a new style. :dd - -{No Kspace calculation with verlet/split} :dt - -The 2nd partition performs a kspace calculation so the kspace_style -command must be used. :dd - -{No automatic unit conversion to XTC file format conventions possible for units lj} :dt - -This means no scaling will be performed. :dd - -{No fixes defined, atoms won't move} :dt - -If you are not using a fix like nve, nvt, npt then atom velocities and -coordinates will not be updated during timestepping. :dd - -{No joints between rigid bodies, use fix rigid instead} :dt - -The bodies defined by fix poems are not connected by joints. POEMS -will integrate the body motion, but it would be more efficient to use -fix rigid. :dd - -{Not using real units with pair reax} :dt - -This is most likely an error, unless you have created your own ReaxFF -parameter file in a different set of units. :dd - -{Number of MSM mesh points changed to be a multiple of 2} :dt - -MSM requires that the number of grid points in each direction be a multiple -of two and the number of grid points in one or more directions have been -adjusted to meet this requirement. :dd - -{OMP_NUM_THREADS environment is not set.} :dt - -This environment variable must be set appropriately to use the -USER-OMP package. :dd - -{One or more atoms are time integrated more than once} :dt - -This is probably an error since you typically do not want to -advance the positions or velocities of an atom more than once -per timestep. :dd - -{One or more chunks do not contain all atoms in molecule} :dt - -This may not be what you intended. :dd - -{One or more dynamic groups may not be updated at correct point in timestep} :dt - -If there are other fixes that act immediately after the initial stage -of time integration within a timestep (i.e. after atoms move), then -the command that sets up the dynamic group should appear after those -fixes. This will insure that dynamic group assignments are made -after all atoms have moved. :dd - -{One or more respa levels compute no forces} :dt - -This is computationally inefficient. :dd - -{Pair COMB charge %.10f with force %.10f hit max barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair COMB charge %.10f with force %.10f hit min barrier} :dt - -Something is possibly wrong with your model. :dd - -{Pair brownian needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dpd needs newton pair on for momentum conservation} :dt - -Self-explanatory. :dd - -{Pair dsmc: num_of_collisions > number_of_A} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair dsmc: num_of_collisions > number_of_B} :dt - -Collision model in DSMC is breaking down. :dd - -{Pair style in data file differs from currently defined pair style} :dt - -Self-explanatory. :dd - -{Particle deposition was unsuccessful} :dt - -The fix deposit command was not able to insert as many atoms as -needed. The requested volume fraction may be too high, or other atoms -may be in the insertion region. :dd - -{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt - -The decomposition of the physical domain (likely due to load -balancing) has led to a processor's sub-domain being smaller than the -neighbor skin in one or more dimensions. Since reneighboring is -triggered by atoms moving the skin distance, this may lead to lost -atoms, if an atom moves all the way across a neighboring processor's -sub-domain before reneighboring is triggered. :dd - -{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt - -This may lead to a larger grid than desired. See the kspace_modify overlap -command to prevent changing of the PPPM order. :dd - -{Replacing a fix, but new group != old group} :dt - -The ID and style of a fix match for a fix you are changing with a fix -command, but the new group you are specifying does not match the old -group. :dd - -{Replicating in a non-periodic dimension} :dt - -The parameters for a replicate command will cause a non-periodic -dimension to be replicated; this may cause unwanted behavior. :dd - -{Resetting reneighboring criteria during PRD} :dt - -A PRD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during TAD} :dt - -A TAD simulation requires that neigh_modify settings be delay = 0, -every = 1, check = yes. Since these settings were not in place, -LAMMPS changed them and will restore them to their original values -after the PRD simulation. :dd - -{Resetting reneighboring criteria during minimization} :dt - -Minimization requires that neigh_modify settings be delay = 0, every = -1, check = yes. Since these settings were not in place, LAMMPS -changed them and will restore them to their original values after the -minimization. :dd - -{Restart file used different # of processors} :dt - -The restart file was written out by a LAMMPS simulation running on a -different number of processors. Due to round-off, the trajectories of -your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different 3d processor grid} :dt - -The restart file was written out by a LAMMPS simulation running on a -different 3d grid of processors. Due to round-off, the trajectories -of your restarted simulation may diverge a little more quickly than if -you ran on the same # of processors. :dd - -{Restart file used different boundary settings, using restart file values} :dt - -Your input script cannot change these restart file settings. :dd - -{Restart file used different newton bond setting, using restart file value} :dt - -The restart file value will override the setting in the input script. :dd - -{Restart file used different newton pair setting, using input script value} :dt - -The input script value will override the setting in the restart file. :dd - -{Restrain problem: %d %ld %d %d %d %d} :dt - -Conformation of the 4 listed dihedral atoms is extreme; you may want -to check your simulation geometry. :dd - -{Running PRD with only one replica} :dt - -This is allowed, but you will get no parallel speed-up. :dd - -{SRD bin shifting turned on due to small lamda} :dt - -This is done to try to preserve accuracy. :dd - -{SRD bin size for fix srd differs from user request} :dt - -Fix SRD had to adjust the bin size to fit the simulation box. See the -cubic keyword if you want this message to be an error vs warning. :dd - -{SRD bins for fix srd are not cubic enough} :dt - -The bin shape is not within tolerance of cubic. See the cubic -keyword if you want this message to be an error vs warning. :dd - -{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{SRD particle %d started inside wall %d on step %ld bounce %d} :dt - -See the inside keyword if you want this message to be an error vs -warning. :dd - -{Shake determinant < 0.0} :dt - -The determinant of the quadratic equation being solved for a single -cluster specified by the fix shake command is numerically suspect. LAMMPS -will set it to 0.0 and continue. :dd - -{Shell command '%s' failed with error '%s'} :dt - -Self-explanatory. :dd - -{Shell command returned with non-zero status} :dt - -This may indicate the shell command did not operate as expected. :dd - -{Should not allow rigid bodies to bounce off relecting walls} :dt - -LAMMPS allows this, but their dynamics are not computed correctly. :dd - -{Should not use fix nve/limit with fix shake or fix rattle} :dt - -This will lead to invalid constraint forces in the SHAKE/RATTLE -computation. :dd - -{Simulations might be very slow because of large number of structure factors} :dt - -Self-explanatory. :dd - -{Slab correction not needed for MSM} :dt - -Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd - -{System is not charge neutral, net charge = %g} :dt - -The total charge on all atoms on the system is not 0.0. -For some KSpace solvers this is only a warning. :dd - -{Table inner cutoff >= outer cutoff} :dt - -You specified an inner cutoff for a Coulombic table that is longer -than the global cutoff. Probably not what you wanted. :dd - -{Temperature for MSST is not for group all} :dt - -User-assigned temperature to MSST fix does not compute temperature for -all atoms. Since MSST computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by MSST could be inaccurate. :dd - -{Temperature for NPT is not for group all} :dt - -User-assigned temperature to NPT fix does not compute temperature for -all atoms. Since NPT computes a global pressure, the kinetic energy -contribution from the temperature is assumed to also be for all atoms. -Thus the pressure used by NPT could be inaccurate. :dd - -{Temperature for fix modify is not for group all} :dt - -The temperature compute is being used with a pressure calculation -which does operate on group all, so this may be inconsistent. :dd - -{Temperature for thermo pressure is not for group all} :dt - -User-assigned temperature to thermo via the thermo_modify command does -not compute temperature for all atoms. Since thermo computes a global -pressure, the kinetic energy contribution from the temperature is -assumed to also be for all atoms. Thus the pressure printed by thermo -could be inaccurate. :dd - -{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt - -Self-explanatory. :dd - -{The minimizer does not re-orient dipoles when using fix efield} :dt - -This means that only the atom coordinates will be minimized, -not the orientation of the dipoles. :dd - -{Too many common neighbors in CNA %d times} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Too many inner timesteps in fix ttm} :dt - -Self-explanatory. :dd - -{Too many neighbors in CNA for %d atoms} :dt - -More than the maximum # of neighbors was found multiple times. This -was unexpected. :dd - -{Triclinic box skew is large} :dt - -The displacement in a skewed direction is normally required to be less -than half the box length in that dimension. E.g. the xy tilt must be -between -half and +half of the x box length. You have relaxed the -constraint using the box tilt command, but the warning means that a -LAMMPS simulation may be inefficient as a result. :dd - -{Use special bonds = 0,1,1 with bond style fene} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Use special bonds = 0,1,1 with bond style fene/expand} :dt - -Most FENE models need this setting for the special_bonds command. :dd - -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt - -This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential -needs to calculated its terms correctly. :dd - -{Using compute temp/deform with inconsistent fix deform remap option} :dt - -Fix nvt/sllod assumes deforming atoms have a velocity profile provided -by "remap v" or "remap none" as a fix deform option. :dd - -{Using compute temp/deform with no fix deform defined} :dt - -This is probably an error, since it makes little sense to use -compute temp/deform in this case. :dd - -{Using fix srd with box deformation but no SRD thermostat} :dt - -The deformation will heat the SRD particles so this can -be dangerous. :dd - -{Using kspace solver on system with no charge} :dt - -Self-explanatory. :dd - -{Using largest cut-off for lj/long/dipole/long long long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for buck/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for lj/long/coul/long} :dt - -Self-explanatory. :dd - -{Using largest cutoff for pair_style lj/long/tip4p/long} :dt - -Self-explanatory. :dd - -{Using package gpu without any pair style defined} :dt - -Self-explanatory. :dd - -{Using pair potential shift with pair_modify compute no} :dt - -The shift effects will thus not be computed. :dd - -{Using pair tail corrections with nonperiodic system} :dt - -This is probably a bogus thing to do, since tail corrections are -computed by integrating the density of a periodic system out to -infinity. :dd - -{Using pair tail corrections with pair_modify compute no} :dt - -The tail corrections will thus not be computed. :dd - -{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt - -Self-explanatory. :dd - -:dle - diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt new file mode 100644 index 0000000000000000000000000000000000000000..dd3402ba8641c487f1a6a4210fa27f1b6ae062ff --- /dev/null +++ b/doc/src/Errors_warnings.txt @@ -0,0 +1,934 @@ +"Higher level section"_Errors.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Warning messages :h3 + +This is an alphabetic list of the WARNING messages LAMMPS prints out +and the reason why. If the explanation here is not sufficient, the +documentation for the offending command may help. Warning messages +also list the source file and line number where the warning was +generated. For example, a message lile this: + +WARNING: Bond atom missing in box size check (domain.cpp:187) :pre + +means that line #187 in the file src/domain.cpp generated the error. +Looking in the source code may help you figure out what went wrong. + +Note that warning messages from "user-contributed +packages"_Packages_user.html are not listed here. If such a warning +occurs and is not self-explanatory, you'll need to look in the source +code or contact the author of the package. + +Doc page with "ERROR messages"_Errors_messages.html + +:line + +:dlb + +{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt + +The adjust/cutoff command is turned on and the Coulombic cutoff has been +adjusted to match the user-specified accuracy. :dd + +{Angle atoms missing at step %ld} :dt + +One or more of 3 atoms needed to compute a particular angle are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the angle has blown apart and an atom is +too far away. :dd + +{Angle style in data file differs from currently defined angle style} :dt + +Self-explanatory. :dd + +{Atom style in data file differs from currently defined atom style} :dt + +Self-explanatory. :dd + +{Bond atom missing in box size check} :dt + +The 2nd atoms needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond atom missing in image check} :dt + +The 2nd atom in a particular bond is missing on this processor. +Typically this is because the pairwise cutoff is set too short or the +bond has blown apart and an atom is too far away. :dd + +{Bond atoms missing at step %ld} :dt + +The 2nd atom needed to compute a particular bond is missing on this +processor. Typically this is because the pairwise cutoff is set too +short or the bond has blown apart and an atom is too far away. :dd + +{Bond style in data file differs from currently defined bond style} :dt + +Self-explanatory. :dd + +{Bond/angle/dihedral extent > half of periodic box length} :dt + +This is a restriction because LAMMPS can be confused about which image +of an atom in the bonded interaction is the correct one to use. +"Extent" in this context means the maximum end-to-end length of the +bond/angle/dihedral. LAMMPS computes this by taking the maximum bond +length, multiplying by the number of bonds in the interaction (e.g. 3 +for a dihedral) and adding a small amount of stretch. :dd + +{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt + +Self-explanatory. :dd + +{Calling write_dump before a full system init.} :dt + +The write_dump command is used before the system has been fully +initialized as part of a 'run' or 'minimize' command. Not all dump +styles and features are fully supported at this point and thus the +command may fail or produce incomplete or incorrect output. Insert +a "run 0" command, if a full system init is required. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt + +This means the temperature associated with the rigid bodies may be +incorrect on this timestep. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt + +Self-explanatory. :dd + +{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt + +Self-explanatory. :dd + +{Charges are set, but coulombic solver is not used} :dt + +Self-explanatory. :dd + +{Charges did not converge at step %ld: %lg} :dt + +Self-explanatory. :dd + +{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt + +Self-explanatory. :dd + +{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt + +The neighbor cutoff used may not encompass enough ghost atoms +to perform this operation correctly. :dd + +{Computing temperature of portions of rigid bodies} :dt + +The group defined by the temperature compute does not encompass all +the atoms in one or more rigid bodies, so the change in +degrees-of-freedom for the atoms in those partial rigid bodies will +not be accounted for. :dd + +{Create_bonds max distance > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus no bond can be created between them. :dd + +{Delete_atoms cutoff > minimum neighbor cutoff} :dt + +This means atom pairs for some atom types may not be in the neighbor +list and thus an atom in that pair cannot be deleted. :dd + +{Dihedral atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular dihedral are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the dihedral has blown apart and an atom is +too far away. :dd + +{Dihedral problem} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Dihedral style in data file differs from currently defined dihedral style} :dt + +Self-explanatory. :dd + +{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt + +If the fix changes the timestep, the dump dcd file will not +reflect the change. :dd + +{Energy due to X extra global DOFs will be included in minimizer energies} :dt + +When using fixes like box/relax, the potential energy used by the minimizer +is augmented by an additional energy provided by the fix. Thus the printed +converged energy may be different from the total potential energy. :dd + +{Energy tally does not account for 'zero yes'} :dt + +The energy removed by using the 'zero yes' flag is not accounted +for in the energy tally and thus energy conservation cannot be +monitored in this case. :dd + +{Estimated error in splitting of dispersion coeffs is %g} :dt + +Error is greater than 0.0001 percent. :dd + +{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt + +Self-explanatory. Choosing a different cutoff value may help. :dd + +{FENE bond too long} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %d %d %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{FENE bond too long: %ld %g} :dt + +A FENE bond has stretched dangerously far. It's interaction strength +will be truncated to attempt to prevent the bond from blowing up. :dd + +{Fix SRD walls overlap but fix srd overlap not set} :dt + +You likely want to set this in your input script. :dd + +{Fix bond/swap will ignore defined angles} :dt + +See the doc page for fix bond/swap for more info on this +restriction. :dd + +{Fix deposit near setting < possible overlap separation %g} :dt + +This test is performed for finite size particles with a diameter, not +for point particles. The near setting is smaller than the particle +diameter which can lead to overlaps. :dd + +{Fix evaporate may delete atom with non-zero molecule ID} :dt + +This is probably an error, since you should not delete only one atom +of a molecule. :dd + +{Fix gcmc using full_energy option} :dt + +Fix gcmc has automatically turned on the full_energy option since it +is required for systems like the one specified by the user. User input +included one or more of the following: kspace, triclinic, a hybrid +pair style, an eam pair style, or no "single" function for the pair +style. :dd + +{Fix property/atom mol or charge w/out ghost communication} :dt + +A model typically needs these properties defined for ghost atoms. :dd + +{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt + +Self-explanatory. :dd + +{Fix qeq has non-zero lower Taper radius cutoff} :dt + +Absolute value must be <= 0.01. :dd + +{Fix qeq has very low Taper radius cutoff} :dt + +Value should typically be >= 5.0. :dd + +{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt + +Self-explanatory. :dd + +{Fix qeq/fire tolerance may be too small for damped fires} :dt + +Self-explanatory. :dd + +{Fix rattle should come after all other integration fixes} :dt + +This fix is designed to work after all other integration fixes change +atom positions. Thus it should be the last integration fix specified. +If not, it will not satisfy the desired constraints as well as it +otherwise would. :dd + +{Fix recenter should come after all other integration fixes} :dt + +Other fixes may change the position of the center-of-mass, so +fix recenter should come last. :dd + +{Fix srd SRD moves may trigger frequent reneighboring} :dt + +This is because the SRD particles may move long distances. :dd + +{Fix srd grid size > 1/4 of big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd particle moved outside valid domain} :dt + +This may indicate a problem with your simulation parameters. :dd + +{Fix srd particles may move > big particle diameter} :dt + +This may cause accuracy problems. :dd + +{Fix srd viscosity < 0.0 due to low SRD density} :dt + +This may cause accuracy problems. :dd + +{Fix thermal/conductivity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that fix +thermal/conductivity comes first. If you are using fix ave/spatial to +measure the temperature profile induced by fix viscosity, then this +may cause a glitch in the profile since you are averaging immediately +after swaps have occurred. Flipping the order of the 2 fixes +typically helps. :dd + +{Fix viscosity comes before fix ave/spatial} :dt + +The order of these 2 fixes in your input script is such that +fix viscosity comes first. If you are using fix ave/spatial +to measure the velocity profile induced by fix viscosity, then +this may cause a glitch in the profile since you are averaging +immediately after swaps have occurred. Flipping the order +of the 2 fixes typically helps. :dd + +{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt + +This is current restriction with Kokkos. :dd + +{For better accuracy use 'pair_modify table 0'} :dt + +The user-specified force accuracy cannot be achieved unless the table +feature is disabled by using 'pair_modify table 0'. :dd + +{Geometric mixing assumed for 1/r^6 coefficients} :dt + +Self-explanatory. :dd + +{Group for fix_modify temp != fix group} :dt + +The fix_modify command is specifying a temperature computation that +computes a temperature on a different group of atoms than the fix +itself operates on. This is probably not what you want to do. :dd + +{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt + +This is the size of the matrix. :dd + +{Ignoring unknown or incorrect info command flag} :dt + +Self-explanatory. An unknown argument was given to the info command. +Compare your input with the documentation. :dd + +{Improper atoms missing at step %ld} :dt + +One or more of 4 atoms needed to compute a particular improper are +missing on this processor. Typically this is because the pairwise +cutoff is set too short or the improper has blown apart and an atom is +too far away. :dd + +{Improper problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed improper atoms is extreme; you may want +to check your simulation geometry. :dd + +{Improper style in data file differs from currently defined improper style} :dt + +Self-explanatory. :dd + +{Inconsistent image flags} :dt + +The image flags for a pair on bonded atoms appear to be inconsistent. +Inconsistent means that when the coordinates of the two atoms are +unwrapped using the image flags, the two atoms are far apart. +Specifically they are further apart than half a periodic box length. +Or they are more than a box length apart in a non-periodic dimension. +This is usually due to the initial data file not having correct image +flags for the 2 atoms in a bond that straddles a periodic boundary. +They should be different by 1 in that case. This is a warning because +inconsistent image flags will not cause problems for dynamics or most +LAMMPS simulations. However they can cause problems when such atoms +are used with the fix rigid or replicate commands. Note that if you +have an infinite periodic crystal with bonds then it is impossible to +have fully consistent image flags, since some bonds will cross +periodic boundaries and connect two atoms with the same image +flag. :dd + +{KIM Model does not provide 'energy'; Potential energy will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'forces'; Forces will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt + +Self-explanatory. :dd + +{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt + +Self-explanatory. :dd + +{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt + +The kspace_modify slab parameter should be larger to insure periodic +grids padded with empty space do not overlap. :dd + +{Less insertions than requested} :dt + +The fix pour command was unsuccessful at finding open space +for as many particles as it tried to insert. :dd + +{Library error in lammps_gather_atoms} :dt + +This library function cannot be used if atom IDs are not defined +or are not consecutively numbered. :dd + +{Library error in lammps_scatter_atoms} :dt + +This library function cannot be used if atom IDs are not defined or +are not consecutively numbered, or if no atom map is defined. See the +atom_modify command for details about atom maps. :dd + +{Lost atoms via change_box: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms via displace_atoms: original %ld current %ld} :dt + +The command options you have used caused atoms to be lost. :dd + +{Lost atoms: original %ld current %ld} :dt + +Lost atoms are checked for each time thermo output is done. See the +thermo_modify lost command for options. Lost atoms usually indicate +bad dynamics, e.g. atoms have been blown far out of the simulation +box, or moved further than one processor's sub-domain away before +reneighboring. :dd + +{MSM mesh too small, increasing to 2 points in each direction} :dt + +Self-explanatory. :dd + +{Mismatch between velocity and compute groups} :dt + +The temperature computation used by the velocity command will not be +on the same group of atoms that velocities are being set for. :dd + +{Mixing forced for lj coefficients} :dt + +Self-explanatory. :dd + +{Molecule attributes do not match system attributes} :dt + +An attribute is specified (e.g. diameter, charge) that is +not defined for the specified atom style. :dd + +{Molecule has bond topology but no special bond settings} :dt + +This means the bonded atoms will not be excluded in pair-wise +interactions. :dd + +{Molecule template for create_atoms has multiple molecules} :dt + +The create_atoms command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix gcmc has multiple molecules} :dt + +The fix gcmc command will only create molecules of a single type, +i.e. the first molecule in the template. :dd + +{Molecule template for fix shake has multiple molecules} :dt + +The fix shake command will only recognize molecules of a single +type, i.e. the first molecule in the template. :dd + +{More than one compute centro/atom} :dt + +It is not efficient to use compute centro/atom more than once. :dd + +{More than one compute cluster/atom} :dt + +It is not efficient to use compute cluster/atom more than once. :dd + +{More than one compute cna/atom defined} :dt + +It is not efficient to use compute cna/atom more than once. :dd + +{More than one compute contact/atom} :dt + +It is not efficient to use compute contact/atom more than once. :dd + +{More than one compute coord/atom} :dt + +It is not efficient to use compute coord/atom more than once. :dd + +{More than one compute damage/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute dilatation/atom} :dt + +Self-explanatory. :dd + +{More than one compute erotate/sphere/atom} :dt + +It is not efficient to use compute erorate/sphere/atom more than once. :dd + +{More than one compute hexorder/atom} :dt + +It is not efficient to use compute hexorder/atom more than once. :dd + +{More than one compute ke/atom} :dt + +It is not efficient to use compute ke/atom more than once. :dd + +{More than one compute orientorder/atom} :dt + +It is not efficient to use compute orientorder/atom more than once. :dd + +{More than one compute plasticity/atom} :dt + +Self-explanatory. :dd + +{More than one compute sna/atom} :dt + +Self-explanatory. :dd + +{More than one compute snad/atom} :dt + +Self-explanatory. :dd + +{More than one compute snav/atom} :dt + +Self-explanatory. :dd + +{More than one fix poems} :dt + +It is not efficient to use fix poems more than once. :dd + +{More than one fix rigid} :dt + +It is not efficient to use fix rigid more than once. :dd + +{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt + +This is because excluding specific pair interactions also excludes +them from long-range interactions which may not be the desired effect. +The special_bonds command handles this consistently by insuring +excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated +consistently by both the short-range pair style and the long-range +solver. This is not done for exclusions of charged atom pairs via the +neigh_modify exclude command. :dd + +{New thermo_style command, previous thermo_modify settings will be lost} :dt + +If a thermo_style command is used after a thermo_modify command, the +settings changed by the thermo_modify command will be reset to their +default values. This is because the thermo_modify command acts on +the currently defined thermo style, and a thermo_style command creates +a new style. :dd + +{No Kspace calculation with verlet/split} :dt + +The 2nd partition performs a kspace calculation so the kspace_style +command must be used. :dd + +{No automatic unit conversion to XTC file format conventions possible for units lj} :dt + +This means no scaling will be performed. :dd + +{No fixes defined, atoms won't move} :dt + +If you are not using a fix like nve, nvt, npt then atom velocities and +coordinates will not be updated during timestepping. :dd + +{No joints between rigid bodies, use fix rigid instead} :dt + +The bodies defined by fix poems are not connected by joints. POEMS +will integrate the body motion, but it would be more efficient to use +fix rigid. :dd + +{Not using real units with pair reax} :dt + +This is most likely an error, unless you have created your own ReaxFF +parameter file in a different set of units. :dd + +{Number of MSM mesh points changed to be a multiple of 2} :dt + +MSM requires that the number of grid points in each direction be a multiple +of two and the number of grid points in one or more directions have been +adjusted to meet this requirement. :dd + +{OMP_NUM_THREADS environment is not set.} :dt + +This environment variable must be set appropriately to use the +USER-OMP package. :dd + +{One or more atoms are time integrated more than once} :dt + +This is probably an error since you typically do not want to +advance the positions or velocities of an atom more than once +per timestep. :dd + +{One or more chunks do not contain all atoms in molecule} :dt + +This may not be what you intended. :dd + +{One or more dynamic groups may not be updated at correct point in timestep} :dt + +If there are other fixes that act immediately after the initial stage +of time integration within a timestep (i.e. after atoms move), then +the command that sets up the dynamic group should appear after those +fixes. This will insure that dynamic group assignments are made +after all atoms have moved. :dd + +{One or more respa levels compute no forces} :dt + +This is computationally inefficient. :dd + +{Pair COMB charge %.10f with force %.10f hit max barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair COMB charge %.10f with force %.10f hit min barrier} :dt + +Something is possibly wrong with your model. :dd + +{Pair brownian needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dpd needs newton pair on for momentum conservation} :dt + +Self-explanatory. :dd + +{Pair dsmc: num_of_collisions > number_of_A} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair dsmc: num_of_collisions > number_of_B} :dt + +Collision model in DSMC is breaking down. :dd + +{Pair style in data file differs from currently defined pair style} :dt + +Self-explanatory. :dd + +{Pair style restartinfo set but has no restart support} :dt + +This pair style has a bug, where it does not support reading and +writing information to a restart file, but does not set the member +variable "restartinfo" to 0 as required in that case. :dd + +{Particle deposition was unsuccessful} :dt + +The fix deposit command was not able to insert as many atoms as +needed. The requested volume fraction may be too high, or other atoms +may be in the insertion region. :dd + +{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt + +The decomposition of the physical domain (likely due to load +balancing) has led to a processor's sub-domain being smaller than the +neighbor skin in one or more dimensions. Since reneighboring is +triggered by atoms moving the skin distance, this may lead to lost +atoms, if an atom moves all the way across a neighboring processor's +sub-domain before reneighboring is triggered. :dd + +{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt + +This may lead to a larger grid than desired. See the kspace_modify overlap +command to prevent changing of the PPPM order. :dd + +{Replacing a fix, but new group != old group} :dt + +The ID and style of a fix match for a fix you are changing with a fix +command, but the new group you are specifying does not match the old +group. :dd + +{Replicating in a non-periodic dimension} :dt + +The parameters for a replicate command will cause a non-periodic +dimension to be replicated; this may cause unwanted behavior. :dd + +{Resetting reneighboring criteria during PRD} :dt + +A PRD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during TAD} :dt + +A TAD simulation requires that neigh_modify settings be delay = 0, +every = 1, check = yes. Since these settings were not in place, +LAMMPS changed them and will restore them to their original values +after the PRD simulation. :dd + +{Resetting reneighboring criteria during minimization} :dt + +Minimization requires that neigh_modify settings be delay = 0, every = +1, check = yes. Since these settings were not in place, LAMMPS +changed them and will restore them to their original values after the +minimization. :dd + +{Restart file used different # of processors} :dt + +The restart file was written out by a LAMMPS simulation running on a +different number of processors. Due to round-off, the trajectories of +your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different 3d processor grid} :dt + +The restart file was written out by a LAMMPS simulation running on a +different 3d grid of processors. Due to round-off, the trajectories +of your restarted simulation may diverge a little more quickly than if +you ran on the same # of processors. :dd + +{Restart file used different boundary settings, using restart file values} :dt + +Your input script cannot change these restart file settings. :dd + +{Restart file used different newton bond setting, using restart file value} :dt + +The restart file value will override the setting in the input script. :dd + +{Restart file used different newton pair setting, using input script value} :dt + +The input script value will override the setting in the restart file. :dd + +{Restrain problem: %d %ld %d %d %d %d} :dt + +Conformation of the 4 listed dihedral atoms is extreme; you may want +to check your simulation geometry. :dd + +{Running PRD with only one replica} :dt + +This is allowed, but you will get no parallel speed-up. :dd + +{SRD bin shifting turned on due to small lamda} :dt + +This is done to try to preserve accuracy. :dd + +{SRD bin size for fix srd differs from user request} :dt + +Fix SRD had to adjust the bin size to fit the simulation box. See the +cubic keyword if you want this message to be an error vs warning. :dd + +{SRD bins for fix srd are not cubic enough} :dt + +The bin shape is not within tolerance of cubic. See the cubic +keyword if you want this message to be an error vs warning. :dd + +{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{SRD particle %d started inside wall %d on step %ld bounce %d} :dt + +See the inside keyword if you want this message to be an error vs +warning. :dd + +{Shake determinant < 0.0} :dt + +The determinant of the quadratic equation being solved for a single +cluster specified by the fix shake command is numerically suspect. LAMMPS +will set it to 0.0 and continue. :dd + +{Shell command '%s' failed with error '%s'} :dt + +Self-explanatory. :dd + +{Shell command returned with non-zero status} :dt + +This may indicate the shell command did not operate as expected. :dd + +{Should not allow rigid bodies to bounce off relecting walls} :dt + +LAMMPS allows this, but their dynamics are not computed correctly. :dd + +{Should not use fix nve/limit with fix shake or fix rattle} :dt + +This will lead to invalid constraint forces in the SHAKE/RATTLE +computation. :dd + +{Simulations might be very slow because of large number of structure factors} :dt + +Self-explanatory. :dd + +{Slab correction not needed for MSM} :dt + +Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd + +{System is not charge neutral, net charge = %g} :dt + +The total charge on all atoms on the system is not 0.0. +For some KSpace solvers this is only a warning. :dd + +{Table inner cutoff >= outer cutoff} :dt + +You specified an inner cutoff for a Coulombic table that is longer +than the global cutoff. Probably not what you wanted. :dd + +{Temperature for MSST is not for group all} :dt + +User-assigned temperature to MSST fix does not compute temperature for +all atoms. Since MSST computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by MSST could be inaccurate. :dd + +{Temperature for NPT is not for group all} :dt + +User-assigned temperature to NPT fix does not compute temperature for +all atoms. Since NPT computes a global pressure, the kinetic energy +contribution from the temperature is assumed to also be for all atoms. +Thus the pressure used by NPT could be inaccurate. :dd + +{Temperature for fix modify is not for group all} :dt + +The temperature compute is being used with a pressure calculation +which does operate on group all, so this may be inconsistent. :dd + +{Temperature for thermo pressure is not for group all} :dt + +User-assigned temperature to thermo via the thermo_modify command does +not compute temperature for all atoms. Since thermo computes a global +pressure, the kinetic energy contribution from the temperature is +assumed to also be for all atoms. Thus the pressure printed by thermo +could be inaccurate. :dd + +{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt + +Self-explanatory. :dd + +{The minimizer does not re-orient dipoles when using fix efield} :dt + +This means that only the atom coordinates will be minimized, +not the orientation of the dipoles. :dd + +{Too many common neighbors in CNA %d times} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Too many inner timesteps in fix ttm} :dt + +Self-explanatory. :dd + +{Too many neighbors in CNA for %d atoms} :dt + +More than the maximum # of neighbors was found multiple times. This +was unexpected. :dd + +{Triclinic box skew is large} :dt + +The displacement in a skewed direction is normally required to be less +than half the box length in that dimension. E.g. the xy tilt must be +between -half and +half of the x box length. You have relaxed the +constraint using the box tilt command, but the warning means that a +LAMMPS simulation may be inefficient as a result. :dd + +{Use special bonds = 0,1,1 with bond style fene} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Use special bonds = 0,1,1 with bond style fene/expand} :dt + +Most FENE models need this setting for the special_bonds command. :dd + +{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt + +This is likely not what you want to do. The exclusion settings will +eliminate neighbors in the neighbor list, which the manybody potential +needs to calculated its terms correctly. :dd + +{Using compute temp/deform with inconsistent fix deform remap option} :dt + +Fix nvt/sllod assumes deforming atoms have a velocity profile provided +by "remap v" or "remap none" as a fix deform option. :dd + +{Using compute temp/deform with no fix deform defined} :dt + +This is probably an error, since it makes little sense to use +compute temp/deform in this case. :dd + +{Using fix srd with box deformation but no SRD thermostat} :dt + +The deformation will heat the SRD particles so this can +be dangerous. :dd + +{Using kspace solver on system with no charge} :dt + +Self-explanatory. :dd + +{Using largest cut-off for lj/long/dipole/long long long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for buck/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for lj/long/coul/long} :dt + +Self-explanatory. :dd + +{Using largest cutoff for pair_style lj/long/tip4p/long} :dt + +Self-explanatory. :dd + +{Using package gpu without any pair style defined} :dt + +Self-explanatory. :dd + +{Using pair potential shift with pair_modify compute no} :dt + +The shift effects will thus not be computed. :dd + +{Using pair tail corrections with nonperiodic system} :dt + +This is probably a bogus thing to do, since tail corrections are +computed by integrating the density of a periodic system out to +infinity. :dd + +{Using pair tail corrections with pair_modify compute no} :dt + +The tail corrections will thus not be computed. :dd + +{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt + +Self-explanatory. :dd + +:dle diff --git a/doc/src/Section_example.txt b/doc/src/Examples.txt similarity index 95% rename from doc/src/Section_example.txt rename to doc/src/Examples.txt index a2a9940f4845f10c2df5fe3333c8de30cba1ea7d..5bd8da2409185873b745cc87b1ae95b5a0b6ac1b 100644 --- a/doc/src/Section_example.txt +++ b/doc/src/Examples.txt @@ -1,12 +1,14 @@ -"Previous Section"_Section_howto.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_perf.html :c +"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -7. Example problems :h2 +Example scripts :h3 The LAMMPS distribution includes an examples sub-directory with many sample problems. Many are 2d models that run quickly are are @@ -46,7 +48,7 @@ Lists of both kinds of directories are given below. :line -Lowercase directories :h3 +Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) airebo: polyethylene with AIREBO potential @@ -122,7 +124,7 @@ browser. :line -Uppercase directories :h3 +Uppercase directories :h4 ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc COUPLE: examples of how to use LAMMPS as a library @@ -141,5 +143,5 @@ The USER directory has a large number of sub-directories which correspond by name to a USER package. They contain scripts that illustrate how to use the command(s) provided in that package. Many of the sub-directories have their own README files which give further -instructions. See the "Section 4"_Section_packages.html doc +instructions. See the "Packages_details"_Packages_details.html doc page for more info on specific USER packages. diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt new file mode 100644 index 0000000000000000000000000000000000000000..d9a60d1ef4b8e8365683794e5bfc96d5fc325b32 --- /dev/null +++ b/doc/src/Howto.txt @@ -0,0 +1,128 @@ +"Previous Section"_Performance.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Examples.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +How to discussions :h2 + +These doc pages describe how to perform various tasks with LAMMPS, +both for users and developers. The +"glossary"_http://lammps.sandia.gov website page also lists MD +terminology with links to corresponding LAMMPS manual pages. + +The example input scripts included in the examples dir of the LAMMPS +distribution and highlighted on the "Examples"_Examples.html doc page +also show how to setup and run various kinds of simulations. + + + + + +"Using GitHub with LAMMPS"_Howto_github.html +"PyLAMMPS interface to LAMMPS"_Howto_pylammps.html +"Using LAMMPS with bash on Windows"_Howto_bash.html + +"Restart a simulation"_Howto_restart.html +"Visualize LAMMPS snapshots"_Howto_viz.html +"Run multiple simulations from one input script"_Howto_multiple.html +"Multi-replica simulations"_Howto_replica.html +"Library interface to LAMMPS"_Howto_library.html +"Couple LAMMPS to other codes"_Howto_couple.html :all(b) + +"Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_Howto_output.html +"Use chunks to calculate system properties"_Howto_chunk.html :all(b) + +"2d simulations"_Howto_2d.html +"Triclinic (non-orthogonal) simulation boxes"_Howto_triclinic.html +"Walls"_Howto_walls.html +"NEMD simulations"_Howto_nemd.html +"Granular models"_Howto_granular.html +"Finite-size spherical and aspherical particles"_Howto_spherical.html +"Long-range dispersion settings"_Howto_dispersion.html :all(b) + +"Calculate temperature"_Howto_temperature.html +"Thermostats"_Howto_thermostat.html +"Barostats"_Howto_barostat.html +"Calculate elastic constants"_Howto_elastic.html +"Calculate thermal conductivity"_Howto_kappa.html +"Calculate viscosity"_Howto_viscosity.html +"Calculate a diffusion coefficient"_Howto_diffusion.html :all(b) + +"CHARMM, AMBER, and DREIDING force fields"_Howto_bioFF.html +"TIP3P water model"_Howto_tip3p.html +"TIP4P water model"_Howto_tip4p.html +"SPC water model"_Howto_spc.html :all(b) + +"Body style particles"_Howto_body.html +"Polarizable models"_Howto_polarizable.html +"Adiabatic core/shell model"_Howto_coreshell.html +"Drude induced dipoles"_Howto_drude.html +"Drude induced dipoles (extended)"_Howto_drude2.html :all(b) +"Manifolds (surfaces)"_Howto_manifold.html +"Magnetic spins"_Howto_spins.html + + diff --git a/doc/src/Howto_2d.txt b/doc/src/Howto_2d.txt new file mode 100644 index 0000000000000000000000000000000000000000..e1758c05d5ff9fc771e239ba6007f98d3abbbf63 --- /dev/null +++ b/doc/src/Howto_2d.txt @@ -0,0 +1,48 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +2d simulations :h3 + +Use the "dimension"_dimension.html command to specify a 2d simulation. + +Make the simulation box periodic in z via the "boundary"_boundary.html +command. This is the default. + +If using the "create box"_create_box.html command to define a +simulation box, set the z dimensions narrow, but finite, so that the +create_atoms command will tile the 3d simulation box with a single z +plane of atoms - e.g. + +"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre + +If using the "read data"_read_data.html command to read in a file of +atom coordinates, set the "zlo zhi" values to be finite but narrow, +similar to the create_box command settings just described. For each +atom in the file, assign a z coordinate so it falls inside the +z-boundaries of the box - e.g. 0.0. + +Use the "fix enforce2d"_fix_enforce2d.html command as the last +defined fix to insure that the z-components of velocities and forces +are zeroed out every timestep. The reason to make it the last fix is +so that any forces induced by other fixes will be zeroed out. + +Many of the example input scripts included in the LAMMPS distribution +are for 2d models. + +NOTE: Some models in LAMMPS treat particles as finite-size spheres, as +opposed to point particles. See the "atom_style +sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html +commands for details. By default, for 2d simulations, such particles +will still be modeled as 3d spheres, not 2d discs (circles), meaning +their moment of inertia will be that of a sphere. If you wish to +model them as 2d discs, see the "set density/disc"_set.html command +and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html, +"fix nvt/sphere"_fix_nvt_sphere.html, "fix +nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html +commands. diff --git a/doc/src/Howto_barostat.txt b/doc/src/Howto_barostat.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c3db891524379f49fe38134186764e07eeff959 --- /dev/null +++ b/doc/src/Howto_barostat.txt @@ -0,0 +1,75 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Barostats :h3 + +Barostatting means controlling the pressure in an MD simulation. +"Thermostatting"_Howto_thermostat.html means controlling the +temperature of the particles. Since the pressure includes a kinetic +component due to particle velocities, both these operations require +calculation of the temperature. Typically a target temperature (T) +and/or pressure (P) is specified by the user, and the thermostat or +barostat attempts to equilibrate the system to the requested T and/or +P. + +Barostatting in LAMMPS is performed by "fixes"_fix.html. Two +barosttating methods are currently available: Nose-Hoover (npt and +nph) and Berendsen: + +"fix npt"_fix_nh.html +"fix npt/sphere"_fix_npt_sphere.html +"fix npt/asphere"_fix_npt_asphere.html +"fix nph"_fix_nh.html +"fix press/berendsen"_fix_press_berendsen.html :ul + +The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat +and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat; +it does no thermostatting. Both "fix nph"_fix_nh.html and "fix +press/berendsen"_fix_press_berendsen.html can be used in conjunction +with any of the thermostatting fixes. + +As with the "thermostats"_Howto_thermostat.html, "fix npt"_fix_nh.html +and "fix nph"_fix_nh.html only use translational motion of the +particles in computing T and P and performing thermo/barostatting. +"Fix npt/sphere"_fix_npt_sphere.html and "fix +npt/asphere"_fix_npt_asphere.html thermo/barostat using not only +translation velocities but also rotational velocities for spherical +and aspherical particles. + +All of the barostatting fixes use the "compute +pressure"_compute_pressure.html compute to calculate a current +pressure. By default, this compute is created with a simple "compute +temp"_compute_temp.html (see the last argument of the "compute +pressure"_compute_pressure.html command), which is used to calculated +the kinetic component of the pressure. The barostatting fixes can +also use temperature computes that remove bias for the purpose of +computing the kinetic component which contributes to the current +pressure. See the doc pages for the individual fixes and for the +"fix_modify"_fix_modify.html command for instructions on how to assign +a temperature or pressure compute to a barostatting fix. + +NOTE: As with the thermostats, the Nose/Hoover methods ("fix +npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration. +"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should +be used with one of the constant NVE fixes or with one of the NVT +fixes. + +Thermodynamic output, which can be setup via the +"thermo_style"_thermo_style.html command, often includes pressure +values. As explained on the doc page for the +"thermo_style"_thermo_style.html command, the default pressure is +setup by the thermo command itself. It is NOT the presure associated +with any barostatting fix you have defined or with any compute you +have defined that calculates a presure. The doc pages for the +barostatting fixes explain the ID of the pressure compute they create. +Thus if you want to view these pressurse, you need to specify them +explicitly via the "thermo_style custom"_thermo_style.html command. +Or you can use the "thermo_modify"_thermo_modify.html command to +re-define what pressure compute is used for default thermodynamic +output. diff --git a/doc/src/tutorial_bash_on_windows.txt b/doc/src/Howto_bash.txt old mode 100644 new mode 100755 similarity index 99% rename from doc/src/tutorial_bash_on_windows.txt rename to doc/src/Howto_bash.txt index 66712bdffafc8173bef83e5883bae8d3e0843ec0..f1438418e78b2bf97118992dea972e73513e0e29 --- a/doc/src/tutorial_bash_on_windows.txt +++ b/doc/src/Howto_bash.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,6 +10,7 @@ Using LAMMPS with Bash on Windows :h3 [written by Richard Berger] :line + Starting with Windows 10 you can install Linux tools directly in Windows. This allows you to compile LAMMPS following the same procedure as on a real Ubuntu Linux installation. Software can be easily installed using the package manager diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt new file mode 100644 index 0000000000000000000000000000000000000000..afb8a84f2e32ac4397054054c4032ab339629290 --- /dev/null +++ b/doc/src/Howto_bioFF.txt @@ -0,0 +1,101 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +CHARMM, AMBER, and DREIDING force fields :h3 + +A force field has 2 parts: the formulas that define it and the +coefficients used for a particular system. Here we only discuss +formulas implemented in LAMMPS that correspond to formulas commonly +used in the CHARMM, AMBER, and DREIDING force fields. Setting +coefficients is done in the input data file via the +"read_data"_read_data.html command or in the input script with +commands like "pair_coeff"_pair_coeff.html or +"bond_coeff"_bond_coeff.html. See the "Tools"_Tools.html doc page for +additional tools that can use CHARMM or AMBER to assign force field +coefficients and convert their output into LAMMPS input. + +See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force +field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force +field. + +:link(charmm,http://www.scripps.edu/brooks) +:link(amber,http://amber.scripps.edu) + +These style choices compute force field formulas that are consistent +with common options in CHARMM or AMBER. See each command's +documentation for the formula it computes. + +"bond_style"_bond_harmonic.html harmonic +"angle_style"_angle_charmm.html charmm +"dihedral_style"_dihedral_charmm.html charmmfsh +"dihedral_style"_dihedral_charmm.html charmm +"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh +"pair_style"_pair_charmm.html lj/charmmfsw/coul/long +"pair_style"_pair_charmm.html lj/charmm/coul/charmm +"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit +"pair_style"_pair_charmm.html lj/charmm/coul/long :ul + +"special_bonds"_special_bonds.html charmm +"special_bonds"_special_bonds.html amber :ul + +NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were +released in March 2017. We recommend they be used instead of the +older {charmm} styles. See discussion of the differences on the "pair +charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html +doc pages. + +DREIDING is a generic force field developed by the "Goddard +group"_http://www.wag.caltech.edu at Caltech and is useful for +predicting structures and dynamics of organic, biological and +main-group inorganic molecules. The philosophy in DREIDING is to use +general force constants and geometry parameters based on simple +hybridization considerations, rather than individual force constants +and geometric parameters that depend on the particular combinations of +atoms involved in the bond, angle, or torsion terms. DREIDING has an +"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe +interactions involving a hydrogen atom on very electronegative atoms +(N, O, F). + +See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field + +These style choices compute force field formulas that are consistent +with the DREIDING force field. See each command's +documentation for the formula it computes. + +"bond_style"_bond_harmonic.html harmonic +"bond_style"_bond_morse.html morse :ul + +"angle_style"_angle_harmonic.html harmonic +"angle_style"_angle_cosine.html cosine +"angle_style"_angle_cosine_periodic.html cosine/periodic :ul + +"dihedral_style"_dihedral_charmm.html charmm +"improper_style"_improper_umbrella.html umbrella :ul + +"pair_style"_pair_buck.html buck +"pair_style"_pair_buck.html buck/coul/cut +"pair_style"_pair_buck.html buck/coul/long +"pair_style"_pair_lj.html lj/cut +"pair_style"_pair_lj.html lj/cut/coul/cut +"pair_style"_pair_lj.html lj/cut/coul/long :ul + +"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj +"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul + +"special_bonds"_special_bonds.html dreiding :ul + +:line + +:link(howto-MacKerell) +[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, +Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). + +:link(howto-Mayo) +[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). diff --git a/doc/src/body.txt b/doc/src/Howto_body.txt similarity index 52% rename from doc/src/body.txt rename to doc/src/Howto_body.txt index 8d49efdae40eed30f9c7ec82e704adc3aef44771..3535349b461589aa6ddafdf4e9a3d684a546c2e1 100644 --- a/doc/src/body.txt +++ b/doc/src/Howto_body.txt @@ -1,24 +1,24 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -Body particles :h2 +Body particles :h3 [Overview:] -This doc page is not about a LAMMPS input script command, but about -body particles, which are generalized finite-size particles. +In LAMMPS, body particles are generalized finite-size particles. Individual body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. Note that other kinds of finite-size spherical and aspherical particles are also supported by LAMMPS, such as spheres, ellipsoids, line segments, and triangles, but they are -simpler entities that body particles. See "Section -6.14"_Section_howto.html#howto_14 for a general overview of all +simpler entities that body particles. See the "Howto +spherical"_Howto_spherical.html doc page for a general overview of all these particle types. Body particles are used via the "atom_style body"_atom_style.html @@ -27,19 +27,17 @@ styles supported by LAMMPS are as follows. The name in the first column is used as the {bstyle} argument for the "atom_style body"_atom_style.html command. -{nparticle} | rigid body with N sub-particles | -{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|) +{nparticle} : rigid body with N sub-particles +{rounded/polygon} : 2d polygons with N vertices +{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:) The body style determines what attributes are stored for each body and thus how they can be used to compute pairwise body/body or bond/non-body (point particle) interactions. More details of each style are described below. -NOTE: The rounded/polygon style listed in the table above and -described below has not yet been relesed in LAMMPS. It will be soon. - -We hope to add more styles in the future. See "Section -10.12"_Section_modify.html#mod_12 for details on how to add a new body +More styles may be added in the future. See the "Modify +body"_Modify_body.html doc page for details on how to add a new body style to the code. :line @@ -61,7 +59,7 @@ the simple particles. By contrast, when body particles are used, LAMMPS treats an entire body as a single particle for purposes of computing pairwise interactions, building neighbor lists, migrating particles between -processors, outputting particles to a dump file, etc. This means that +processors, output of particles to a dump file, etc. This means that interactions between pairs of bodies or between a body and non-body (point) particle need to be encoded in an appropriate pair style. If such a pair style were to mimic the "fix rigid"_fix_rigid.html model, @@ -72,17 +70,20 @@ single body/body interaction was computed. Thus it only makes sense to use body particles and develop such a pair style, when particle/particle interactions are more complex than what the "fix rigid"_fix_rigid.html command can already calculate. For -example, if particles have one or more of the following attributes: +example, consider particles with one or more of the following +attributes: represented by a surface mesh represented by a collection of geometric entities (e.g. planes + spheres) deformable internal stress that induces fragmentation :ul -then the interaction between pairs of particles is likely to be more -complex than the summation of simple sub-particle interactions. An -example is contact or frictional forces between particles with planar -surfaces that inter-penetrate. +For these models, the interaction between pairs of particles is likely +to be more complex than the summation of simple pairwise interactions. +An example is contact or frictional forces between particles with +planar surfaces that inter-penetrate. Likewise, the body particle may +store internal state, such as a stress tensor used to compute a +fracture criterion. These are additional LAMMPS commands that can be used with body particles of different styles @@ -130,7 +131,9 @@ x1 y1 z1 ... xN yN zN :pre -N is the number of sub-particles in the body particle. M = 6 + 3*N. +where M = 6 + 3*N, and N is the number of sub-particles in the body +particle. + The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N sub-particles (x1 to zN) as 3N values. These values can be listed on @@ -148,8 +151,8 @@ center-of-mass position of the particle is specified by the x,y,z values in the {Atoms} section of the data file, as is the total mass of the body particle. -The "pair_style body"_pair_body.html command can be used with this -body style to compute body/body and body/non-body interactions. +The "pair_style body/nparticle"_pair_body_nparticle.html command can be used +with this body style to compute body/body and body/non-body interactions. For output purposes via the "compute body/local"_compute_body_local.html and "dump local"_dump.html @@ -175,15 +178,18 @@ The {bflag2} argument is ignored. [Specifics of body style rounded/polygon:] -NOTE: Aug 2016 - This body style has not yet been added to LAMMPS. -The info below is a placeholder. +The {rounded/polygon} body style represents body particles as a 2d +polygon with a variable number of N vertices. This style can only be +used for 2d models; see the "boundary"_boundary.html command. See the +"pair_style body/rounded/polygon" doc page for a diagram of two +squares with rounded circles at the vertices. Special cases for N = 1 +(circle) and N = 2 (rod with rounded ends) can also be specified. + +One use of this body style is for 2d discrete element models, as +described in "Fraige"_#body-Fraige. -The {rounded/polygon} body style represents body particles as a convex -polygon with a variable number N > 2 of vertices, which can only be -used for 2d models. One example use of this body style is for 2d -discrete element models, as described in "Fraige"_#Fraige. Similar to -body style {nparticle}, the atom_style body command for this body -style takes two additional arguments: +Similar to body style {nparticle}, the atom_style body command for +this body style takes two additional arguments: atom_style body rounded/polygon Nmin Nmax Nmin = minimum # of vertices in any body in the system @@ -203,17 +209,20 @@ x1 y1 z1 ... xN yN zN i j j k k ... -radius :pre +diameter :pre -N is the number of vertices in the body particle. M = 6 + 3*N + 2*N + -1. The integer line has a single value N. The floating point line(s) +where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the +body particle. + +The integer line has a single value N. The floating point line(s) list 6 moments of inertia followed by the coordinates of the N -vertices (x1 to zN) as 3N values, followed by 2N vertex indices -corresponding to the end points of the N edges, followed by a single -radius value = the smallest circle encompassing the polygon. That -last value is used to facilitate the body/body contact detection. -These floating-point values can be listed on as many lines as you -wish; see the "read_data"_read_data.html command for more details. +vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by +2N vertex indices corresponding to the end points of the N edges, +followed by a single diameter value = the rounded diameter of the +circle that surrounds each vertex. The diameter value can be different +for each body particle. These floating-point values can be listed on +as many lines as you wish; see the "read_data"_read_data.html command +for more details. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with the current orientation of the rigid body @@ -225,8 +234,11 @@ from the center-of-mass of the body particle. The center-of-mass position of the particle is specified by the x,y,z values in the {Atoms} section of the data file. -For example, the following information would specify a square -particles whose edge length is sqrt(2): +For example, the following information would specify a square particle +whose edge length is sqrt(2) and rounded diameter is 1.0. The +orientation of the square is aligned with the xy coordinate axes which +is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz = +1 1 4 0 0 0. Note that only Izz matters in 2D simulations. 3 1 27 4 @@ -235,12 +247,178 @@ particles whose edge length is sqrt(2): -0.7071 0.7071 0 0.7071 0.7071 0 0.7071 -0.7071 0 -0 1 1 2 2 3 3 0 +0 1 +1 2 +2 3 +3 0 1.0 :pre +A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +1 1 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A disk, whose diameter is 3.0, mass 1.0, is specified as follows: + +1 1 10 +1 +1 1 4.5 0 0 0 +0 0 0 +3.0 :pre + The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html command can be used with this body style to compute body/body -interactions. +interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html +command can be used with this body style to compute the interaction of +body particles with a wall. + +:line + +[Specifics of body style rounded/polyhedron:] + +The {rounded/polyhedron} body style represents body particles as a 3d +polyhedron with a variable number of N vertices, E edges and F faces. +This style can only be used for 3d models; see the +"boundary"_boundary.html command. See the "pair_style +body/rounded/polygon" doc page for a diagram of a two 2d squares with +rounded circles at the vertices. A 3d cube with rounded spheres at +the 8 vertices and 12 rounded edges would be similar. Special cases +for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be +specified. + +This body style is for 3d discrete element models, as described in +"Wang"_#body-Wang. + +Similar to body style {rounded/polygon}, the atom_style body command +for this body style takes two additional arguments: + +atom_style body rounded/polyhedron Nmin Nmax +Nmin = minimum # of vertices in any body in the system +Nmax = maximum # of vertices in any body in the system :pre + +The Nmin and Nmax arguments are used to bound the size of data +structures used internally by each particle. + +When the "read_data"_read_data.html command reads a data file for this +body style, the following information must be provided for each entry +in the {Bodies} section of the data file: + +atom-ID 3 M +N E F +ixx iyy izz ixy ixz iyz +x1 y1 z1 +... +xN yN zN +0 1 +1 2 +2 3 +... +0 1 2 -1 +0 2 3 -1 +... +1 2 3 4 +diameter :pre + +where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in +the body particle, E = number of edges, F = number of faces. + +The integer line has three values: number of vertices (N), number of +edges (E) and number of faces (F). The floating point line(s) list 6 +moments of inertia followed by the coordinates of the N vertices (x1 +to zN) as 3N values, followed by 2N vertex indices corresponding to +the end points of the E edges, then 4*F vertex indices defining F +faces. The last value is the diameter value = the rounded diameter of +the sphere that surrounds each vertex. The diameter value can be +different for each body particle. These floating-point values can be +listed on as many lines as you wish; see the +"read_data"_read_data.html command for more details. Because the +maxmimum vertices per face is hard-coded to be 4 +(i.e. quadrilaterals), faces with more than 4 vertices need to be +split into triangles or quadrilaterals. For triangular faces, the +last vertex index should be set to -1. + +The ordering of the 4 vertices within a face should follow +the right-hand rule so that the normal vector of the face points +outwards from the center of mass. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the principal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. +The coordinates of each vertex are specified as its x,y,z displacement +from the center-of-mass of the body particle. The center-of-mass +position of the particle is specified by the x,y,z values in the +{Atoms} section of the data file. + +For example, the following information would specify a cubic particle +whose edge length is 2.0 and rounded diameter is 0.5. +The orientation of the cube is aligned with the xyz coordinate axes +which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz +iyz = 0.667 0.667 0.667 0 0 0. + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 :pre + +A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends +by circles of diameter 0.5, is specified as follows: + +1 1 13 +2 +0 1.33333 1.33333 0 0 0 +-2 0 0 +2 0 0 +0.5 :pre + +A sphere whose diameter is 3.0 and mass 1.0, is specified as follows: + +1 1 10 +1 +0.9 0.9 0.9 0 0 0 +0 0 0 +3.0 :pre + +The "pair_style +body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can +be used with this body style to compute body/body interactions. The +"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be +used with this body style to compute the interaction of body particles +with a wall. + +:line For output purposes via the "compute body/local"_compute_body_local.html and "dump local"_dump.html @@ -257,10 +435,10 @@ the body particle itself. These values are calculated using the current COM and orientation of the body particle. For images created by the "dump image"_dump_image.html command, if the -{body} keyword is set, then each body particle is drawn as a convex -polygon consisting of N line segments. Note that the line segments -are drawn between the N vertices, which does not correspond exactly to -the physical extent of the body (because the "pair_style +{body} keyword is set, then each body particle is drawn as a polygon +consisting of N line segments. Note that the line segments are drawn +between the N vertices, which does not correspond exactly to the +physical extent of the body (because the "pair_style rounded/polygon"_pair_body_rounded_polygon.html defines finite-size spheres at those point and the line segments between the spheres are tangent to the spheres). The drawn diameter of each line segment is @@ -269,6 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword. The :line -:link(Fraige) +:link(body-Fraige) [(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008). + +:link(body-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). diff --git a/doc/src/Howto_chunk.txt b/doc/src/Howto_chunk.txt new file mode 100644 index 0000000000000000000000000000000000000000..8e52acf4b8693569bac54304bb5f2c0ffd56d0fb --- /dev/null +++ b/doc/src/Howto_chunk.txt @@ -0,0 +1,166 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Use chunks to calculate system properties :h3 + +In LAMMS, "chunks" are collections of atoms, as defined by the +"compute chunk/atom"_compute_chunk_atom.html command, which assigns +each atom to a chunk ID (or to no chunk at all). The number of chunks +and the assignment of chunk IDs to atoms can be static or change over +time. Examples of "chunks" are molecules or spatial bins or atoms +with similar values (e.g. coordination number or potential energy). + +The per-atom chunk IDs can be used as input to two other kinds of +commands, to calculate various properties of a system: + +"fix ave/chunk"_fix_ave_chunk.html +any of the "compute */chunk"_compute.html commands :ul + +Here, each of the 3 kinds of chunk-related commands is briefly +overviewed. Then some examples are given of how to compute different +properties with chunk commands. + +Compute chunk/atom command: :h4 + +This compute can assign atoms to chunks of various styles. Only atoms +in the specified group and optional specified region are assigned to a +chunk. Here are some possible chunk definitions: + +atoms in same molecule | chunk ID = molecule ID | +atoms of same atom type | chunk ID = atom type | +all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | +atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | +atoms in same spatial bin | chunk ID = bin ID | +atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | +atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | +atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) + +Note that chunk IDs are integer values, so for atom properties or +computes that produce a floating point value, they will be truncated +to an integer. You could also use the compute in a variable that +scales the floating point value to spread it across multiple integers. + +Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = +pencils, 3d bins = boxes, spherical bins, cylindrical bins. + +This compute also calculates the number of chunks {Nchunk}, which is +used by other commands to tally per-chunk data. {Nchunk} can be a +static value or change over time (e.g. the number of clusters). The +chunk ID for an individual atom can also be static (e.g. a molecule +ID), or dynamic (e.g. what spatial bin an atom is in as it moves). + +Note that this compute allows the per-atom output of other +"computes"_compute.html, "fixes"_fix.html, and +"variables"_variable.html to be used to define chunk IDs for each +atom. This means you can write your own compute or fix to output a +per-atom quantity to use as chunk ID. See the "Modify"_Modify.html +doc pages for info on how to do this. You can also define a "per-atom +variable"_variable.html in the input script that uses a formula to +generate a chunk ID for each atom. + +Fix ave/chunk command: :h4 + +This fix takes the ID of a "compute +chunk/atom"_compute_chunk_atom.html command as input. For each chunk, +it then sums one or more specified per-atom values over the atoms in +each chunk. The per-atom values can be any atom property, such as +velocity, force, charge, potential energy, kinetic energy, stress, +etc. Additional keywords are defined for per-chunk properties like +density and temperature. More generally any per-atom value generated +by other "computes"_compute.html, "fixes"_fix.html, and "per-atom +variables"_variable.html, can be summed over atoms in each chunk. + +Similar to other averaging fixes, this fix allows the summed per-chunk +values to be time-averaged in various ways, and output to a file. The +fix produces a global array as output with one row of values per +chunk. + +Compute */chunk commands: :h4 + +Currently the following computes operate on chunks of atoms to produce +per-chunk values. + +"compute com/chunk"_compute_com_chunk.html +"compute gyration/chunk"_compute_gyration_chunk.html +"compute inertia/chunk"_compute_inertia_chunk.html +"compute msd/chunk"_compute_msd_chunk.html +"compute property/chunk"_compute_property_chunk.html +"compute temp/chunk"_compute_temp_chunk.html +"compute torque/chunk"_compute_vcm_chunk.html +"compute vcm/chunk"_compute_vcm_chunk.html :ul + +They each take the ID of a "compute +chunk/atom"_compute_chunk_atom.html command as input. As their names +indicate, they calculate the center-of-mass, radius of gyration, +moments of inertia, mean-squared displacement, temperature, torque, +and velocity of center-of-mass for each chunk of atoms. The "compute +property/chunk"_compute_property_chunk.html command can tally the +count of atoms in each chunk and extract other per-chunk properties. + +The reason these various calculations are not part of the "fix +ave/chunk command"_fix_ave_chunk.html, is that each requires a more +complicated operation than simply summing and averaging over per-atom +values in each chunk. For example, many of them require calculation +of a center of mass, which requires summing mass*position over the +atoms and then dividing by summed mass. + +All of these computes produce a global vector or global array as +output, wih one or more values per chunk. They can be used +in various ways: + +As input to the "fix ave/time"_fix_ave_time.html command, which can +write the values to a file and optionally time average them. :ulb,l + +As input to the "fix ave/histo"_fix_ave_histo.html command to +histogram values across chunks. E.g. a histogram of cluster sizes or +molecule diffusion rates. :l + +As input to special functions of "equal-style +variables"_variable.html, like sum() and max(). E.g. to find the +largest cluster or fastest diffusing molecule. :l +:ule + +Example calculations with chunks :h4 + +Here are examples using chunk commands to calculate various +properties: + +(1) Average velocity in each of 1000 2d spatial bins: + +compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced +fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre + +(2) Temperature in each spatial bin, after subtracting a flow +velocity: + +compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced +compute vbias all temp/profile 1 0 0 y 10 +fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre + +(3) Center of mass of each molecule: + +compute cc1 all chunk/atom molecule +compute myChunk all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre + +(4) Total force on each molecule and ave/max across all molecules: + +compute cc1 all chunk/atom molecule +fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out +variable xave equal ave(f_1\[2\]) +variable xmax equal max(f_1\[2\]) +thermo 1000 +thermo_style custom step temp v_xave v_xmax :pre + +(5) Histogram of cluster sizes: + +compute cluster all cluster/atom 1.0 +compute cc1 all chunk/atom c_cluster compress yes +compute size all property/chunk cc1 count +fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre diff --git a/doc/src/Howto_coreshell.txt b/doc/src/Howto_coreshell.txt new file mode 100644 index 0000000000000000000000000000000000000000..4f1cd64384e696dbf00eccf023a3a10be8f40cc9 --- /dev/null +++ b/doc/src/Howto_coreshell.txt @@ -0,0 +1,253 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Adiabatic core/shell model :h3 + +The adiabatic core-shell model by "Mitchell and +Fincham"_#MitchellFincham is a simple method for adding polarizability +to a system. In order to mimic the electron shell of an ion, a +satellite particle is attached to it. This way the ions are split into +a core and a shell where the latter is meant to react to the +electrostatic environment inducing polarizability. See the "Howto +polarizable"_Howto_polarizable.html doc page for a discussion of all +the polarizable models available in LAMMPS. + +Technically, shells are attached to the cores by a spring force f = +k*r where k is a parametrized spring constant and r is the distance +between the core and the shell. The charges of the core and the shell +add up to the ion charge, thus q(ion) = q(core) + q(shell). This +setup introduces the ion polarizability (alpha) given by +alpha = q(shell)^2 / k. In a +similar fashion the mass of the ion is distributed on the core and the +shell with the core having the larger mass. + +To run this model in LAMMPS, "atom_style"_atom_style.html {full} can +be used since atom charge and bonds are needed. Each kind of +core/shell pair requires two atom types and a bond type. The core and +shell of a core/shell pair should be bonded to each other with a +harmonic bond that provides the spring force. For example, a data file +for NaCl, as found in examples/coreshell, has this format: + +432 atoms # core and shell atoms +216 bonds # number of core/shell springs :pre + +4 atom types # 2 cores and 2 shells for Na and Cl +2 bond types :pre + +0.0 24.09597 xlo xhi +0.0 24.09597 ylo yhi +0.0 24.09597 zlo zhi :pre + +Masses # core/shell mass ratio = 0.1 :pre + +1 20.690784 # Na core +2 31.90500 # Cl core +3 2.298976 # Na shell +4 3.54500 # Cl shell :pre + +Atoms :pre + +1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 +2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 +3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 +4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 +(...) :pre + +Bonds # Bond topology for spring forces :pre + +1 2 1 2 # spring for core/shell pair 1 +2 2 3 4 # spring for core/shell pair 2 +(...) :pre + +Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only +defined between the shells. Coulombic interactions are defined +between all cores and shells. If desired, additional bonds can be +specified between cores. + +The "special_bonds"_special_bonds.html command should be used to +turn-off the Coulombic interaction within core/shell pairs, since that +interaction is set by the bond spring. This is done using the +"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0, +which is the default value. It needs to be considered whether one has +to adjust the "special_bonds"_special_bonds.html weighting according +to the molecular topology since the interactions of the shells are +bypassed over an extra bond. + +Note that this core/shell implementation does not require all ions to +be polarized. One can mix core/shell pairs and ions without a +satellite particle if desired. + +Since the core/shell model permits distances of r = 0.0 between the +core and shell, a pair style with a "cs" suffix needs to be used to +implement a valid long-range Coulombic correction. Several such pair +styles are provided in the CORESHELL package. See "this doc +page"_pair_cs.html for details. All of the core/shell enabled pair +styles require the use of a long-range Coulombic solver, as specified +by the "kspace_style"_kspace_style.html command. Either the PPPM or +Ewald solvers can be used. + +For the NaCL example problem, these pair style and bond style settings +are used: + +pair_style born/coul/long/cs 20.0 20.0 +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 :pre + +When running dynamics with the adiabatic core/shell model, the +following issues should be considered. The relative motion of +the core and shell particles corresponds to the polarization, +hereby an instantaneous relaxation of the shells is approximated +and a fast core/shell spring frequency ensures a nearly constant +internal kinetic energy during the simulation. +Thermostats can alter this polarization behaviour, by scaling the +internal kinetic energy, meaning the shell will not react freely to +its electrostatic environment. +Therefore it is typically desirable to decouple the relative motion of +the core/shell pair, which is an imaginary degree of freedom, from the +real physical system. To do that, the "compute +temp/cs"_compute_temp_cs.html command can be used, in conjunction with +any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix +langevin"_fix_langevin. This compute uses the center-of-mass velocity +of the core/shell pairs to calculate a temperature, and insures that +velocity is what is rescaled for thermostatting purposes. This +compute also works for a system with both core/shell pairs and +non-polarized ions (ions without an attached satellite particle). The +"compute temp/cs"_compute_temp_cs.html command requires input of two +groups, one for the core atoms, another for the shell atoms. +Non-polarized ions which might also be included in the treated system +should not be included into either of these groups, they are taken +into account by the {group-ID} (2nd argument) of the compute. The +groups can be defined using the "group {type}"_group.html command. +Note that to perform thermostatting using this definition of +temperature, the "fix modify temp"_fix_modify.html command should be +used to assign the compute to the thermostat fix. Likewise the +"thermo_modify temp"_thermo_modify.html command can be used to make +this temperature be output for the overall system. + +For the NaCl example, this can be done as follows: + +group cores type 1 2 +group shells type 3 4 +compute CSequ all temp/cs cores shells +fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system +fix thermostatequ all nve # integrator as needed for the berendsen thermostat +fix_modify thermoberendsen temp CSequ +thermo_modify temp CSequ # output of center-of-mass derived temperature :pre + +The pressure for the core/shell system is computed via the regular +LAMMPS convention by "treating the cores and shells as individual +particles"_#MitchellFincham2. For the thermo output of the pressure +as well as for the application of a barostat, it is necessary to +use an additional "pressure"_compute_pressure compute based on the +default "temperature"_compute_temp and specifying it as a second +argument in "fix modify"_fix_modify.html and +"thermo_modify"_thermo_modify.html resulting in: + +(...) +compute CSequ all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles +thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure +fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 +fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre + +If "compute temp/cs"_compute_temp_cs.html is used, the decoupled +relative motion of the core and the shell should in theory be +stable. However numerical fluctuation can introduce a small +momentum to the system, which is noticable over long trajectories. +Therefore it is recommendable to use the "fix +momentum"_fix_momentum.html command in combination with "compute +temp/cs"_compute_temp_cs.html when equilibrating the system to +prevent any drift. + +When initializing the velocities of a system with core/shell pairs, it +is also desirable to not introduce energy into the relative motion of +the core/shell particles, but only assign a center-of-mass velocity to +the pairs. This can be done by using the {bias} keyword of the +"velocity create"_velocity.html command and assigning the "compute +temp/cs"_compute_temp_cs.html command to the {temp} keyword of the +"velocity"_velocity.html command, e.g. + +velocity all create 1427 134 bias yes temp CSequ +velocity all scale 1427 temp CSequ :pre + +To maintain the correct polarizability of the core/shell pairs, the +kinetic energy of the internal motion shall remain nearly constant. +Therefore the choice of spring force and mass ratio need to ensure +much faster relative motion of the 2 atoms within the core/shell pair +than their center-of-mass velocity. This allows the shells to +effectively react instantaneously to the electrostatic environment and +limits energy transfer to or from the core/shell oscillators. +This fast movement also dictates the timestep that can be used. + +The primary literature of the adiabatic core/shell model suggests that +the fast relative motion of the core/shell pairs only allows negligible +energy transfer to the environment. +The mentioned energy transfer will typically lead to a small drift +in total energy over time. This internal energy can be monitored +using the "compute chunk/atom"_compute_chunk_atom.html and "compute +temp/chunk"_compute_temp_chunk.html commands. The internal kinetic +energies of each core/shell pair can then be summed using the sum() +special function of the "variable"_variable.html command. Or they can +be time/averaged and output using the "fix ave/time"_fix_ave_time.html +command. To use these commands, each core/shell pair must be defined +as a "chunk". If each core/shell pair is defined as its own molecule, +the molecule ID can be used to define the chunks. If cores are bonded +to each other to form larger molecules, the chunks can be identified +by the "fix property/atom"_fix_property_atom.html via assigning a +core/shell ID to each atom using a special field in the data file read +by the "read_data"_read_data.html command. This field can then be +accessed by the "compute property/atom"_compute_property_atom.html +command, to use as input to the "compute +chunk/atom"_compute_chunk_atom.html command to define the core/shell +pairs as chunks. + +For example if core/shell pairs are the only molecules: + +read_data NaCl_CS_x0.1_prop.data +compute prop all property/atom molecule +compute cs_chunk all chunk/atom c_prop +compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs +fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre + +For example if core/shell pairs and other molecules are present: + +fix csinfo all property/atom i_CSID # property/atom command +read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file +compute prop all property/atom i_CSID +(...) :pre + +The additional section in the date file would be formatted like this: + +CS-Info # header of additional section :pre + +1 1 # column 1 = atom ID, column 2 = core/shell ID +2 1 +3 2 +4 2 +5 3 +6 3 +7 4 +8 4 +(...) :pre + +:line + +:link(MitchellFincham) +[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, +5, 1031-1038 (1993). + +:link(MitchellFincham2) +[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, +6, 393-404 (1994). diff --git a/doc/src/Howto_couple.txt b/doc/src/Howto_couple.txt new file mode 100644 index 0000000000000000000000000000000000000000..38595a9d1641ddb869cf5606ce003c2189690813 --- /dev/null +++ b/doc/src/Howto_couple.txt @@ -0,0 +1,105 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Coupling LAMMPS to other codes :h3 + +LAMMPS is designed to allow it to be coupled to other codes. For +example, a quantum mechanics code might compute forces on a subset of +atoms and pass those forces to LAMMPS. Or a continuum finite element +(FE) simulation might use atom positions as boundary conditions on FE +nodal points, compute a FE solution, and return interpolated forces on +MD atoms. + +LAMMPS can be coupled to other codes in at least 3 ways. Each has +advantages and disadvantages, which you'll have to think about in the +context of your application. + +(1) Define a new "fix"_fix.html command that calls the other code. In +this scenario, LAMMPS is the driver code. During its timestepping, +the fix is invoked, and can make library calls to the other code, +which has been linked to LAMMPS as a library. This is the way the +"POEMS"_poems package that performs constrained rigid-body motion on +groups of atoms is hooked to LAMMPS. See the "fix +poems"_fix_poems.html command for more details. See the +"Modify"_Modify.html doc pages for info on how to add a new fix to +LAMMPS. + +:link(poems,http://www.rpi.edu/~anderk5/lab) + +(2) Define a new LAMMPS command that calls the other code. This is +conceptually similar to method (1), but in this case LAMMPS and the +other code are on a more equal footing. Note that now the other code +is not called during the timestepping of a LAMMPS run, but between +runs. The LAMMPS input script can be used to alternate LAMMPS runs +with calls to the other code, invoked via the new command. The +"run"_run.html command facilitates this with its {every} option, which +makes it easy to run a few steps, invoke the command, run a few steps, +invoke the command, etc. + +In this scenario, the other code can be called as a library, as in +(1), or it could be a stand-alone code, invoked by a system() call +made by the command (assuming your parallel machine allows one or more +processors to start up another program). In the latter case the +stand-alone code could communicate with LAMMPS thru files that the +command writes and reads. + +See the "Modify command"_Modify_command.html doc page for info on how +to add a new command to LAMMPS. + +(3) Use LAMMPS as a library called by another code. In this case the +other code is the driver and calls LAMMPS as needed. Or a wrapper +code could link and call both LAMMPS and another code as libraries. +Again, the "run"_run.html command has options that allow it to be +invoked with minimal overhead (no setup or clean-up) if you wish to do +multiple short runs, driven by another program. + +Examples of driver codes that call LAMMPS as a library are included in +the examples/COUPLE directory of the LAMMPS distribution; see +examples/COUPLE/README for more details: + +simple: simple driver programs in C++ and C which invoke LAMMPS as a +library :ulb,l + +lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical +MD with quantum forces calculated by a density functional code :l + +lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple +a kinetic Monte Carlo model for grain growth using MD to calculate +strain induced across grain boundaries :l +:ule + +:link(quest,http://dft.sandia.gov/Quest) +:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) + +"This section"_Section_start.html#start_5 of the documentation +describes how to build LAMMPS as a library. Once this is done, you +can interface with LAMMPS either via C++, C, Fortran, or Python (or +any other language that supports a vanilla C-like interface). For +example, from C++ you could create one (or more) "instances" of +LAMMPS, pass it an input script to process, or execute individual +commands, all by invoking the correct class methods in LAMMPS. From C +or Fortran you can make function calls to do the same things. See the +"Python"_Python.html doc pages for a description of the Python wrapper +provided with LAMMPS that operates through the LAMMPS library +interface. + +The files src/library.cpp and library.h contain the C-style interface +to LAMMPS. See the "Howto library"_Howto_library.html doc page for a +description of the interface and how to extend it for your needs. + +Note that the lammps_open() function that creates an instance of +LAMMPS takes an MPI communicator as an argument. This means that +instance of LAMMPS will run on the set of processors in the +communicator. Thus the calling code can run LAMMPS on all or a subset +of processors. For example, a wrapper script might decide to +alternate between LAMMPS and another code, allowing them both to run +on all the processors. Or it might allocate half the processors to +LAMMPS and half to the other code and run both codes simultaneously +before syncing them up periodically. Or it might instantiate multiple +instances of LAMMPS to perform different calculations. diff --git a/doc/src/Howto_diffusion.txt b/doc/src/Howto_diffusion.txt new file mode 100644 index 0000000000000000000000000000000000000000..401c1e359c05ee83ef37ecbae44073cdd4ecfacf --- /dev/null +++ b/doc/src/Howto_diffusion.txt @@ -0,0 +1,31 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate a diffusion coefficient :h3 + +The diffusion coefficient D of a material can be measured in at least +2 ways using various options in LAMMPS. See the examples/DIFFUSE +directory for scripts that implement the 2 methods discussed here for +a simple Lennard-Jones fluid model. + +The first method is to measure the mean-squared displacement (MSD) of +the system, via the "compute msd"_compute_msd.html command. The slope +of the MSD versus time is proportional to the diffusion coefficient. +The instantaneous MSD values can be accumulated in a vector via the +"fix vector"_fix_vector.html command, and a line fit to the vector to +compute its slope via the "variable slope"_variable.html function, and +thus extract D. + +The second method is to measure the velocity auto-correlation function +(VACF) of the system, via the "compute vacf"_compute_vacf.html +command. The time-integral of the VACF is proportional to the +diffusion coefficient. The instantaneous VACF values can be +accumulated in a vector via the "fix vector"_fix_vector.html command, +and time integrated via the "variable trap"_variable.html function, +and thus extract D. diff --git a/doc/src/Howto_dispersion.txt b/doc/src/Howto_dispersion.txt new file mode 100644 index 0000000000000000000000000000000000000000..4ea286258e11a38aa07e6e93df4c3e22cb0aca0a --- /dev/null +++ b/doc/src/Howto_dispersion.txt @@ -0,0 +1,108 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Long-raage dispersion settings :h3 + +The PPPM method computes interactions by splitting the pair potential +into two parts, one of which is computed in a normal pairwise fashion, +the so-called real-space part, and one of which is computed using the +Fourier transform, the so called reciprocal-space or kspace part. For +both parts, the potential is not computed exactly but is approximated. +Thus, there is an error in both parts of the computation, the +real-space and the kspace error. The just mentioned facts are true +both for the PPPM for Coulomb as well as dispersion interactions. The +deciding difference - and also the reason why the parameters for +pppm/disp have to be selected with more care - is the impact of the +errors on the results: The kspace error of the PPPM for Coulomb and +dispersion interaction and the real-space error of the PPPM for +Coulomb interaction have the character of noise. In contrast, the +real-space error of the PPPM for dispersion has a clear physical +interpretation: the underprediction of cohesion. As a consequence, the +real-space error has a much stronger effect than the kspace error on +simulation results for pppm/disp. Parameters must thus be chosen in a +way that this error is much smaller than the kspace error. + +When using pppm/disp and not making any specifications on the PPPM +parameters via the kspace modify command, parameters will be tuned +such that the real-space error and the kspace error are equal. This +will result in simulations that are either inaccurate or slow, both of +which is not desirable. For selecting parameters for the pppm/disp +that provide fast and accurate simulations, there are two approaches, +which both have their up- and downsides. + +The first approach is to set desired real-space an kspace accuracies +via the {kspace_modify force/disp/real} and {kspace_modify +force/disp/kspace} commands. Note that the accuracies have to be +specified in force units and are thus dependent on the chosen unit +settings. For real units, 0.0001 and 0.002 seem to provide reasonable +accurate and efficient computations for the real-space and kspace +accuracies. 0.002 and 0.05 work well for most systems using lj +units. PPPM parameters will be generated based on the desired +accuracies. The upside of this approach is that it usually provides a +good set of parameters and will work for both the {kspace_modify diff +ad} and {kspace_modify diff ik} options. The downside of the method +is that setting the PPPM parameters will take some time during the +initialization of the simulation. + +The second approach is to set the parameters for the pppm/disp +explicitly using the {kspace_modify mesh/disp}, {kspace_modify +order/disp}, and {kspace_modify gewald/disp} commands. This approach +requires a more experienced user who understands well the impact of +the choice of parameters on the simulation accuracy and +performance. This approach provides a fast initialization of the +simulation. However, it is sensitive to errors: A combination of +parameters that will perform well for one system might result in +far-from-optimal conditions for other simulations. For example, +parameters that provide accurate and fast computations for +all-atomistic force fields can provide insufficient accuracy or +united-atomistic force fields (which is related to that the latter +typically have larger dispersion coefficients). + +To avoid inaccurate or inefficient simulations, the pppm/disp stops +simulations with an error message if no action is taken to control the +PPPM parameters. If the automatic parameter generation is desired and +real-space and kspace accuracies are desired to be equal, this error +message can be suppressed using the {kspace_modify disp/auto yes} +command. + +A reasonable approach that combines the upsides of both methods is to +make the first run using the {kspace_modify force/disp/real} and +{kspace_modify force/disp/kspace} commands, write down the PPPM +parameters from the outut, and specify these parameters using the +second approach in subsequent runs (which have the same composition, +force field, and approximately the same volume). + +Concerning the performance of the pppm/disp there are two more things +to consider. The first is that when using the pppm/disp, the cutoff +parameter does no longer affect the accuracy of the simulation +(subject to that gewald/disp is adjusted when changing the cutoff). +The performance can thus be increased by examining different values +for the cutoff parameter. A lower bound for the cutoff is only set by +the truncation error of the repulsive term of pair potentials. + +The second is that the mixing rule of the pair style has an impact on +the computation time when using the pppm/disp. Fastest computations +are achieved when using the geometric mixing rule. Using the +arithmetic mixing rule substantially increases the computational cost. +The computational overhead can be reduced using the {kspace_modify +mix/disp geom} and {kspace_modify splittol} commands. The first +command simply enforces geometric mixing of the dispersion +coefficients in kspace computations. This introduces some error in +the computations but will also significantly speed-up the +simulations. The second keyword sets the accuracy with which the +dispersion coefficients are approximated using a matrix factorization +approach. This may result in better accuracy then using the first +command, but will usually also not provide an equally good increase of +efficiency. + +Finally, pppm/disp can also be used when no mixing rules apply. +This can be achieved using the {kspace_modify mix/disp none} command. +Note that the code does not check automatically whether any mixing +rule is fulfilled. If mixing rules do not apply, the user will have +to specify this command explicitly. diff --git a/doc/src/Howto_drude.txt b/doc/src/Howto_drude.txt new file mode 100644 index 0000000000000000000000000000000000000000..ebdf5f865824a365220f1a58214fd06f111dcae2 --- /dev/null +++ b/doc/src/Howto_drude.txt @@ -0,0 +1,77 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Drude induced dipoles :h3 + +The thermalized Drude model represents induced dipoles by a pair of +charges (the core atom and the Drude particle) connected by a harmonic +spring. See the "Howto polarizable"_Howto_polarizable.html doc page +for a discussion of all the polarizable models available in LAMMPS. + +The Drude model has a number of features aimed at its use in +molecular systems ("Lamoureux and Roux"_#howto-Lamoureux): + +Thermostating of the additional degrees of freedom associated with the +induced dipoles at very low temperature, in terms of the reduced +coordinates of the Drude particles with respect to their cores. This +makes the trajectory close to that of relaxed induced dipoles. :ulb,l + +Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle +pair represents a single (polarizable) atom, so the special screening +factors in a covalent structure should be the same for the core and +the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 +special neighbor relations from their respective cores. :l + +Stabilization of the interactions between induced dipoles. Drude +dipoles on covalently bonded atoms interact too strongly due to the +short distances, so an atom may capture the Drude particle of a +neighbor, or the induced dipoles within the same molecule may align +too much. To avoid this, damping at short range can be done by Thole +functions (for which there are physical grounds). This Thole damping +is applied to the point charges composing the induced dipole (the +charge of the Drude particle and the opposite charge on the core, not +to the total charge of the core atom). :l,ule + +A detailed tutorial covering the usage of Drude induced dipoles in +LAMMPS is on the "Howto drude2e"_Howto_drude2.html doc page. + +As with the core-shell model, the cores and Drude particles should +appear in the data file as standard atoms. The same holds for the +springs between them, which are described by standard harmonic bonds. +The nature of the atoms (core, Drude particle or non-polarizable) is +specified via the "fix drude"_fix_drude.html command. The special +list of neighbors is automatically refactored to account for the +equivalence of core and Drude particles as regards special 1-2 to 1-4 +screening. It may be necessary to use the {extra/special/per/atom} +keyword of the "read_data"_read_data.html command. If using "fix +shake"_fix_shake.html, make sure no Drude particle is in this fix +group. + +There are two ways to thermostat the Drude particles at a low +temperature: use either "fix langevin/drude"_fix_langevin_drude.html +for a Langevin thermostat, or "fix +drude/transform/*"_fix_drude_transform.html for a Nose-Hoover +thermostat. The former requires use of the command "comm_modify vel +yes"_comm_modify.html. The latter requires two separate integration +fixes like {nvt} or {npt}. The correct temperatures of the reduced +degrees of freedom can be calculated using the "compute +temp/drude"_compute_temp_drude.html. This requires also to use the +command {comm_modify vel yes}. + +Short-range damping of the induced dipole interactions can be achieved +using Thole functions through the "pair style +thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html +with a Coulomb pair style. It may be useful to use {coul/long/cs} or +similar from the CORESHELL package if the core and Drude particle come +too close, which can cause numerical issues. + +:line + +:link(howto-Lamoureux) +[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/src/tutorial_drude.txt b/doc/src/Howto_drude2.txt similarity index 99% rename from doc/src/tutorial_drude.txt rename to doc/src/Howto_drude2.txt index f6e7eed40bd84cde46e30213c0a14c22244eae86..a342d4a87d1deec93cbb9820a39099aaf5fb75a6 100644 --- a/doc/src/tutorial_drude.txt +++ b/doc/src/Howto_drude2.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/Howto_elastic.txt b/doc/src/Howto_elastic.txt new file mode 100644 index 0000000000000000000000000000000000000000..68b30970ca33a84308b32bb1516081f49470367e --- /dev/null +++ b/doc/src/Howto_elastic.txt @@ -0,0 +1,47 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate elastic constants :h3 + +Elastic constants characterize the stiffness of a material. The formal +definition is provided by the linear relation that holds between the +stress and strain tensors in the limit of infinitesimal deformation. +In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where +the repeated indices imply summation. s_ij are the elements of the +symmetric stress tensor. e_kl are the elements of the symmetric strain +tensor. C_ijkl are the elements of the fourth rank tensor of elastic +constants. In three dimensions, this tensor has 3^4=81 elements. Using +Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij +is now the derivative of s_i w.r.t. e_j. Because s_i is itself a +derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at +most 7*6/2 = 21 distinct elements. + +At zero temperature, it is easy to estimate these derivatives by +deforming the simulation box in one of the six directions using the +"change_box"_change_box.html command and measuring the change in the +stress tensor. A general-purpose script that does this is given in the +examples/elastic directory described on the "Examples"_Examples.html +doc page. + +Calculating elastic constants at finite temperature is more +challenging, because it is necessary to run a simulation that perfoms +time averages of differential properties. One way to do this is to +measure the change in average stress tensor in an NVT simulations when +the cell volume undergoes a finite deformation. In order to balance +the systematic and statistical errors in this method, the magnitude of +the deformation must be chosen judiciously, and care must be taken to +fully equilibrate the deformed cell before sampling the stress +tensor. Another approach is to sample the triclinic cell fluctuations +that occur in an NPT simulation. This method can also be slow to +converge and requires careful post-processing "(Shinoda)"_#Shinoda1 + +:line + +:link(Shinoda1) +[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). diff --git a/doc/src/tutorial_github.txt b/doc/src/Howto_github.txt similarity index 98% rename from doc/src/tutorial_github.txt rename to doc/src/Howto_github.txt index 3e10b821aecf3b8bce1f1f9e54198720bd521ce5..720b3317f012eb3eaf3f32f65fc1542185359721 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/Howto_github.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ work required by the LAMMPS developers. Consequently, creating a pull request will increase your chances to have your contribution included and will reduce the time until the integration is complete. For more information on the requirements to have your code included into LAMMPS -please see "Section 10.15"_Section_modify.html#mod_15 +please see the "Modify contribute"_Modify_contribute.html doc page. :line @@ -124,7 +124,7 @@ unrelated feature, you should switch branches! After everything is done, add the files to the branch and commit them: - $ git add doc/src/tutorial_github.txt + $ git add doc/src/Howto_github.txt $ git add doc/src/JPG/tutorial*.png :pre IMPORTANT NOTE: Do not use {git commit -a} (or {git add -A}). The -a @@ -318,7 +318,7 @@ Because the changes are OK with us, we are going to merge by clicking on Now, since in the meantime our local text for the tutorial also changed, we need to pull Axel's change back into our branch, and merge them: - $ git add tutorial_github.txt + $ git add Howto_github.txt $ git add JPG/tutorial_reverse_pull_request*.png $ git commit -m "Updated text and images on reverse pull requests" $ git pull :pre @@ -331,7 +331,7 @@ With Axel's changes merged in and some final text updates, our feature branch is now perfect as far as we are concerned, so we are going to commit and push again: - $ git add tutorial_github.txt + $ git add Howto_github.txt $ git add JPG/tutorial_reverse_pull_request6.png $ git commit -m "Merged Axel's suggestions and updated text" $ git push git@github.com:Pakketeretet2/lammps :pre diff --git a/doc/src/Howto_granular.txt b/doc/src/Howto_granular.txt new file mode 100644 index 0000000000000000000000000000000000000000..8027369501eb0730dd4008b56503d95642ee9380 --- /dev/null +++ b/doc/src/Howto_granular.txt @@ -0,0 +1,57 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Granular models :h3 + +Granular system are composed of spherical particles with a diameter, +as opposed to point particles. This means they have an angular +velocity and torque can be imparted to them to cause them to rotate. + +To run a simulation of a granular model, you will want to use +the following commands: + +"atom_style sphere"_atom_style.html +"fix nve/sphere"_fix_nve_sphere.html +"fix gravity"_fix_gravity.html :ul + +This compute + +"compute erotate/sphere"_compute_erotate_sphere.html :ul + +calculates rotational kinetic energy which can be "output with +thermodynamic info"_Howto_output.html. + +Use one of these 3 pair potentials, which compute forces and torques +between interacting pairs of particles: + +"pair_style"_pair_style.html gran/history +"pair_style"_pair_style.html gran/no_history +"pair_style"_pair_style.html gran/hertzian :ul + +These commands implement fix options specific to granular systems: + +"fix freeze"_fix_freeze.html +"fix pour"_fix_pour.html +"fix viscous"_fix_viscous.html +"fix wall/gran"_fix_wall_gran.html :ul + +The fix style {freeze} zeroes both the force and torque of frozen +atoms, and should be used for granular system instead of the fix style +{setforce}. + +For computational efficiency, you can eliminate needless pairwise +computations between frozen atoms by using this command: + +"neigh_modify"_neigh_modify.html exclude :ul + +NOTE: By default, for 2d systems, granular particles are still modeled +as 3d spheres, not 2d discs (circles), meaning their moment of inertia +will be the same as in 3d. If you wish to model granular particles in +2d as 2d discs, see the note on this topic on the "Howto 2d"_Howto_2d +doc page, where 2d simulations are discussed. diff --git a/doc/src/Howto_kappa.txt b/doc/src/Howto_kappa.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2a57ef49b82461b89a72cda29c9785297a877f0 --- /dev/null +++ b/doc/src/Howto_kappa.txt @@ -0,0 +1,90 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate thermal conductivity :h3 + +The thermal conductivity kappa of a material can be measured in at +least 4 ways using various options in LAMMPS. See the examples/KAPPA +directory for scripts that implement the 4 methods discussed here for +a simple Lennard-Jones fluid model. Also, see the "Howto +viscosity"_Howto_viscosity.html doc page for an analogous discussion +for viscosity. + +The thermal conductivity tensor kappa is a measure of the propensity +of a material to transmit heat energy in a diffusive manner as given +by Fourier's law + +J = -kappa grad(T) + +where J is the heat flux in units of energy per area per time and +grad(T) is the spatial gradient of temperature. The thermal +conductivity thus has units of energy per distance per time per degree +K and is often approximated as an isotropic quantity, i.e. as a +scalar. + +The first method is to setup two thermostatted regions at opposite +ends of a simulation box, or one in the middle and one at the end of a +periodic box. By holding the two regions at different temperatures +with a "thermostatting fix"_Howto_thermostat.html, the energy added to +the hot region should equal the energy subtracted from the cold region +and be proportional to the heat flux moving between the regions. See +the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji and +"Wirnsberger et al"_#howto-Wirnsberger for details of this idea. Note +that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix +langevin"_fix_langevin.html, and "fix +temp/rescale"_fix_temp_rescale.html store the cumulative energy they +add/subtract. + +Alternatively, as a second method, the "fix heat"_fix_heat.html or +"fix ehex"_fix_ehex.html commands can be used in place of thermostats +on each of two regions to add/subtract specified amounts of energy to +both regions. In both cases, the resulting temperatures of the two +regions can be monitored with the "compute temp/region" command and +the temperature profile of the intermediate region can be monitored +with the "fix ave/chunk"_fix_ave_chunk.html and "compute +ke/atom"_compute_ke_atom.html commands. + +The third method is to perform a reverse non-equilibrium MD simulation +using the "fix thermal/conductivity"_fix_thermal_conductivity.html +command which implements the rNEMD algorithm of Muller-Plathe. +Kinetic energy is swapped between atoms in two different layers of the +simulation box. This induces a temperature gradient between the two +layers which can be monitored with the "fix +ave/chunk"_fix_ave_chunk.html and "compute +ke/atom"_compute_ke_atom.html commands. The fix tallies the +cumulative energy transfer that it performs. See the "fix +thermal/conductivity"_fix_thermal_conductivity.html command for +details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the heat flux +to kappa. The heat flux can be calculated from the fluctuations of +per-atom potential and kinetic energies and per-atom stress tensor in +a steady-state equilibrated simulation. This is in contrast to the +two preceding non-equilibrium methods, where energy flows continuously +between hot and cold regions of the simulation box. + +The "compute heat/flux"_compute_heat_flux.html command can calculate +the needed heat flux and describes how to implement the Green_Kubo +formalism using additional LAMMPS commands, such as the "fix +ave/correlate"_fix_ave_correlate.html command to calculate the needed +auto-correlation. See the doc page for the "compute +heat/flux"_compute_heat_flux.html command for an example input script +that calculates the thermal conductivity of solid Ar via the GK +formalism. + +:line + +:link(howto-Ikeshoji) +[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 +(1994). + +:link(howto-Wirnsberger) +[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 +(2015). diff --git a/doc/src/Howto_library.txt b/doc/src/Howto_library.txt new file mode 100644 index 0000000000000000000000000000000000000000..0d4852fbf247adee92be56045d7b98af7e5a3542 --- /dev/null +++ b/doc/src/Howto_library.txt @@ -0,0 +1,208 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Library interface to LAMMPS :h3 + +As described in "Section 2.5"_Section_start.html#start_5, LAMMPS can +be built as a library, so that it can be called by another code, used +in a "coupled manner"_Howto_couple.html with other codes, or driven +through a "Python interface"_Python.html. + +All of these methodologies use a C-style interface to LAMMPS that is +provided in the files src/library.cpp and src/library.h. The +functions therein have a C-style argument list, but contain C++ code +you could write yourself in a C++ application that was invoking LAMMPS +directly. The C++ code in the functions illustrates how to invoke +internal LAMMPS operations. Note that LAMMPS classes are defined +within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ +application. + +The examples/COUPLE and python/examples directories have example C++ +and C and Python codes which show how a driver code can link to LAMMPS +as a library, run LAMMPS on a subset of processors, grab data from +LAMMPS, change it, and put it back into LAMMPS. + +The file src/library.cpp contains the following functions for creating +and destroying an instance of LAMMPS and sending it commands to +execute. See the documentation in the src/library.cpp file for +details. + +NOTE: You can write code for additional functions as needed to define +how your code talks to LAMMPS and add them to src/library.cpp and +src/library.h, as well as to the "Python interface"_Python.html. The +added functions can access or change any internal LAMMPS data you +wish. + +void lammps_open(int, char **, MPI_Comm, void **) +void lammps_open_no_mpi(int, char **, void **) +void lammps_close(void *) +int lammps_version(void *) +void lammps_file(void *, char *) +char *lammps_command(void *, char *) +void lammps_commands_list(void *, int, char **) +void lammps_commands_string(void *, char *) +void lammps_free(void *) :pre + +The lammps_open() function is used to initialize LAMMPS, passing in a +list of strings as if they were "command-line +arguments"_Section_start.html#start_6 when LAMMPS is run in +stand-alone mode from the command line, and a MPI communicator for +LAMMPS to run under. It returns a ptr to the LAMMPS object that is +created, and which is used in subsequent library calls. The +lammps_open() function can be called multiple times, to create +multiple instances of LAMMPS. + +LAMMPS will run on the set of processors in the communicator. This +means the calling code can run LAMMPS on all or a subset of +processors. For example, a wrapper script might decide to alternate +between LAMMPS and another code, allowing them both to run on all the +processors. Or it might allocate half the processors to LAMMPS and +half to the other code and run both codes simultaneously before +syncing them up periodically. Or it might instantiate multiple +instances of LAMMPS to perform different calculations. + +The lammps_open_no_mpi() function is similar except that no MPI +communicator is passed from the caller. Instead, MPI_COMM_WORLD is +used to instantiate LAMMPS, and MPI is initialized if necessary. + +The lammps_close() function is used to shut down an instance of LAMMPS +and free all its memory. + +The lammps_version() function can be used to determined the specific +version of the underlying LAMMPS code. This is particularly useful +when loading LAMMPS as a shared library via dlopen(). The code using +the library interface can than use this information to adapt to +changes to the LAMMPS command syntax between versions. The returned +LAMMPS version code is an integer (e.g. 2 Sep 2015 results in +20150902) that grows with every new LAMMPS version. + +The lammps_file(), lammps_command(), lammps_commands_list(), and +lammps_commands_string() functions are used to pass one or more +commands to LAMMPS to execute, the same as if they were coming from an +input script. + +Via these functions, the calling code can read or generate a series of +LAMMPS commands one or multiple at a time and pass it thru the library +interface to setup a problem and then run it in stages. The caller +can interleave the command function calls with operations it performs, +calls to extract information from or set information within LAMMPS, or +calls to another code's library. + +The lammps_file() function passes the filename of an input script. +The lammps_command() function passes a single command as a string. +The lammps_commands_list() function passes multiple commands in a +char** list. In both lammps_command() and lammps_commands_list(), +individual commands may or may not have a trailing newline. The +lammps_commands_string() function passes multiple commands +concatenated into one long string, separated by newline characters. +In both lammps_commands_list() and lammps_commands_string(), a single +command can be spread across multiple lines, if the last printable +character of all but the last line is "&", the same as if the lines +appeared in an input script. + +The lammps_free() function is a clean-up function to free memory that +the library allocated previously via other function calls. See +comments in src/library.cpp file for which other functions need this +clean-up. + +The file src/library.cpp also contains these functions for extracting +information from LAMMPS and setting value within LAMMPS. Again, see +the documentation in the src/library.cpp file for details, including +which quantities can be queried by name: + +int lammps_extract_setting(void *, char *) +void *lammps_extract_global(void *, char *) +void lammps_extract_box(void *, double *, double *, + double *, double *, double *, int *, int *) +void *lammps_extract_atom(void *, char *) +void *lammps_extract_compute(void *, char *, int, int) +void *lammps_extract_fix(void *, char *, int, int, int, int) +void *lammps_extract_variable(void *, char *, char *) :pre + +The extract_setting() function returns info on the size +of data types (e.g. 32-bit or 64-bit atom IDs) used +by the LAMMPS executable (a compile-time choice). + +The other extract functions return a pointer to various global or +per-atom quantities stored in LAMMPS or to values calculated by a +compute, fix, or variable. The pointer returned by the +extract_global() function can be used as a permanent reference to a +value which may change. For the extract_atom() method, see the +extract() method in the src/atom.cpp file for a list of valid per-atom +properties. New names could easily be added if the property you want +is not listed. For the other extract functions, the underlying +storage may be reallocated as LAMMPS runs, so you need to re-call the +function to assure a current pointer or returned value(s). + +double lammps_get_thermo(void *, char *) +int lammps_get_natoms(void *) :pre + +int lammps_set_variable(void *, char *, char *) +void lammps_reset_box(void *, double *, double *, double, double, double) :pre + +The lammps_get_thermo() function returns the current value of a thermo +keyword as a double precision value. + +The lammps_get_natoms() function returns the total number of atoms in +the system and can be used by the caller to allocate memory for the +lammps_gather_atoms() and lammps_scatter_atoms() functions. + +The lammps_set_variable() function can set an existing string-style +variable to a new string value, so that subsequent LAMMPS commands can +access the variable. + +The lammps_reset_box() function resets the size and shape of the +simulation box, e.g. as part of restoring a previously extracted and +saved state of a simulation. + +void lammps_gather_atoms(void *, char *, int, int, void *) +void lammps_gather_atoms_concat(void *, char *, int, int, void *) +void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) +void lammps_scatter_atoms(void *, char *, int, int, void *) +void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre + +void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, + imageint *, int) :pre + +The gather functions collect peratom info of the requested type (atom +coords, atom types, forces, etc) from all processors, and returns the +same vector of values to each callling processor. The scatter +functions do the inverse. They distribute a vector of peratom values, +passed by all calling processors, to invididual atoms, which may be +owned by different processos. + +The lammps_gather_atoms() function does this for all N atoms in the +system, ordered by atom ID, from 1 to N. The +lammps_gather_atoms_concat() function does it for all N atoms, but +simply concatenates the subset of atoms owned by each processor. The +resulting vector is not ordered by atom ID. Atom IDs can be requetsed +by the same function if the caller needs to know the ordering. The +lammps_gather_subset() function allows the caller to request values +for only a subset of atoms (identified by ID). +For all 3 gather function, per-atom image flags can be retrieved in 2 ways. +If the count is specified as 1, they are returned +in a packed format with all three image flags stored in a single integer. +If the count is specified as 3, the values are unpacked into xyz flags +by the library before returning them. + +The lammps_scatter_atoms() function takes a list of values for all N +atoms in the system, ordered by atom ID, from 1 to N, and assigns +those values to each atom in the system. The +lammps_scatter_atoms_subset() function takes a subset of IDs as an +argument and only scatters those values to the owning atoms. + +The lammps_create_atoms() function takes a list of N atoms as input +with atom types and coords (required), an optionally atom IDs and +velocities and image flags. It uses the coords of each atom to assign +it as a new atom to the processor that owns it. This function is +useful to add atoms to a simulation or (in tandem with +lammps_reset_box()) to restore a previously extracted and saved state +of a simulation. Additional properties for the new atoms can then be +assigned via the lammps_scatter_atoms() or lammps_extract_atom() +functions. diff --git a/doc/src/manifolds.txt b/doc/src/Howto_manifold.txt similarity index 97% rename from doc/src/manifolds.txt rename to doc/src/Howto_manifold.txt index 1013d8fab68f91cb2d5113b0cde132d7fc1f4385..09a936f7d3adec5cec22b820be9e9c54a2e4dfd0 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/Howto_manifold.txt @@ -2,11 +2,11 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -Manifolds (surfaces) :h2 +Manifolds (surfaces) :h3 [Overview:] diff --git a/doc/src/Howto_multiple.txt b/doc/src/Howto_multiple.txt new file mode 100644 index 0000000000000000000000000000000000000000..edcb8196cf015543db85b6ab83411d4d13373758 --- /dev/null +++ b/doc/src/Howto_multiple.txt @@ -0,0 +1,95 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Run multiple simulations from one input script :h3 + +This can be done in several ways. See the documentation for +individual commands for more details on how these examples work. + +If "multiple simulations" means continue a previous simulation for +more timesteps, then you simply use the "run"_run.html command +multiple times. For example, this script + +units lj +atom_style atomic +read_data data.lj +run 10000 +run 10000 +run 10000 +run 10000 +run 10000 :pre + +would run 5 successive simulations of the same system for a total of +50,000 timesteps. + +If you wish to run totally different simulations, one after the other, +the "clear"_clear.html command can be used in between them to +re-initialize LAMMPS. For example, this script + +units lj +atom_style atomic +read_data data.lj +run 10000 +clear +units lj +atom_style atomic +read_data data.lj.new +run 10000 :pre + +would run 2 independent simulations, one after the other. + +For large numbers of independent simulations, you can use +"variables"_variable.html and the "next"_next.html and +"jump"_jump.html commands to loop over the same input script +multiple times with different settings. For example, this +script, named in.polymer + +variable d index run1 run2 run3 run4 run5 run6 run7 run8 +shell cd $d +read_data data.polymer +run 10000 +shell cd .. +clear +next d +jump in.polymer :pre + +would run 8 simulations in different directories, using a data.polymer +file in each directory. The same concept could be used to run the +same system at 8 different temperatures, using a temperature variable +and storing the output in different log and dump files, for example + +variable a loop 8 +variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15 +log log.$a +read data.polymer +velocity all create $t 352839 +fix 1 all nvt $t $t 100.0 +dump 1 all atom 1000 dump.$a +run 100000 +clear +next t +next a +jump in.polymer :pre + +All of the above examples work whether you are running on 1 or +multiple processors, but assumed you are running LAMMPS on a single +partition of processors. LAMMPS can be run on multiple partitions via +the "-partition" command-line switch as described in "this +section"_Section_start.html#start_6 of the manual. + +In the last 2 examples, if LAMMPS were run on 3 partitions, the same +scripts could be used if the "index" and "loop" variables were +replaced with {universe}-style variables, as described in the +"variable"_variable.html command. Also, the "next t" and "next a" +commands would need to be replaced with a single "next a t" command. +With these modifications, the 8 simulations of each script would run +on the 3 partitions one after the other until all were finished. +Initially, 3 simulations would be started simultaneously, one on each +partition. When one finished, that partition would then start +the 4th simulation, and so forth, until all 8 were completed. diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt new file mode 100644 index 0000000000000000000000000000000000000000..f787801c36745d934abbfb1c26462734014d1c0c --- /dev/null +++ b/doc/src/Howto_nemd.txt @@ -0,0 +1,48 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +NEMD simulations :h3 + +Non-equilibrium molecular dynamics or NEMD simulations are typically +used to measure a fluid's rheological properties such as viscosity. +In LAMMPS, such simulations can be performed by first setting up a +non-orthogonal simulation box (see the preceding Howto section). + +A shear strain can be applied to the simulation box at a desired +strain rate by using the "fix deform"_fix_deform.html command. The +"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat +the sheared fluid and integrate the SLLOD equations of motion for the +system. Fix nvt/sllod uses "compute +temp/deform"_compute_temp_deform.html to compute a thermal temperature +by subtracting out the streaming velocity of the shearing atoms. The +velocity profile or other properties of the fluid can be monitored via +the "fix ave/chunk"_fix_ave_chunk.html command. + +As discussed in the previous section on non-orthogonal simulation +boxes, the amount of tilt or skew that can be applied is limited by +LAMMPS for computational efficiency to be 1/2 of the parallel box +length. However, "fix deform"_fix_deform.html can continuously strain +a box by an arbitrary amount. As discussed in the "fix +deform"_fix_deform.html command, when the tilt value reaches a limit, +the box is flipped to the opposite limit which is an equivalent tiling +of periodic space. The strain rate can then continue to change as +before. In a long NEMD simulation these box re-shaping events may +occur many times. + +In a NEMD simulation, the "remap" option of "fix +deform"_fix_deform.html should be set to "remap v", since that is what +"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity +profile consistent with the applied shear strain rate. + +An alternative method for calculating viscosities is provided via the +"fix viscosity"_fix_viscosity.html command. + +NEMD simulations can also be used to measure transport properties of a fluid +through a pore or channel. Simulations of steady-state flow can be performed +using the "fix flow/gauss"_fix_flow_gauss.html command. diff --git a/doc/src/Howto_output.txt b/doc/src/Howto_output.txt new file mode 100644 index 0000000000000000000000000000000000000000..a204a3cc96c3a0f2cebdc97fbc4ac7d2b78e8420 --- /dev/null +++ b/doc/src/Howto_output.txt @@ -0,0 +1,307 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Output from LAMMPS (thermo, dumps, computes, fixes, variables) :h3 + +There are four basic kinds of LAMMPS output: + +"Thermodynamic output"_thermo_style.html, which is a list +of quantities printed every few timesteps to the screen and logfile. :ulb,l + +"Dump files"_dump.html, which contain snapshots of atoms and various +per-atom values and are written at a specified frequency. :l + +Certain fixes can output user-specified quantities to files: "fix +ave/time"_fix_ave_time.html for time averaging, "fix +ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix +print"_fix_print.html for single-line output of +"variables"_variable.html. Fix print can also output to the +screen. :l + +"Restart files"_restart.html. :l +:ule + +A simulation prints one set of thermodynamic output and (optionally) +restart files. It can generate any number of dump files and fix +output files, depending on what "dump"_dump.html and "fix"_fix.html +commands you specify. + +As discussed below, LAMMPS gives you a variety of ways to determine +what quantities are computed and printed when the thermodynamics, +dump, or fix commands listed above perform output. Throughout this +discussion, note that users can also "add their own computes and fixes +to LAMMPS"_Modify.html which can then generate values that can then be +output with these commands. + +The following sub-sections discuss different LAMMPS command related +to output and the kind of data they operate on and produce: + +"Global/per-atom/local data"_#global +"Scalar/vector/array data"_#scalar +"Thermodynamic output"_#thermo +"Dump file output"_#dump +"Fixes that write output files"_#fixoutput +"Computes that process output quantities"_#computeoutput +"Fixes that process output quantities"_#fixprocoutput +"Computes that generate values to output"_#compute +"Fixes that generate values to output"_#fix +"Variables that generate values to output"_#variable +"Summary table of output options and data flow between commands"_#table :ul + +Global/per-atom/local data :h4,link(global) + +Various output-related commands work with three different styles of +data: global, per-atom, or local. A global datum is one or more +system-wide values, e.g. the temperature of the system. A per-atom +datum is one or more values per atom, e.g. the kinetic energy of each +atom. Local datums are calculated by each processor based on the +atoms it owns, but there may be zero or more per atom, e.g. a list of +bond distances. + +Scalar/vector/array data :h4,link(scalar) + +Global, per-atom, and local datums can each come in three kinds: a +single scalar value, a vector of values, or a 2d array of values. The +doc page for a "compute" or "fix" or "variable" that generates data +will specify both the style and kind of data it produces, e.g. a +per-atom vector. + +When a quantity is accessed, as in many of the output commands +discussed below, it can be referenced via the following bracket +notation, where ID in this case is the ID of a compute. The leading +"c_" would be replaced by "f_" for a fix, or "v_" for a variable: + +c_ID | entire scalar, vector, or array +c_ID\[I\] | one element of vector, one column of array +c_ID\[I\]\[J\] | one element of array :tb(s=|) + +In other words, using one bracket reduces the dimension of the data +once (vector -> scalar, array -> vector). Using two brackets reduces +the dimension twice (array -> scalar). Thus a command that uses +scalar values as input can typically also process elements of a vector +or array. + +Thermodynamic output :h4,link(thermo) + +The frequency and format of thermodynamic output is set by the +"thermo"_thermo.html, "thermo_style"_thermo_style.html, and +"thermo_modify"_thermo_modify.html commands. The +"thermo_style"_thermo_style.html command also specifies what values +are calculated and written out. Pre-defined keywords can be specified +(e.g. press, etotal, etc). Three additional kinds of keywords can +also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html +or "fix"_fix.html or "variable"_variable.html provides the value to be +output. In each case, the compute, fix, or variable must generate +global values for input to the "thermo_style custom"_dump.html +command. + +Note that thermodynamic output values can be "extensive" or +"intensive". The former scale with the number of atoms in the system +(e.g. total energy), the latter do not (e.g. temperature). The +setting for "thermo_modify norm"_thermo_modify.html determines whether +extensive quantities are normalized or not. Computes and fixes +produce either extensive or intensive values; see their individual doc +pages for details. "Equal-style variables"_variable.html produce only +intensive values; you can include a division by "natoms" in the +formula if desired, to make an extensive calculation produce an +intensive result. + +Dump file output :h4,link(dump) + +Dump file output is specified by the "dump"_dump.html and +"dump_modify"_dump_modify.html commands. There are several +pre-defined formats (dump atom, dump xtc, etc). + +There is also a "dump custom"_dump.html format where the user +specifies what values are output with each atom. Pre-defined atom +attributes can be specified (id, x, fx, etc). Three additional kinds +of keywords can also be specified (c_ID, f_ID, v_name), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute, fix, or +variable must generate per-atom values for input to the "dump +custom"_dump.html command. + +There is also a "dump local"_dump.html format where the user specifies +what local values to output. A pre-defined index keyword can be +specified to enumerate the local values. Two additional kinds of +keywords can also be specified (c_ID, f_ID), where a +"compute"_compute.html or "fix"_fix.html or "variable"_variable.html +provides the values to be output. In each case, the compute or fix +must generate local values for input to the "dump local"_dump.html +command. + +Fixes that write output files :h4,link(fixoutput) + +Several fixes take various quantities as input and can write output +files: "fix ave/time"_fix_ave_time.html, "fix +ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, +"fix ave/correlate"_fix_ave_correlate.html, and "fix +print"_fix_print.html. + +The "fix ave/time"_fix_ave_time.html command enables direct output to +a file and/or time-averaging of global scalars or vectors. The user +specifies one or more quantities as input. These can be global +"compute"_compute.html values, global "fix"_fix.html values, or +"variables"_variable.html of any style except the atom style which +produces per-atom values. Since a variable can refer to keywords used +by the "thermo_style custom"_thermo_style.html command (like temp or +press) and individual per-atom values, a wide variety of quantities +can be time averaged and/or output in this way. If the inputs are one +or more scalar values, then the fix generate a global scalar or vector +of output. If the inputs are one or more vector values, then the fix +generates a global vector or array of output. The time-averaged +output of this fix can also be used as input to other output commands. + +The "fix ave/chunk"_fix_ave_chunk.html command enables direct output +to a file of chunk-averaged per-atom quantities like those output in +dump files. Chunks can represent spatial bins or other collections of +atoms, e.g. individual molecules. The per-atom quantities can be atom +density (mass or number) or atom attributes such as position, +velocity, force. They can also be per-atom quantities calculated by a +"compute"_compute.html, by a "fix"_fix.html, or by an atom-style +"variable"_variable.html. The chunk-averaged output of this fix can +also be used as input to other output commands. + +The "fix ave/histo"_fix_ave_histo.html command enables direct output +to a file of histogrammed quantities, which can be global or per-atom +or local quantities. The histogram output of this fix can also be +used as input to other output commands. + +The "fix ave/correlate"_fix_ave_correlate.html command enables direct +output to a file of time-correlated quantities, which can be global +values. The correlation matrix output of this fix can also be used as +input to other output commands. + +The "fix print"_fix_print.html command can generate a line of output +written to the screen and log file or to a separate file, periodically +during a running simulation. The line can contain one or more +"variable"_variable.html values for any style variable except the +vector or atom styles). As explained above, variables themselves can +contain references to global values generated by "thermodynamic +keywords"_thermo_style.html, "computes"_compute.html, +"fixes"_fix.html, or other "variables"_variable.html, or to per-atom +values for a specific atom. Thus the "fix print"_fix_print.html +command is a means to output a wide variety of quantities separate +from normal thermodynamic or dump file output. + +Computes that process output quantities :h4,link(computeoutput) + +The "compute reduce"_compute_reduce.html and "compute +reduce/region"_compute_reduce.html commands take one or more per-atom +or local vector quantities as inputs and "reduce" them (sum, min, max, +ave) to scalar quantities. These are produced as output values which +can be used as input to other output commands. + +The "compute slice"_compute_slice.html command take one or more global +vector or array quantities as inputs and extracts a subset of their +values to create a new vector or array. These are produced as output +values which can be used as input to other output commands. + +The "compute property/atom"_compute_property_atom.html command takes a +list of one or more pre-defined atom attributes (id, x, fx, etc) and +stores the values in a per-atom vector or array. These are produced +as output values which can be used as input to other output commands. +The list of atom attributes is the same as for the "dump +custom"_dump.html command. + +The "compute property/local"_compute_property_local.html command takes +a list of one or more pre-defined local attributes (bond info, angle +info, etc) and stores the values in a local vector or array. These +are produced as output values which can be used as input to other +output commands. + +Fixes that process output quantities :h4,link(fixprocoutput) + +The "fix vector"_fix_vector.html command can create global vectors as +output from global scalars as input, accumulating them one element at +a time. + +The "fix ave/atom"_fix_ave_atom.html command performs time-averaging +of per-atom vectors. The per-atom quantities can be atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a "compute"_compute.html, by a +"fix"_fix.html, or by an atom-style "variable"_variable.html. The +time-averaged per-atom output of this fix can be used as input to +other output commands. + +The "fix store/state"_fix_store_state.html command can archive one or +more per-atom attributes at a particular time, so that the old values +can be used in a future calculation or output. The list of atom +attributes is the same as for the "dump custom"_dump.html command, +including per-atom quantities calculated by a "compute"_compute.html, +by a "fix"_fix.html, or by an atom-style "variable"_variable.html. +The output of this fix can be used as input to other output commands. + +Computes that generate values to output :h4,link(compute) + +Every "compute"_compute.html in LAMMPS produces either global or +per-atom or local values. The values can be scalars or vectors or +arrays of data. These values can be output using the other commands +described in this section. The doc page for each compute command +describes what it produces. Computes that produce per-atom or local +values have the word "atom" or "local" in their style name. Computes +without the word "atom" or "local" produce global values. + +Fixes that generate values to output :h4,link(fix) + +Some "fixes"_fix.html in LAMMPS produces either global or per-atom or +local values which can be accessed by other commands. The values can +be scalars or vectors or arrays of data. These values can be output +using the other commands described in this section. The doc page for +each fix command tells whether it produces any output quantities and +describes them. + +Variables that generate values to output :h4,link(variable) + +"Variables"_variable.html defined in an input script can store one or +more strings. But equal-style, vector-style, and atom-style or +atomfile-style variables generate a global scalar value, global vector +or values, or a per-atom vector, respectively, when accessed. The +formulas used to define these variables can contain references to the +thermodynamic keywords and to global and per-atom data generated by +computes, fixes, and other variables. The values generated by +variables can be used as input to and thus output by the other +commands described in this section. + +Summary table of output options and data flow between commands :h4,link(table) + +This table summarizes the various commands that can be used for +generating output from LAMMPS. Each command produces output data of +some kind and/or writes data to a file. Most of the commands can take +data from other commands as input. Thus you can link many of these +commands together in pipeline form, where data produced by one command +is used as input to another command and eventually written to the +screen or to a file. Note that to hook two commands together the +output and input data types must match, e.g. global/per-atom/local +data and scalar/vector/array data. + +Also note that, as described above, when a command takes a scalar as +input, that could be an element of a vector or array. Likewise a +vector input could be a column of an array. + +Command: Input: Output: +"thermo_style custom"_thermo_style.html: global scalars: screen, log file: +"dump custom"_dump.html: per-atom vectors: dump file: +"dump local"_dump.html: local vectors: dump file: +"fix print"_fix_print.html: global scalar from variable: screen, file: +"print"_print.html: global scalar from variable: screen: +"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: +"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array: +"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector: +"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector: +"compute slice"_compute_slice.html: global vectors/arrays: global vector/array: +"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: +"compute property/local"_compute_property_local.html: local vectors: local vector/array: +"fix vector"_fix_vector.html: global scalars: global vector: +"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: +"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: +"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file: +"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: +"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file: +"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:) diff --git a/doc/src/Howto_polarizable.txt b/doc/src/Howto_polarizable.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2653b117e9caed203f1a9127575278f1747fcb4 --- /dev/null +++ b/doc/src/Howto_polarizable.txt @@ -0,0 +1,81 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Polarizable models :h3 + +In polarizable force fields the charge distributions in molecules and +materials respond to their electrostatic environments. Polarizable +systems can be simulated in LAMMPS using three methods: + +the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html +package, :ulb,l +the adiabatic core-shell method, implemented in the +"CORESHELL"_Howto_coreshell.html package, :l +the thermalized Drude dipole method, implemented in the +"USER-DRUDE"_Howto_drude.html package. :l,ule + +The fluctuating charge method calculates instantaneous charges on +interacting atoms based on the electronegativity equalization +principle. It is implemented in the "fix qeq"_fix_qeq.html which is +available in several variants. It is a relatively efficient technique +since no additional particles are introduced. This method allows for +charge transfer between molecules or atom groups. However, because the +charges are located at the interaction sites, off-plane components of +polarization cannot be represented in planar molecules or atom groups. + +The two other methods share the same basic idea: polarizable atoms are +split into one core atom and one satellite particle (called shell or +Drude particle) attached to it by a harmonic spring. Both atoms bear +a charge and they represent collectively an induced electric dipole. +These techniques are computationally more expensive than the QEq +method because of additional particles and bonds. These two +charge-on-spring methods differ in certain features, with the +core-shell model being normally used for ionic/crystalline materials, +whereas the so-called Drude model is normally used for molecular +systems and fluid states. + +The core-shell model is applicable to crystalline materials where the +high symmetry around each site leads to stable trajectories of the +core-shell pairs. However, bonded atoms in molecules can be so close +that a core would interact too strongly or even capture the Drude +particle of a neighbor. The Drude dipole model is relatively more +complex in order to remediate this and other issues. Specifically, the +Drude model includes specific thermostating of the core-Drude pairs +and short-range damping of the induced dipoles. + +The three polarization methods can be implemented through a +self-consistent calculation of charges or induced dipoles at each +timestep. In the fluctuating charge scheme this is done by the matrix +inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell +or Drude-dipoles the relaxed-dipoles technique would require an slow +iterative procedure. These self-consistent solutions yield accurate +trajectories since the additional degrees of freedom representing +polarization are massless. An alternative is to attribute a mass to +the additional degrees of freedom and perform time integration using +an extended Lagrangian technique. For the fluctuating charge scheme +this is done by "fix qeq/dynamic"_fix_qeq.html, and for the +charge-on-spring models by the methods outlined in the next two +sections. The assignment of masses to the additional degrees of +freedom can lead to unphysical trajectories if care is not exerted in +choosing the parameters of the polarizable models and the simulation +conditions. + +In the core-shell model the vibration of the shells is kept faster +than the ionic vibrations to mimic the fast response of the +polarizable electrons. But in molecular systems thermalizing the +core-Drude pairs at temperatures comparable to the rest of the +simulation leads to several problems (kinetic energy transfer, too +short a timestep, etc.) In order to avoid these problems the relative +motion of the Drude particles with respect to their cores is kept +"cold" so the vibration of the core-Drude pairs is very slow, +approaching the self-consistent regime. In both models the +temperature is regulated using the velocities of the center of mass of +core+shell (or Drude) pairs, but in the Drude model the actual +relative core-Drude particle motion is thermostated separately as +well. diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/Howto_pylammps.txt similarity index 95% rename from doc/src/tutorial_pylammps.txt rename to doc/src/Howto_pylammps.txt index 11cddb3cbf3fa7abc4350c9fe0cfb685f19b7b47..8be4b66e78a511b404987929d247ce3836a40086 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/Howto_pylammps.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -15,13 +15,19 @@ END_RST --> Overview :h4 -PyLammps is a Python wrapper class which can be created on its own or use an -existing lammps Python object. It creates a simpler, Python-like interface to -common LAMMPS functionality. Unlike the original flat C-types interface, it -exposes a discoverable API. It no longer requires knowledge of the underlying -C++ code implementation. Finally, the IPyLammps wrapper builds on top of -PyLammps and adds some additional features for IPython integration into IPython -notebooks, e.g. for embedded visualization output from dump/image. +PyLammps is a Python wrapper class which can be created on its own or +use an existing lammps Python object. It creates a simpler, +Python-like interface to common LAMMPS functionality, in contrast to +the lammps.py wrapper on the C-style LAMMPS library interface which is +written using Python ctypes. The lammps.py wrapper is discussed on +the "Python library"_Python_library.html doc page. + +Unlike the flat ctypes interface, PyLammps exposes a discoverable API. +It no longer requires knowledge of the underlying C++ code +implementation. Finally, the IPyLammps wrapper builds on top of +PyLammps and adds some additional features for IPython integration +into IPython notebooks, e.g. for embedded visualization output from +dump/image. Comparison of lammps and PyLammps interfaces :h5 @@ -40,7 +46,6 @@ communication with LAMMPS is hidden from API user shorter, more concise Python better IPython integration, designed for quick prototyping :ul - Quick Start :h4 System-wide Installation :h5 diff --git a/doc/src/Howto_replica.txt b/doc/src/Howto_replica.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b44fe53748d4dc1adf35aebe333b97bea4c33ac --- /dev/null +++ b/doc/src/Howto_replica.txt @@ -0,0 +1,61 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Multi-replica simulations :h3 + +Several commands in LAMMPS run mutli-replica simulations, meaning +that multiple instances (replicas) of your simulation are run +simultaneously, with small amounts of data exchanged between replicas +periodically. + +These are the relevant commands: + +"neb"_neb.html for nudged elastic band calculations +"prd"_prd.html for parallel replica dynamics +"tad"_tad.html for temperature accelerated dynamics +"temper"_temper.html for parallel tempering +"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul + +NEB is a method for finding transition states and barrier energies. +PRD and TAD are methods for performing accelerated dynamics to find +and perform infrequent events. Parallel tempering or replica exchange +runs different replicas at a series of temperature to facilitate +rare-event sampling. + +These commands can only be used if LAMMPS was built with the REPLICA +package. See the "Making LAMMPS"_Section_start.html#start_3 section +for more info on packages. + +PIMD runs different replicas whose individual particles are coupled +together by springs to model a system or ring-polymers. + +This commands can only be used if LAMMPS was built with the USER-MISC +package. See the "Making LAMMPS"_Section_start.html#start_3 section +for more info on packages. + +In all these cases, you must run with one or more processors per +replica. The processors assigned to each replica are determined at +run-time by using the "-partition command-line +switch"_Section_start.html#start_6 to launch LAMMPS on multiple +partitions, which in this context are the same as replicas. E.g. +these commands: + +mpirun -np 16 lmp_linux -partition 8x2 -in in.temper +mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre + +would each run 8 replicas, on either 16 or 8 processors. Note the use +of the "-in command-line switch"_Section_start.html#start_6 to specify +the input script which is required when running in multi-replica mode. + +Also note that with MPI installed on a machine (e.g. your desktop), +you can run on more (virtual) processors than you have physical +processors. Thus the above commands could be run on a +single-processor (or few-processor) desktop so that you can run +a multi-replica simulation on more replicas than you have +physical processors. diff --git a/doc/src/Howto_restart.txt b/doc/src/Howto_restart.txt new file mode 100644 index 0000000000000000000000000000000000000000..b211775479bfc367301a408ef15e45f8bd46cca0 --- /dev/null +++ b/doc/src/Howto_restart.txt @@ -0,0 +1,97 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Restart a simulation :h3 + +There are 3 ways to continue a long LAMMPS simulation. Multiple +"run"_run.html commands can be used in the same input script. Each +run will continue from where the previous run left off. Or binary +restart files can be saved to disk using the "restart"_restart.html +command. At a later time, these binary files can be read via a +"read_restart"_read_restart.html command in a new script. Or they can +be converted to text data files using the "-r command-line +switch"_Section_start.html#start_6 and read by a +"read_data"_read_data.html command in a new script. + +Here we give examples of 2 scripts that read either a binary restart +file or a converted data file and then issue a new run command to +continue where the previous run left off. They illustrate what +settings must be made in the new script. Details are discussed in the +documentation for the "read_restart"_read_restart.html and +"read_data"_read_data.html commands. + +Look at the {in.chain} input script provided in the {bench} directory +of the LAMMPS distribution to see the original script that these 2 +scripts are based on. If that script had the line + +restart 50 tmp.restart :pre + +added to it, it would produce 2 binary restart files (tmp.restart.50 +and tmp.restart.100) as it ran. + +This script could be used to read the 1st restart file and re-run the +last 50 timesteps: + +read_restart tmp.restart.50 :pre + +neighbor 0.4 bin +neigh_modify every 1 delay 1 :pre + +fix 1 all nve +fix 2 all langevin 1.0 1.0 10.0 904297 :pre + +timestep 0.012 :pre + +run 50 :pre + +Note that the following commands do not need to be repeated because +their settings are included in the restart file: {units, atom_style, +special_bonds, pair_style, bond_style}. However these commands do +need to be used, since their settings are not in the restart file: +{neighbor, fix, timestep}. + +If you actually use this script to perform a restarted run, you will +notice that the thermodynamic data match at step 50 (if you also put a +"thermo 50" command in the original script), but do not match at step +100. This is because the "fix langevin"_fix_langevin.html command +uses random numbers in a way that does not allow for perfect restarts. + +As an alternate approach, the restart file could be converted to a data +file as follows: + +lmp_g++ -r tmp.restart.50 tmp.restart.data :pre + +Then, this script could be used to re-run the last 50 steps: + +units lj +atom_style bond +pair_style lj/cut 1.12 +pair_modify shift yes +bond_style fene +special_bonds 0.0 1.0 1.0 :pre + +read_data tmp.restart.data :pre + +neighbor 0.4 bin +neigh_modify every 1 delay 1 :pre + +fix 1 all nve +fix 2 all langevin 1.0 1.0 10.0 904297 :pre + +timestep 0.012 :pre + +reset_timestep 50 +run 50 :pre + +Note that nearly all the settings specified in the original {in.chain} +script must be repeated, except the {pair_coeff} and {bond_coeff} +commands since the new data file lists the force field coefficients. +Also, the "reset_timestep"_reset_timestep.html command is used to tell +LAMMPS the current timestep. This value is stored in restart files, +but not in data files. diff --git a/doc/src/Howto_spc.txt b/doc/src/Howto_spc.txt new file mode 100644 index 0000000000000000000000000000000000000000..2cbf16547be6f318794d837d832d3651edd072be --- /dev/null +++ b/doc/src/Howto_spc.txt @@ -0,0 +1,54 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +SPC water model :h3 + +The SPC water model specifies a 3-site rigid water molecule with +charges and Lennard-Jones parameters assigned to each of the 3 atoms. +In LAMMPS the "fix shake"_fix_shake.html command can be used to hold +the two O-H bonds and the H-O-H angle rigid. A bond style of +{harmonic} and an angle style of {harmonic} or {charmm} should also be +used. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid SPC model. + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.820 +H charge = 0.410 +LJ epsilon of OO = 0.1553 +LJ sigma of OO = 3.166 +LJ epsilon, sigma of OH, HH = 0.0 +r0 of OH bond = 1.0 +theta of HOH angle = 109.47 :all(b),p + +Note that as originally proposed, the SPC model was run with a 9 +Angstrom cutoff for both LJ and Coulommbic terms. It can also be used +with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing +any of the parameters above, though it becomes a different model in +that mode of usage. + +The SPC/E (extended) water model is the same, except +the partial charge assignments change: + +O charge = -0.8476 +H charge = 0.4238 :all(b),p + +See the "(Berendsen)"_#howto-Berendsen reference for more details on both +the SPC and SPC/E models. + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(howto-Berendsen) +[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, +6269-6271 (1987). diff --git a/doc/src/Howto_spherical.txt b/doc/src/Howto_spherical.txt new file mode 100644 index 0000000000000000000000000000000000000000..1e737df655462c2fc0e1059ac7bc56ecdb120287 --- /dev/null +++ b/doc/src/Howto_spherical.txt @@ -0,0 +1,243 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Finite-size spherical and aspherical particles :h3 + +Typical MD models treat atoms or particles as point masses. Sometimes +it is desirable to have a model with finite-size particles such as +spheroids or ellipsoids or generalized aspherical bodies. The +difference is that such particles have a moment of inertia, rotational +energy, and angular momentum. Rotation is induced by torque coming +from interactions with other particles. + +LAMMPS has several options for running simulations with these kinds of +particles. The following aspects are discussed in turn: + +atom styles +pair potentials +time integration +computes, thermodynamics, and dump output +rigid bodies composed of finite-size particles :ul + +Example input scripts for these kinds of models are in the body, +colloid, dipole, ellipse, line, peri, pour, and tri directories of the +"examples directory"_Examples.html in the LAMMPS distribution. + +Atom styles :h4 + +There are several "atom styles"_atom_style.html that allow for +definition of finite-size particles: sphere, dipole, ellipsoid, line, +tri, peri, and body. + +The sphere style defines particles that are spheriods and each +particle can have a unique diameter and mass (or density). These +particles store an angular velocity (omega) and can be acted upon by +torque. The "set" command can be used to modify the diameter and mass +of individual particles, after then are created. + +The dipole style does not actually define finite-size particles, but +is often used in conjunction with spherical particles, via a command +like + +atom_style hybrid sphere dipole :pre + +This is because when dipoles interact with each other, they induce +torques, and a particle must be finite-size (i.e. have a moment of +inertia) in order to respond and rotate. See the "atom_style +dipole"_atom_style.html command for details. The "set" command can be +used to modify the orientation and length of the dipole moment of +individual particles, after then are created. + +The ellipsoid style defines particles that are ellipsoids and thus can +be aspherical. Each particle has a shape, specified by 3 diameters, +and mass (or density). These particles store an angular momentum and +their orientation (quaternion), and can be acted upon by torque. They +do not store an angular velocity (omega), which can be in a different +direction than angular momentum, rather they compute it as needed. +The "set" command can be used to modify the diameter, orientation, and +mass of individual particles, after then are created. It also has a +brief explanation of what quaternions are. + +The line style defines line segment particles with two end points and +a mass (or density). They can be used in 2d simulations, and they can +be joined together to form rigid bodies which represent arbitrary +polygons. + +The tri style defines triangular particles with three corner points +and a mass (or density). They can be used in 3d simulations, and they +can be joined together to form rigid bodies which represent arbitrary +particles with a triangulated surface. + +The peri style is used with "Peridynamic models"_pair_peri.html and +defines particles as having a volume, that is used internally in the +"pair_style peri"_pair_peri.html potentials. + +The body style allows for definition of particles which can represent +complex entities, such as surface meshes of discrete points, +collections of sub-particles, deformable objects, etc. The body style +is discussed in more detail on the "Howto body"_Howto_body.html doc +page. + +Note that if one of these atom styles is used (or multiple styles via +the "atom_style hybrid"_atom_style.html command), not all particles in +the system are required to be finite-size or aspherical. + +For example, in the ellipsoid style, if the 3 shape parameters are set +to the same value, the particle will be a sphere rather than an +ellipsoid. If the 3 shape parameters are all set to 0.0 or if the +diameter is set to 0.0, it will be a point particle. In the line or +tri style, if the lineflag or triflag is specified as 0, then it +will be a point particle. + +Some of the pair styles used to compute pairwise interactions between +finite-size particles also compute the correct interaction with point +particles as well, e.g. the interaction between a point particle and a +finite-size particle or between two point particles. If necessary, +"pair_style hybrid"_pair_hybrid.html can be used to insure the correct +interactions are computed for the appropriate style of interactions. +Likewise, using groups to partition particles (ellipsoids versus +spheres versus point particles) will allow you to use the appropriate +time integrators and temperature computations for each class of +particles. See the doc pages for various commands for details. + +Also note that for "2d simulations"_dimension.html, atom styles sphere +and ellipsoid still use 3d particles, rather than as circular disks or +ellipses. This means they have the same moment of inertia as the 3d +object. When temperature is computed, the correct degrees of freedom +are used for rotation in a 2d versus 3d system. + +Pair potentials :h4 + +When a system with finite-size particles is defined, the particles +will only rotate and experience torque if the force field computes +such interactions. These are the various "pair +styles"_pair_style.html that generate torque: + +"pair_style gran/history"_pair_gran.html +"pair_style gran/hertzian"_pair_gran.html +"pair_style gran/no_history"_pair_gran.html +"pair_style dipole/cut"_pair_dipole.html +"pair_style gayberne"_pair_gayberne.html +"pair_style resquared"_pair_resquared.html +"pair_style brownian"_pair_brownian.html +"pair_style lubricate"_pair_lubricate.html +"pair_style line/lj"_pair_line_lj.html +"pair_style tri/lj"_pair_tri_lj.html +"pair_style body/nparticle"_pair_body_nparticle.html :ul + +The granular pair styles are used with spherical particles. The +dipole pair style is used with the dipole atom style, which could be +applied to spherical or ellipsoidal particles. The GayBerne and +REsquared potentials require ellipsoidal particles, though they will +also work if the 3 shape parameters are the same (a sphere). The +Brownian and lubrication potentials are used with spherical particles. +The line, tri, and body potentials are used with line segment, +triangular, and body particles respectively. + +Time integration :h4 + +There are several fixes that perform time integration on finite-size +spherical particles, meaning the integrators update the rotational +orientation and angular velocity or angular momentum of the particles: + +"fix nve/sphere"_fix_nve_sphere.html +"fix nvt/sphere"_fix_nvt_sphere.html +"fix npt/sphere"_fix_npt_sphere.html :ul + +Likewise, there are 3 fixes that perform time integration on +ellipsoidal particles: + +"fix nve/asphere"_fix_nve_asphere.html +"fix nvt/asphere"_fix_nvt_asphere.html +"fix npt/asphere"_fix_npt_asphere.html :ul + +The advantage of these fixes is that those which thermostat the +particles include the rotational degrees of freedom in the temperature +calculation and thermostatting. The "fix langevin"_fix_langevin +command can also be used with its {omgea} or {angmom} options to +thermostat the rotational degrees of freedom for spherical or +ellipsoidal particles. Other thermostatting fixes only operate on the +translational kinetic energy of finite-size particles. + +These fixes perform constant NVE time integration on line segment, +triangular, and body particles: + +"fix nve/line"_fix_nve_line.html +"fix nve/tri"_fix_nve_tri.html +"fix nve/body"_fix_nve_body.html :ul + +Note that for mixtures of point and finite-size particles, these +integration fixes can only be used with "groups"_group.html which +contain finite-size particles. + +Computes, thermodynamics, and dump output :h4 + +There are several computes that calculate the temperature or +rotational energy of spherical or ellipsoidal particles: + +"compute temp/sphere"_compute_temp_sphere.html +"compute temp/asphere"_compute_temp_asphere.html +"compute erotate/sphere"_compute_erotate_sphere.html +"compute erotate/asphere"_compute_erotate_asphere.html :ul + +These include rotational degrees of freedom in their computation. If +you wish the thermodynamic output of temperature or pressure to use +one of these computes (e.g. for a system entirely composed of +finite-size particles), then the compute can be defined and the +"thermo_modify"_thermo_modify.html command used. Note that by default +thermodynamic quantities will be calculated with a temperature that +only includes translational degrees of freedom. See the +"thermo_style"_thermo_style.html command for details. + +These commands can be used to output various attributes of finite-size +particles: + +"dump custom"_dump.html +"compute property/atom"_compute_property_atom.html +"dump local"_dump.html +"compute body/local"_compute_body_local.html :ul + +Attributes include the dipole moment, the angular velocity, the +angular momentum, the quaternion, the torque, the end-point and +corner-point coordinates (for line and tri particles), and +sub-particle attributes of body particles. + +Rigid bodies composed of finite-size particles :h4 + +The "fix rigid"_fix_rigid.html command treats a collection of +particles as a rigid body, computes its inertia tensor, sums the total +force and torque on the rigid body each timestep due to forces on its +constituent particles, and integrates the motion of the rigid body. + +If any of the constituent particles of a rigid body are finite-size +particles (spheres or ellipsoids or line segments or triangles), then +their contribution to the inertia tensor of the body is different than +if they were point particles. This means the rotational dynamics of +the rigid body will be different. Thus a model of a dimer is +different if the dimer consists of two point masses versus two +spheroids, even if the two particles have the same mass. Finite-size +particles that experience torque due to their interaction with other +particles will also impart that torque to a rigid body they are part +of. + +See the "fix rigid" command for example of complex rigid-body models +it is possible to define in LAMMPS. + +Note that the "fix shake"_fix_shake.html command can also be used to +treat 2, 3, or 4 particles as a rigid body, but it always assumes the +particles are point masses. + +Also note that body particles cannot be modeled with the "fix +rigid"_fix_rigid.html command. Body particles are treated by LAMMPS +as single particles, though they can store internal state, such as a +list of sub-particles. Individual body partices are typically treated +as rigid bodies, and their motion integrated with a command like "fix +nve/body"_fix_nve_body.html. Interactions between pairs of body +particles are computed via a command like "pair_style +body/nparticle"_pair_body_nparticle.html. diff --git a/doc/src/Howto_spins.txt b/doc/src/Howto_spins.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b9adb49a5701789dafc9f86cebc23a87623411c --- /dev/null +++ b/doc/src/Howto_spins.txt @@ -0,0 +1,59 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Magnetic spins :h3 + +The magnetic spin simualtions are enabled by the SPIN package, whose +implementation is detailed in "Tranchida"_#Tranchida7. + +The model representents the simulation of atomic magnetic spins coupled +to lattice vibrations. The dynamics of those magnetic spins can be used +to simulate a broad range a phenomena related to magneto-elasticity, or +or to study the influence of defects on the magnetic properties of +materials. + +The magnetic spins are interacting with each others and with the +lattice via pair interactions. Typically, the magnetic exchange +interaction can be defined using the +"pair/spin/exchange"_pair_spin_exchange.html command. This exchange +applies a magnetic torque to a given spin, considering the orientation +of its neighboring spins and their relative distances. +It also applies a force on the atoms as a function of the spin +orientations and their associated inter-atomic distances. + +The command "fix precession/spin"_fix_precession_spin.html allows to +apply a constant magnetic torque on all the spins in the system. This +torque can be an external magnetic field (Zeeman interaction), or an +uniaxial magnetic anisotropy. + +A Langevin thermostat can be applied to those magnetic spins using +"fix langevin/spin"_fix_langevin_spin.html. Typically, this thermostat +can be coupled to another Langevin thermostat applied to the atoms +using "fix langevin"_fix_langevin.html in order to simulate +thermostated spin-lattice system. + +The magnetic Gilbert damping can also be applied using "fix +langevin/spin"_fix_langevin_spin.html. It allows to either dissipate +the thermal energy of the Langevin thermostat, or to perform a +relaxation of the magnetic configuration toward an equilibrium state. + +All the computed magnetic properties can be outputed by two main +commands. The first one is "compute spin"_compute_spin.html, that +enables to evaluate magnetic averaged quantities, such as the total +magnetization of the system along x, y, or z, the spin temperature, or +the magnetic energy. The second command is "compute +property/atom"_compute_property_atom.html. It enables to output all the +per atom magnetic quantities. Typically, the orientation of a given +magnetic spin, or the magnetic force acting on this spin. + +:line + +:link(Tranchida7) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +arXiv preprint arXiv:1801.10233, (2018). diff --git a/doc/src/Howto_temperature.txt b/doc/src/Howto_temperature.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a318250cffa956692693e601638e749cc4d6df4 --- /dev/null +++ b/doc/src/Howto_temperature.txt @@ -0,0 +1,40 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calcalate temperature :h3 + +Temperature is computed as kinetic energy divided by some number of +degrees of freedom (and the Boltzmann constant). Since kinetic energy +is a function of particle velocity, there is often a need to +distinguish between a particle's advection velocity (due to some +aggregate motion of particles) and its thermal velocity. The sum of +the two is the particle's total velocity, but the latter is often what +is wanted to compute a temperature. + +LAMMPS has several options for computing temperatures, any of which can be used in "thermostatting"_Howto_thermostat.html and "barostatting"_Howto_barostat.html. These "compute commands"_compute.html calculate temperature: + +"compute temp"_compute_temp.html +"compute temp/sphere"_compute_temp_sphere.html +"compute temp/asphere"_compute_temp_asphere.html +"compute temp/com"_compute_temp_com.html +"compute temp/deform"_compute_temp_deform.html +"compute temp/partial"_compute_temp_partial.html +"compute temp/profile"_compute_temp_profile.html +"compute temp/ramp"_compute_temp_ramp.html +"compute temp/region"_compute_temp_region.html :ul + +All but the first 3 calculate velocity biases directly (e.g. advection +velocities) that are removed when computing the thermal temperature. +"Compute temp/sphere"_compute_temp_sphere.html and "compute +temp/asphere"_compute_temp_asphere.html compute kinetic energy for +finite-size particles that includes rotational degrees of freedom. +They both allow for velocity biases indirectly, via an optional extra +argument which is another temperature compute that subtracts a velocity bias. +This allows the translational velocity of spherical or aspherical +particles to be adjusted in prescribed ways. diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e2feb18699cd993abf78df4542b599431d8512a --- /dev/null +++ b/doc/src/Howto_thermostat.txt @@ -0,0 +1,89 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Thermostats :h3 + +Thermostatting means controlling the temperature of particles in an MD +simulation. "Barostatting"_Howto_barostat.html means controlling the +pressure. Since the pressure includes a kinetic component due to +particle velocities, both these operations require calculation of the +temperature. Typically a target temperature (T) and/or pressure (P) +is specified by the user, and the thermostat or barostat attempts to +equilibrate the system to the requested T and/or P. + +Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one +case by a pair style. Several thermostatting fixes are available: +Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling +(temp/rescale). Dissipative particle dynamics (DPD) thermostatting +can be invoked via the {dpd/tstat} pair style: + +"fix nvt"_fix_nh.html +"fix nvt/sphere"_fix_nvt_sphere.html +"fix nvt/asphere"_fix_nvt_asphere.html +"fix nvt/sllod"_fix_nvt_sllod.html +"fix temp/berendsen"_fix_temp_berendsen.html +"fix temp/csvr"_fix_temp_csvr.html +"fix langevin"_fix_langevin.html +"fix temp/rescale"_fix_temp_rescale.html +"pair_style dpd/tstat"_pair_dpd.html :ul + +"Fix nvt"_fix_nh.html only thermostats the translational velocity of +particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except +that it subtracts out a velocity bias due to a deforming box and +integrates the SLLOD equations of motion. See the "Howto +nemd"_Howto_nemd.html doc page for further details. "Fix +nvt/sphere"_fix_nvt_sphere.html and "fix +nvt/asphere"_fix_nvt_asphere.html thermostat not only translation +velocities but also rotational velocities for spherical and aspherical +particles. + +DPD thermostatting alters pairwise interactions in a manner analogous +to the per-particle thermostatting of "fix +langevin"_fix_langevin.html. + +Any of the thermostatting fixes can use "temperature +computes"_Howto_thermostat.html that remove bias which has two +effects. First, the current calculated temperature, which is compared +to the requested target temperature, is calculated with the velocity +bias removed. Second, the thermostat adjusts only the thermal +temperature component of the particle's velocities, which are the +velocities with the bias removed. The removed bias is then added back +to the adjusted velocities. See the doc pages for the individual +fixes and for the "fix_modify"_fix_modify.html command for +instructions on how to assign a temperature compute to a +thermostatting fix. For example, you can apply a thermostat to only +the x and z components of velocity by using it in conjunction with +"compute temp/partial"_compute_temp_partial.html. Of you could +thermostat only the thermal temperature of a streaming flow of +particles without affecting the streaming velocity, by using "compute +temp/profile"_compute_temp_profile.html. + +NOTE: Only the nvt fixes perform time integration, meaning they update +the velocities and positions of particles due to forces and velocities +respectively. The other thermostat fixes only adjust velocities; they +do NOT perform time integration updates. Thus they should be used in +conjunction with a constant NVE integration fix such as these: + +"fix nve"_fix_nve.html +"fix nve/sphere"_fix_nve_sphere.html +"fix nve/asphere"_fix_nve_asphere.html :ul + +Thermodynamic output, which can be setup via the +"thermo_style"_thermo_style.html command, often includes temperature +values. As explained on the doc page for the +"thermo_style"_thermo_style.html command, the default temperature is +setup by the thermo command itself. It is NOT the temperature +associated with any thermostatting fix you have defined or with any +compute you have defined that calculates a temperature. The doc pages +for the thermostatting fixes explain the ID of the temperature compute +they create. Thus if you want to view these temperatures, you need to +specify them explicitly via the "thermo_style +custom"_thermo_style.html command. Or you can use the +"thermo_modify"_thermo_modify.html command to re-define what +temperature compute is used for default thermodynamic output. diff --git a/doc/src/Howto_tip3p.txt b/doc/src/Howto_tip3p.txt new file mode 100644 index 0000000000000000000000000000000000000000..942b42aea16ea63d2541ca839646f4b77dc9c079 --- /dev/null +++ b/doc/src/Howto_tip3p.txt @@ -0,0 +1,69 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +TIP3P water model :h3 + +The TIP3P water model as implemented in CHARMM +"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with +charges and Lennard-Jones parameters assigned to each of the 3 atoms. +In LAMMPS the "fix shake"_fix_shake.html command can be used to hold +the two O-H bonds and the H-O-H angle rigid. A bond style of +{harmonic} and an angle style of {harmonic} or {charmm} should also be +used. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid TIP3P-CHARMM model with a +cutoff. The K values can be used if a flexible TIP3P model (without +fix shake) is desired. If the LJ epsilon and sigma for HH and OH are +set to 0.0, it corresponds to the original 1983 TIP3P model +"(Jorgensen)"_#Jorgensen1. + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.834 +H charge = 0.417 +LJ epsilon of OO = 0.1521 +LJ sigma of OO = 3.1507 +LJ epsilon of HH = 0.0460 +LJ sigma of HH = 0.4000 +LJ epsilon of OH = 0.0836 +LJ sigma of OH = 1.7753 +K of OH bond = 450 +r0 of OH bond = 0.9572 +K of HOH angle = 55 +theta of HOH angle = 104.52 :all(b),p + +These are the parameters to use for TIP3P with a long-range Coulombic +solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for +details: + +O mass = 15.9994 +H mass = 1.008 +O charge = -0.830 +H charge = 0.415 +LJ epsilon of OO = 0.102 +LJ sigma of OO = 3.188 +LJ epsilon, sigma of OH, HH = 0.0 +K of OH bond = 450 +r0 of OH bond = 0.9572 +K of HOH angle = 55 +theta of HOH angle = 104.52 :all(b),p + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(Jorgensen1) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). + +:link(Price1) +[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). + diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt new file mode 100644 index 0000000000000000000000000000000000000000..f9e548e26896c1143f1cead59e3c0a1effb015c3 --- /dev/null +++ b/doc/src/Howto_tip4p.txt @@ -0,0 +1,112 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +TIP4P water model :h3 + +The four-point TIP4P rigid water model extends the traditional +three-point TIP3P model by adding an additional site, usually +massless, where the charge associated with the oxygen atom is placed. +This site M is located at a fixed distance away from the oxygen along +the bisector of the HOH bond angle. A bond style of {harmonic} and an +angle style of {harmonic} or {charmm} should also be used. + +A TIP4P model is run with LAMMPS using either this command +for a cutoff model: + +"pair_style lj/cut/tip4p/cut"_pair_lj.html + +or these two commands for a long-range model: + +"pair_style lj/cut/tip4p/long"_pair_lj.html +"kspace_style pppm/tip4p"_kspace_style.html :ul + +For both models, the bond lengths and bond angles should be held fixed +using the "fix shake"_fix_shake.html command. + +These are the additional parameters (in real units) to set for O and H +atoms and the water molecule to run a rigid TIP4P model with a cutoff +"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in +the "pair_style"_pair_style.html command, not as part of the pair +coefficients. + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.040 +H charge = 0.520 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.15 +LJ epsilon of O-O = 0.1550 +LJ sigma of O-O = 3.1536 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); +http://dx.doi.org/10.1063/1.1931662) these values can be used: + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.1794 +H charge = 0.5897 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1577 +LJ epsilon of O-O = 0.21084 +LJ sigma of O-O = 3.1668 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); +http://dx.doi.org/10.1063/1.2121687), these values can be used: + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.1128 +H charge = 0.5564 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1546 +LJ epsilon of O-O = 0.1852 +LJ sigma of O-O = 3.1589 +LJ epsilon, sigma of OH, HH = 0.0 +Coulombic cutoff = 8.5 :all(b),p + +These are the parameters to use for TIP4P with a long-range Coulombic +solver (e.g. Ewald or PPPM in LAMMPS): + +O mass = 15.9994 +H mass = 1.008 +O charge = -1.0484 +H charge = 0.5242 +r0 of OH bond = 0.9572 +theta of HOH angle = 104.52 +OM distance = 0.1250 +LJ epsilon of O-O = 0.16275 +LJ sigma of O-O = 3.16435 +LJ epsilon, sigma of OH, HH = 0.0 :all(b),p + +Note that the when using the TIP4P pair style, the neighbor list +cutoff for Coulomb interactions is effectively extended by a distance +2 * (OM distance), to account for the offset distance of the +fictitious charges on O atoms in water molecules. Thus it is +typically best in an efficiency sense to use a LJ cutoff >= Coulomb +cutoff + 2*(OM distance), to shrink the size of the neighbor list. +This leads to slightly larger cost for the long-range calculation, so +you can test the trade-off for your model. The OM distance and the LJ +and Coulombic cutoffs are set in the "pair_style +lj/cut/tip4p/long"_pair_lj.html command. + +Wikipedia also has a nice article on "water +models"_http://en.wikipedia.org/wiki/Water_model. + +:line + +:link(Jorgensen1) +[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem +Phys, 79, 926 (1983). diff --git a/doc/src/Howto_triclinic.txt b/doc/src/Howto_triclinic.txt new file mode 100644 index 0000000000000000000000000000000000000000..4b299e5ae1ecc024c3be42bbc019bc8d9550c54d --- /dev/null +++ b/doc/src/Howto_triclinic.txt @@ -0,0 +1,213 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +Triclinic (non-orthogonal) simulation boxes :h3 + +By default, LAMMPS uses an orthogonal simulation box to encompass the +particles. The "boundary"_boundary.html command sets the boundary +conditions of the box (periodic, non-periodic, etc). The orthogonal +box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors +starting from the origin given by [a] = (xhi-xlo,0,0); [b] = +(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters +(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box +is created, e.g. by the "create_box"_create_box.html or +"read_data"_read_data.html or "read_restart"_read_restart.html +commands. Additionally, LAMMPS defines box size parameters lx,ly,lz +where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 +parameters, as well as lx,ly,lz, can be output via the "thermo_style +custom"_thermo_style.html command. + +LAMMPS also allows simulations to be performed in triclinic +(non-orthogonal) simulation boxes shaped as a parallelepiped with +triclinic symmetry. The parallelepiped has its "origin" at +(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the +origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] = +(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values +and are called "tilt factors" because they are the amount of +displacement applied to faces of an originally orthogonal box to +transform it into the parallelepiped. In LAMMPS the triclinic +simulation box edge vectors [a], [b], and [c] cannot be arbitrary +vectors. As indicated, [a] must lie on the positive x axis. [b] must +lie in the xy plane, with strictly positive y component. [c] may have +any orientation with strictly positive z component. The requirement +that [a], [b], and [c] have strictly positive x, y, and z components, +respectively, ensures that [a], [b], and [c] form a complete +right-handed basis. These restrictions impose no loss of generality, +since it is possible to rotate/invert any set of 3 crystal basis +vectors so that they conform to the restrictions. + +For example, assume that the 3 vectors [A],[B],[C] are the edge +vectors of a general parallelepiped, where there is no restriction on +[A],[B],[C] other than they form a complete right-handed basis i.e. +[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear +rotation of [A], [B], and [C] and can be computed as follows: + +:c,image(Eqs/transform.jpg) + +where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) +indicates the corresponding unit vector. {beta} and {gamma} are angles +between the vectors described below. Note that by construction, +[a], [b], and [c] have strictly positive x, y, and z components, respectively. +If it should happen that +[A], [B], and [C] form a left-handed basis, then the above equations +are not valid for [c]. In this case, it is necessary +to first apply an inversion. This can be achieved +by interchanging two basis vectors or by changing the sign of one of them. + +For consistency, the same rotation/inversion applied to the basis vectors +must also be applied to atom positions, velocities, +and any other vector quantities. +This can be conveniently achieved by first converting to +fractional coordinates in the +old basis and then converting to distance coordinates in the new basis. +The transformation is given by the following equation: + +:c,image(Eqs/rotate.jpg) + +where {V} is the volume of the box, [X] is the original vector quantity and +[x] is the vector in the LAMMPS basis. + +There is no requirement that a triclinic box be periodic in any +dimension, though it typically should be in at least the 2nd dimension +of the tilt (y in xy) if you want to enforce a shift in periodic +boundary conditions across that boundary. Some commands that work +with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix +npt"_fix_nh.html commands, require periodicity or non-shrink-wrap +boundary conditions in specific dimensions. See the command doc pages +for details. + +The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the +time the simulation box is created. This happens in one of 3 ways. +If the "create_box"_create_box.html command is used with a region of +style {prism}, then a triclinic box is setup. See the +"region"_region.html command for details. If the +"read_data"_read_data.html command is used to define the simulation +box, and the header of the data file contains a line with the "xy xz +yz" keyword, then a triclinic box is setup. See the +"read_data"_read_data.html command for details. Finally, if the +"read_restart"_read_restart.html command reads a restart file which +was written from a simulation using a triclinic box, then a triclinic +box will be setup for the restarted simulation. + +Note that you can define a triclinic box with all 3 tilt factors = +0.0, so that it is initially orthogonal. This is necessary if the box +will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or +"fix deform"_fix_deform.html commands. Alternatively, you can use the +"change_box"_change_box.html command to convert a simulation box from +orthogonal to triclinic and vice versa. + +As with orthogonal boxes, LAMMPS defines triclinic box size parameters +lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. +The 9 parameters, as well as lx,ly,lz, can be output via the +"thermo_style custom"_thermo_style.html command. + +To avoid extremely tilted boxes (which would be computationally +inefficient), LAMMPS normally requires that no tilt factor can skew +the box more than half the distance of the parallel box length, which +is the 1st dimension in the tilt factor (x for xz). This is required +both when the simulation box is created, e.g. via the +"create_box"_create_box.html or "read_data"_read_data.html commands, +as well as when the box shape changes dynamically during a simulation, +e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html +commands. + +For example, if xlo = 2 and xhi = 12, then the x box length is 10 and +the xy tilt factor must be between -5 and 5. Similarly, both xz and +yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is +not a limitation, since if the maximum tilt factor is 5 (as in this +example), then configurations with tilt = ..., -15, -5, 5, 15, 25, +... are geometrically all equivalent. If the box tilt exceeds this +limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html +command), then the box is "flipped" to an equivalent shape with a tilt +factor within the bounds, so the run can continue. See the "fix +deform"_fix_deform.html doc page for further details. + +One exception to this rule is if the 1st dimension in the tilt +factor (x for xy) is non-periodic. In that case, the limits on the +tilt factor are not enforced, since flipping the box in that dimension +does not change the atom positions due to non-periodicity. In this +mode, if you tilt the system to extreme angles, the simulation will +simply become inefficient, due to the highly skewed simulation box. + +The limitation on not creating a simulation box with a tilt factor +skewing the box more than half the distance of the parallel box length +can be overridden via the "box"_box.html command. Setting the {tilt} +keyword to {large} allows any tilt factors to be specified. + +Box flips that may occur using the "fix deform"_fix_deform.html or +"fix npt"_fix_nh.html commands can be turned off using the {flip no} +option with either of the commands. + +Note that if a simulation box has a large tilt factor, LAMMPS will run +less efficiently, due to the large volume of communication needed to +acquire ghost atoms around a processor's irregular-shaped sub-domain. +For extreme values of tilt, LAMMPS may also lose atoms and generate an +error. + +Triclinic crystal structures are often defined using three lattice +constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and +{gamma}. Note that in this nomenclature, the a, b, and c lattice +constants are the scalar lengths of the edge vectors [a], [b], and [c] +defined above. The relationship between these 6 quantities +(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = +(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: + +:c,image(Eqs/box.jpg) + +The inverse relationship can be written as follows: + +:c,image(Eqs/box_inverse.jpg) + +The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed +out or accessed by computes using the +"thermo_style custom"_thermo_style.html keywords +{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, +respectively. + +As discussed on the "dump"_dump.html command doc page, when the BOX +BOUNDS for a snapshot is written to a dump file for a triclinic box, +an orthogonal bounding box which encloses the triclinic simulation box +is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic +box, formatted as follows: + +ITEM: BOX BOUNDS xy xz yz +xlo_bound xhi_bound xy +ylo_bound yhi_bound xz +zlo_bound zhi_bound yz :pre + +This bounding box is convenient for many visualization programs and is +calculated from the 9 triclinic box parameters +(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: + +xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) +xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz) +ylo_bound = ylo + MIN(0.0,yz) +yhi_bound = yhi + MAX(0.0,yz) +zlo_bound = zlo +zhi_bound = zhi :pre + +These formulas can be inverted if you need to convert the bounding box +back into the triclinic box parameters, e.g. xlo = xlo_bound - +MIN(0.0,xy,xz,xy+xz). + +One use of triclinic simulation boxes is to model solid-state crystals +with triclinic symmetry. The "lattice"_lattice.html command can be +used with non-orthogonal basis vectors to define a lattice that will +tile a triclinic simulation box via the +"create_atoms"_create_atoms.html command. + +A second use is to run Parinello-Rahman dynamics via the "fix +npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt +factors to compensate for off-diagonal components of the pressure +tensor. The analog for an "energy minimization"_minimize.html is +the "fix box/relax"_fix_box_relax.html command. + +A third use is to shear a bulk solid to study the response of the +material. The "fix deform"_fix_deform.html command can be used for +this purpose. It allows dynamic control of the xy, xz, yz tilt +factors as a simulation runs. This is discussed in the next section +on non-equilibrium MD (NEMD) simulations. diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt new file mode 100644 index 0000000000000000000000000000000000000000..8bcab6dd247f02de5dbb3135e67fe76cc32efb01 --- /dev/null +++ b/doc/src/Howto_viscosity.txt @@ -0,0 +1,133 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Calculate viscosity :h3 + +The shear viscosity eta of a fluid can be measured in at least 5 ways +using various options in LAMMPS. See the examples/VISCOSITY directory +for scripts that implement the 5 methods discussed here for a simple +Lennard-Jones fluid model. Also, see the "Howto +kappa"_Howto_kappa.html doc page for an analogous discussion for +thermal conductivity. + +Eta is a measure of the propensity of a fluid to transmit momentum in +a direction perpendicular to the direction of velocity or momentum +flow. Alternatively it is the resistance the fluid has to being +sheared. It is given by + +J = -eta grad(Vstream) + +where J is the momentum flux in units of momentum per area per time. +and grad(Vstream) is the spatial gradient of the velocity of the fluid +moving in another direction, normal to the area through which the +momentum flows. Viscosity thus has units of pressure-time. + +The first method is to perform a non-equilibrium MD (NEMD) simulation +by shearing the simulation box via the "fix deform"_fix_deform.html +command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to +thermostat the fluid via the SLLOD equations of motion. +Alternatively, as a second method, one or more moving walls can be +used to shear the fluid in between them, again with some kind of +thermostat that modifies only the thermal (non-shearing) components of +velocity to prevent the fluid from heating up. + +In both cases, the velocity profile setup in the fluid by this +procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html +command, which determines grad(Vstream) in the equation above. +E.g. the derivative in the y-direction of the Vx component of fluid +motion or grad(Vstream) = dVx/dy. The Pxy off-diagonal component of +the pressure or stress tensor, as calculated by the "compute +pressure"_compute_pressure.html command, can also be monitored, which +is the J term in the equation above. See the "Howto +nemd"_Howto_nemd.html doc page for details on NEMD simulations. + +The third method is to perform a reverse non-equilibrium MD simulation +using the "fix viscosity"_fix_viscosity.html command which implements +the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is +swapped between atoms in two different layers of the simulation box in +a different dimension. This induces a velocity gradient which can be +monitored with the "fix ave/chunk"_fix_ave_chunk.html command. +The fix tallies the cumulative momentum transfer that it performs. +See the "fix viscosity"_fix_viscosity.html command for details. + +The fourth method is based on the Green-Kubo (GK) formula which +relates the ensemble average of the auto-correlation of the +stress/pressure tensor to eta. This can be done in a fully +equilibrated simulation which is in contrast to the two preceding +non-equilibrium methods, where momentum flows continuously through the +simulation box. + +Here is an example input script that calculates the viscosity of +liquid Ar via the GK formalism: + +# Sample LAMMPS input script for viscosity of liquid Ar :pre + +units real +variable T equal 86.4956 +variable V equal vol +variable dt equal 4.0 +variable p equal 400 # correlation length +variable s equal 5 # sample interval +variable d equal $p*$s # dump interval :pre + +# convert from LAMMPS real units to SI :pre + +variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann +variable atm2Pa equal 101325.0 +variable A2m equal 1.0e-10 +variable fs2s equal 1.0e-15 +variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre + +# setup problem :pre + +dimension 3 +boundary p p p +lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box +mass 1 39.948 +pair_style lj/cut 13.0 +pair_coeff * * 0.2381 3.405 +timestep $\{dt\} +thermo $d :pre + +# equilibration and thermalization :pre + +velocity all create $T 102486 mom yes rot yes dist gaussian +fix NVT all nvt temp $T $T 10 drag 0.2 +run 8000 :pre + +# viscosity calculation, switch to NVE if desired :pre + +#unfix NVT +#fix NVE all nve :pre + +reset_timestep 0 +variable pxy equal pxy +variable pxz equal pxz +variable pyz equal pyz +fix SS all ave/correlate $s $p $d & + v_pxy v_pxz v_pyz type auto file S0St.dat ave running +variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\} +variable v11 equal trap(f_SS\[3\])*$\{scale\} +variable v22 equal trap(f_SS\[4\])*$\{scale\} +variable v33 equal trap(f_SS\[5\])*$\{scale\} +thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 +run 100000 +variable v equal (v_v11+v_v22+v_v33)/3.0 +variable ndens equal count(all)/vol +print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre + +The fifth method is related to the above Green-Kubo method, +but uses the Einstein formulation, analogous to the Einstein +mean-square-displacement formulation for self-diffusivity. The +time-integrated momentum fluxes play the role of Cartesian +coordinates, whose mean-square displacement increases linearly +with time at sufficiently long times. diff --git a/doc/src/Howto_viz.txt b/doc/src/Howto_viz.txt new file mode 100644 index 0000000000000000000000000000000000000000..00c329c50b1a7f5685d31b4f9a59b3affa2dcb4f --- /dev/null +++ b/doc/src/Howto_viz.txt @@ -0,0 +1,40 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Visualize LAMMPS snapshots :h3 + +LAMMPS itself does not do visualization, but snapshots from LAMMPS +simulations can be visualized (and analyzed) in a variety of ways. + +Mention dump image and dump movie. + +LAMMPS snapshots are created by the "dump"_dump.html command which can +create files in several formats. The native LAMMPS dump format is a +text file (see "dump atom" or "dump custom") which can be visualized +by several popular visualization tools. The "dump +image"_dump_image.html and "dump movie"_dump_image.html styles can +output internally rendered images and convert a sequence of them to a +movie during the MD run. Several programs included with LAMMPS as +auxiliary tools can convert between LAMMPS format files and other +formats. See the "Tools"_Tools.html doc page for details. + +A Python-based toolkit distributed by our group can read native LAMMPS +dump files, including custom dump files with additional columns of +user-specified atom information, and convert them to various formats +or pipe them into visualization software directly. See the "Pizza.py +WWW site"_pizza for details. Specifically, Pizza.py can convert +LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. +Pizza.py can pipe LAMMPS dump files directly into the Raster3d and +RasMol visualization programs. Pizza.py has tools that do interactive +3d OpenGL visualization and one that creates SVG images of dump file +snapshots. + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(ensight,http://www.ensight.com) +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) diff --git a/doc/src/Howto_walls.txt b/doc/src/Howto_walls.txt new file mode 100644 index 0000000000000000000000000000000000000000..75221185829cfbb3c6b4f9489ee1a3cd47764b43 --- /dev/null +++ b/doc/src/Howto_walls.txt @@ -0,0 +1,80 @@ +"Higher level section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Walls :h3 + +Walls in an MD simulation are typically used to bound particle motion, +i.e. to serve as a boundary condition. + +Walls in LAMMPS can be of rough (made of particles) or idealized +surfaces. Ideal walls can be smooth, generating forces only in the +normal direction, or frictional, generating forces also in the +tangential direction. + +Rough walls, built of particles, can be created in various ways. The +particles themselves can be generated like any other particle, via the +"lattice"_lattice.html and "create_atoms"_create_atoms.html commands, +or read in via the "read_data"_read_data.html command. + +Their motion can be constrained by many different commands, so that +they do not move at all, move together as a group at constant velocity +or in response to a net force acting on them, move in a prescribed +fashion (e.g. rotate around a point), etc. Note that if a time +integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html +is not used with the group that contains wall particles, their +positions and velocities will not be updated. + +"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together +"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0 +"fix freeze"_fix_freeze.html - freeze particles for use as granular walls +"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force +"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul + +The "fix move"_fix_move.html command offers the most generality, since +the motion of individual particles can be specified with +"variable"_variable.html formula which depends on time and/or the +particle position. + +For rough walls, it may be useful to turn off pairwise interactions +between wall particles via the "neigh_modify +exclude"_neigh_modify.html command. + +Rough walls can also be created by specifying frozen particles that do +not move and do not interact with mobile particles, and then tethering +other particles to the fixed particles, via a "bond"_bond_style.html. +The bonded particles do interact with other mobile particles. + +Idealized walls can be specified via several fix commands. "Fix +wall/gran"_fix_wall_gran.html creates frictional walls for use with +granular particles; all the other commands create smooth walls. + +"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls +"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential +"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential +"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential +"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential +"fix wall/region"_fix_wall_region.html - use region surface as wall +"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul + +The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the +flat walls to move with a constant velocity, or oscillate in time. +The "fix wall/region"_fix_wall_region.html command offers the most +generality, since the region surface is treated as a wall, and the +geometry of the region can be a simple primitive volume (e.g. a +sphere, or cube, or plane), or a complex volume made from the union +and intersection of primitive volumes. "Regions"_region.html can also +specify a volume "interior" or "exterior" to the specified primitive +shape or {union} or {intersection}. "Regions"_region.html can also be +"dynamic" meaning they move with constant velocity, oscillate, or +rotate. + +The only frictional idealized walls currently in LAMMPS are flat or +curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html +command. At some point we plan to allow regoin surfaces to be used as +frictional walls, as well as triangulated surfaces. diff --git a/doc/src/Intro.txt b/doc/src/Intro.txt new file mode 100644 index 0000000000000000000000000000000000000000..e3eaa404376015a1bec4d63d34397456b9c425dd --- /dev/null +++ b/doc/src/Intro.txt @@ -0,0 +1,37 @@ +"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Install.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Introduction :h2 + +These pages provide a brief introduction to LAMMPS. + + + + + +"Overview of LAMMPS"_Intro_overview.html +"LAMMPS features"_Intro_features.html +"LAMMPS non-features"_Intro_nonfeatures.html +"LAMMPS open-source license"_Intro_license.html +"LAMMPS authors"_Intro_authors.html +"Additional website links"_Intro_website.html :all(b) + + diff --git a/doc/src/Intro_authors.txt b/doc/src/Intro_authors.txt new file mode 100644 index 0000000000000000000000000000000000000000..ce418d0ce1cfc4463581ceadc5057cb4556ecc65 --- /dev/null +++ b/doc/src/Intro_authors.txt @@ -0,0 +1,379 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS authors :h3 + +The primary LAMMPS developers are at Sandia National Labs and Temple +University: + +"Steve Plimpton"_sjp, sjplimp at sandia.gov +Aidan Thompson, athomps at sandia.gov +Stan Moore, stamoor at sandia.gov +Axel Kohlmeyer, akohlmey at gmail.com :ul + +:link(sjp,http://www.cs.sandia.gov/~sjplimp) + +Past developers include Paul Crozier and Mark Stevens, both at Sandia, +and Ray Shan, now at Materials Design. + +:line + +The following folks are responsible for significant contributions to +the code, or other aspects of the LAMMPS development effort. Many of +the packages they have written are somewhat unique to LAMMPS and the +code would not be as general-purpose as it is without their expertise +and efforts. + +Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CG-CMM, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM packages +Roy Pollock (LLNL), Ewald and PPPM solvers +Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL packages +Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential +Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics +Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion +Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling +Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD +Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages +Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field +Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling +Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF +Georg Gunzenmueller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages +Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul + +:line + +As discussed on the "History +page"_http://lammps.sandia.gov/history.html of the website, LAMMPS +originated as a cooperative project between DOE labs and industrial +partners. Folks involved in the design and testing of the original +version of LAMMPS were the following: + +John Carpenter (Mayo Clinic, formerly at Cray Research) +Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) +Steve Lustig (Dupont) +Jim Belak and Roy Pollock (LLNL) :ul + +:line +:line + +Here is a timeline for when various individuals contributed to a new +feature or command or tool added to LAMMPS: + +Jul18 : DEM polygonal and polyhedron particles : Trung Nguyen (Northwestern U) +Jun18 : SPIN package : Julien Tranchida (Sandia and CEA) +Jun18 : compute entropy/atom : Pablo Piaggi (EPLF, Switzerland) +May18 : fix bond/react : Jake Gissinger (CU Boulder) +Apr18 : USER-BOCS package : Nicholas Dunn and Michael DeLyser (Penn State U) +Mar18: pair coul/shield, kolmogorov/crespi/full, ilp/graphene/hbn : Wengen Ouyang (Tel Aviv U) +Feb18 : pair lj/cut/coul/wolf : Vishal Boddu (U of Erlangen-Nuremberg) +Feb18 : USER-MOFFF package : Hendrik Heenen (Technical U of Munich) and Rochus Schmid (Ruhr-University Bochum) +Feb18 : pair ufm : Rodolfo Paula Leite and Maurice de Koning (Unicamp/Brazil) +Dec17 : fix python/move : Richard Berger (Temple U) +Nov17 : pair extep : Jaap Kroes (Radboud U) +Oct17 : USER-UEF package : David Nicholson (MIT) +Oct17 : fix rhok : Ulf Pederson (Roskilde U) +Oct17 : bond gromos : Axel Kohlmeyer (Temple U) +Oct17 : pair born/coul/wolf/cs and coul/wolf/cs : Vishal Boddu +Sep17 : fix latte : Christian Negre (LANL) +Sep17 : temper_npt : Amulya Pervaje and Cody Addington (NCSU) +Aug17 : USER-MESO package : Zhen Li (Brown University) +Aug17 : compute aggregate/atom & fragment/atom : Axel Kohlmeyer (Temple U) +Jul17 : pair meam/c : Sebastian Hutter (Otto-von-Guericke University) +Jun17 : pair reaxc/omp : Metin Aktulga (MSU) and Axel Kohlmeyer (Temple U) +Jun17 : pair vashishita/gpu : Anders Hafreager (UiO) +Jun17 : kspace pppm/disp/intel and pair lj/long/coul/long/intel : Mike Brown (Intel) and William McDoniel (RWTH Aachen U) +Jun17 : compute cnp/atom : Paulo Branicio (USC) +May17 : fix python and pair python : Richard Berger (Temple U) +May17 : pair edip/multi : Chao Jiang (U Wisconsin) +May17 : pair gw and gw/zbl : German Samolyuk (ORNL) +Mar17 : pair charmm fsw and fsh : Robert Meissner & Lucio Colombi Ciacchi (Bremen U), Robert Latour (Clemson U) +Mar17 : pair momb : Ya Zhou, Kristen Fichthorn, and Tonnam Balankura (PSU) +Mar17 : fix filter/corotate : Lukas Fath (KIT) +Mar17 : pair kolmogorov/crespi/z : Jaap Kroes (Radboud Universiteit) +Feb17 : Kokkos versions of the class2 bond/angle/dihedral/improper : Ray Shan (Materials Design) +Jan17 : USER-CGDNA package : Oliver Henrich (U Edinburgh) +Jan17 : fix mscg : Lauren Abbott (Sandia) +Nov16 : temper/grem and fix grem : David Stelter (BU), Edyta Malolepsza (Broad Institute), Tom Keyes (BU) +Nov16 : pair agni : Axel Kohlmeyer (Temple U) and Venkatesh Botu +Nov16 : pair tersoff/mod.c : Ganga P Purja Pun (George Mason University) +Nov16 : pair born/coul/dsf and pair born/coul/dsf/cs : Ariel Lozano +Nov16 : fix reaxc/species/kk & fix reaxc/bonds/kk : Stan Moore (Sandia) +Oct16 : fix wall/gran/region : Dan Bolintineanu (Sandia) +Sep16 : weight options for balance & fix balance : Axel Kohlmeyer (Temple U) & Iain Bethune (EPCC) +Sep16 : fix cmap : Xiaohu Hu (ORNL), David Hyde-Volpe & Tigran Abramyan & Robert Latour (Clemson U), Chris Lorenz (Kings College, London) +Sep16 : pair vashishta/table : Anders Hafreager (U Oslo) +Sep16 : kspace pppm/kk : Stan Moore (Sandia) +Aug16 : fix flow/gauss : Steve Strong and Joel Eaves (U Colorado) +Aug16 : fix controller : Aidan Thompson (Sandia) +Jul16 : dipole integration by DLM method : Iain Bethune (EPCC) +Jul16 : dihedral spherical : Andrew Jewett +Jun16 : pair reax/c/kk : Ray Shan (Materials Design), Stan Moore (Sandia) +Jun16 : fix orient/bcc : Tegar Wicaksono (UBC) +Jun16 : fix ehex : Peter Wirnsberger (University of Cambridge) +Jun16 : reactive DPD extensions to USER-DPD : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL), Christopher Stone (Computational Science & Engineering, LLC) +May16 : USER-MANIFOLD package : Stefan Paquay (Eindhoven U of Tech, The Netherlands) +Apr16 : write_coeff : Axel Kohlmeyer (Temple U) +Apr16 : pair morse/soft : Stefan Paquay (Eindhoven U of Tech, The Netherlands) +Apr16 : compute dipole/chunk : Axel Kohlmeyer (Temple U) +Apr16 : bond write : Axel Kohlmeyer (Temple U) +Mar16 : pair morse/smooth/linear : Stefan Paquay (Eindhoven U of Tech, The Netherlands) +Feb16 : pair/bond/angle/dihedral/improper zero : Carsten Svaneborg (SDU) +Feb16 : dump custom/vtk : Richard Berger (JKU) and Daniel Queteschiner (DCS Computing) +Feb16 : fix (nvt/npt/nph)/body and compute temp/body : Trung Nguyen +Feb16 : USER-DPD package : James Larentzos (ARL), Timothy Mattox (Engility Corp), John Brennan (ARL) +Dec15 : fix qeq/fire : Ray Shan (Sandia) +Dec15 : pair lj/mdf, pair lennard/mdf, pair buck/mdf, improper distance : Paolo Raiteri (Curtin University) +Nov15 : compute orientorder/atom : Aidan Thompson (Sandia) and Axel Kohlmeyer (U Temple) +Nov15 : compute hexorder/atom : Aidan Thompson (Sandia) +Oct15 : displace_atoms variable option : Reese Jones (Sandia) +Oct15 : pair mgpt & USER-MGPT package : Tomas Oppelstrup and John Moriarty (LLNL) +Oct15 : pair smtbq & USER-SMTBQ package : Nicolas Salles, Emile Maras, Olivier Politano, and Robert Tetot (LAAS-CNRS) +Oct15 : fix ave/correlate/long command : Jorge Ramirez (UPM) and Alexei Likhtman (U Reading) +Oct15 : pair vashishta command : Aidan Thompson (Sandia) and Yongnan Xiong (HNU) +Aug15 : USER-TALLY package : Axel Kohlmeyer (Temple U) +Aug15 : timer command : Axel Kohlmeyer (Temple U) +Aug15 : USER-H5MD package : Pierre de Buyl (KU Leuven) +Aug15 : COMPRESS package : Axel Kohlmeyer (Temple U) +Aug15 : USER-SMD package : Georg Gunzenmueller (EMI) +Jul15 : new HTML format for "doc pages"_Manual.html with search option : Richard Berger (JKU) +Jul15 : rRESPA with pair hybrid : Sam Genheden (U of Southampton) +Jul15 : pair_modify special : Axel Kohlmeyer (Temple U) +Jul15 : pair polymorphic : Xiaowang Zhou and Reese Jones (Sandia) +Jul15 : USER-DRUDE package : Alain Dequidt and Agilio Padua (U Blaise Pascal Clermont-Ferrand) and Julien Devemy (CNRS) +Jul15 : USER-QTB package : Yuan Shen, Tingting Qi, and Evan Reed (Stanford U) +Jul15 : USER-DIFFRACTION package : Shawn Coleman (ARL) +Mar15 : fix temp/csld : Axel Kohlmeyer (Temple U) +Mar15 : CORESHELL package : Hendrik Heenen (Technical University of Munich) +Feb15 : pair quip for GAP and other potentials : Albert Bartok-Partay (U Cambridge) +Feb15 : pair coul/streitz for Streitz-Mintmire potential : Ray Shan (Sandia) +Feb15 : fix tfmc : Kristof Bal (U of Antwerp) +Feb15 : fix ttm/mod : Sergey Starikov and Vasily Pisarev (JIHT of RAS) +Jan15 : fix atom/swap for MC swaps of atom types/charge : Paul Crozier (Sandia) +Nov14 : fix pimd for path-integral MD : Chris Knight and Yuxing Peng (U Chicago) +Nov14 : fix gle and fix ipi for path-integral MD : Michele Ceriotti (EPFL) +Nov14 : pair style srp : Tim Sirk (ARL) and Pieter in 't Veld (BASF) +Nov14 : fix ave/spatial/sphere : Niall Jackson (Imperial College) +Sep14 : QEQ package and several fix qeq/variant styles : Ray Shan (Sandia) +Sep14 : SNAP package and pair style : Aidan Thompson (Sandia) and collaborators +Aug14 : USER-INTEL package : Mike Brown (Intel) +May14 : KOKKOS pacakge : Christian Trott and Carter Edwards (Sandia) +May14 : USER-FEP pacakge : Agilio Padua (U Blaise Pascal Clermont-Ferrand) +Apr14 : fix rigid/small NVE/NVT/NPH/NPT : Trung Nguyen (ORNL) +Apr14 : fix qmmm for QM/MM coupling : Axel Kohlmeyer (Temple U) +Mar14 : kspace_modify collective for faster FFTs on BG/Q : Paul Coffman (IBM) +Mar14 : fix temp/csvr and fix oneway : Axel Kohlmeyer (Temple U) +Feb14 : pair peri/eps, compute dilatation/atom, compute plasticity/atom : Rezwanur Rahman and John Foster (UTSA) +Jan14 : MPI-IO options for dump and restart files : Paul Coffman (IBM) +Nov13 : USER-LB package for Lattice Boltzmann : Francis Mackay and Colin Denniston (U Western Ontario) +Nov13 : fix ti/rs and ti/spring : Rodrigo Freitas (UC Berkeley) +Nov13 : pair comb3 : Ray Shan (Sandia), Tao Liang and Dundar Yilmaz (U Florida) +Nov13 : write_dump and dump movie : Axel Kohlmeyer (Temple U) +Sep13 : xmgrace tool : Vikas Varshney +Sep13 : pair zbl : Aidan Thompson and Stephen Foiles (Sandia) +Aug13 : pair nm and variants : Julien Devemy (ICCF) +Aug13 : fix wall/lj1043 : Jonathan Lee (Sandia) +Jul13 : pair peri/ves : Rezwan Rahman, JT Foster (U Texas San Antonio) +Jul13 : pair tersoff/mod : Vitaly Dozhdikov (JIHT of RAS) +Jul13 : compute basal/atom : Christopher Barrett,(Mississippi State) +Jul13 : polybond tool : Zachary Kraus (Georgia Tech) +Jul13 : fix gld : Stephen Bond and Andrew Baczewski (Sandia) +Jun13 : pair nb3b/harmonic : Todd Zeitler (Sandia) +Jun13 : kspace_style pppm/stagger : Stan Moore (Sandia) +Jun13 : fix tune/kspace : Paul Crozier (Sandia) +Jun13 : long-range point dipoles : Stan Moore (Sandia) and Pieter in 't Veld (BASF) +May13 : compute msd/nongauss : Rob Hoy +May13 : pair list : Axel Kohlmeyer (Temple U) +May13 : triclinic support for long-range solvers : Stan Moore (Sandia) +Apr13 : dump_modify nfile and fileper : Christopher Knight +Mar13 : fix phonon : Ling-Ti Kong (Shanghai Jiao Tong University) +Mar13 : pair_style lj/cut/tip4p/cut : Pavel Elkind (Gothenburg University) +Feb13 : immediate variables in input script : Daniel Moller (Autonomous University of Barcelona) +Feb13 : fix species : Ray Shan (Sandia) +Jan13 : compute voronoi/atom : Daniel Schwen +Nov12 : pair_style mie/cut : Cassiano Aimoli Petrobras (U Notre Dame) +Oct12 : pair_style meam/sw/spline : Robert Rudd (LLNL) +Oct12 : angle_style fourier and fourier/simple and quartic : Loukas Peristeras (Scienomics) +Oct12 : dihedral_style fourier and nharmonic and quadratic : Loukas Peristeras (Scienomics) +Oct12 : improper_style fourier : Loukas Peristeras (Scienomics) +Oct12 : kspace_style pppm/disp for 1/r^6 : Rolf Isele-Holder (Aachen University) +Oct12 : moltemplate molecular builder tool : Andrew Jewett (UCSB) +Sep12 : pair_style lj/cut/coul/dsf and coul/dsf : Trung Nguyen (ORNL) +Sep12 : multi-level summation long-range solver : Stan Moore, Stephen Bond, and Paul Crozier (Sandia) +Aug12 : fix rigid/npt and fix rigid/nph : Trung Nguyen (ORNL) +Aug12 : Fortran wrapper on lib interface : Karl Hammond (UT, Knoxville) +Aug12 : kspace_modify diff for 2-FFT PPPM : Rolf Isele-Holder (Aachen University), Stan Moore (BYU), Paul Crozier (Sandia) +Jun12 : pair_style bop : Don Ward and Xiaowang Zhou (Sandia) +Jun12 : USER-MOLFILE package : Axel Kohlmeyer (U Temple) +Jun12 : USER-COLVARS package : Axel Kohlmeyer (U Temple) +May12 : read_dump : Tim Sirk (ARL) +May12 : improper_style cossq and ring : Georgios Vogiatzis (CoMSE, NTU Athens) +May12 : pair_style lcbop : Dominik Wojt (Wroclaw University of Technology) +Feb12 : PPPM per-atom energy/virial : Stan Moore (BYU) +Feb12 : Ewald per-atom energy/virial : German Samolyuk (ORNL), Stan Moore (BYU) +Feb12 : minimize forcezero linesearch : Asad Hasan (CMU) +Feb12 : pair_style beck : Jon Zimmerman (Sandia) +Feb12 : pair_style meam/spline : Alex Stukowski (LLNL) +Jan12 : pair_style kim : Valeriu Smirichinski, Ryan Elliott, Ellad Tadmor (U Minn) +Jan12 : dihedral_style table : Andrew Jewett (UCSB) +Jan12 : angle_style dipole : Mario Orsi +Jan12 : pair_style lj/smooth/linear : Jon Zimmerman (Sandia) +Jan12 : fix reax/c/bond : Tzu-Ray Shan (Sandia) +Dec11 : pair_style coul/wolf : Yongfeng Zhang (INL) +Dec11 : run_style verlet/split : Yuxing Peng and Chris Knight (U Chicago) +Dec11 : pair_style tersoff/table : Luca Ferraro (CASPUR) +Nov11 : per-atom energy/stress for reax/c : Tzu-Ray Shan (Sandia) +Oct11 : Fast Lubrication Dynamics (FLD) package: Amit Kumar, Michael Bybee, Jonathan Higdon (UIUC) +Oct11 : USER-OMP package : Axel Kohlmeyer (Temple U) +Sep11 : pair_style edip : Luca Ferraro (CASPUR) +Aug11 : USER-SPH package : Georg Ganzenmuller (FIHSD, EMI, Germany) +Aug11 : fix restrain : Craig Tenney (Sandia) +Aug11 : USER-CUDA package : Christian Trott (U Tech Ilmenau) +Aug11 : pair_style lj/sf : Laurent Joly (U Lyon) +Aug11 : bond_style harmonic/shift and harmonic/shift/cut : Carsten Svaneborg +Aug11 : angle_style cosine/shift and cosine/shift/exp : Carsten Svaneborg +Aug11 : dihedral_style cosine/shift/exp : Carsten Svaneborg +Aug11 : pair_style dipole/sf : Mario Orsi +Aug11 : fix addtorque and compute temp/rotate : Laurent Joly (U Lyon) +Aug11 : FFT support via FFTW3, MKL, ACML, KISSFFT libraries : \ + Axel Kohlmeyer (Temple U) +Jun11 : pair_style adp : Chris Weinberger (Sandia), Stephen Foiles (Sandia), \ + Chandra Veer Singh (Cornell) +Jun11 : Windows build option via Microsoft Visual Studio : \ + Ilya Valuev (JIHT, Moscow, Russia) +Jun11 : antisymmetrized wave packet MD : Ilya Valuev (JIHT, Moscow, Russia) +Jun11 : dump image : Nathan Fabian (Sandia) +May11 : pppm GPU single and double : Mike Brown (ORNL) +May11 : pair_style lj/expand/gpu : Inderaj Bains (NVIDIA) +2010 : pair_style reax/c and fix qeq/reax : Metin Aktulga (Purdue, now LBNL) +- : DREIDING force field, pair_style hbond/dreiding, etc : Tod Pascal (Caltech) +- : fix adapt and compute ti for thermodynamic integration for \ + free energies : Sai Jayaraman (Sandia) +- : pair_style born and gauss : Sai Jayaraman (Sandia) +- : stochastic rotation dynamics (SRD) via fix srd : \ + Jeremy Lechman (Sandia) and Pieter in 't Veld (BASF) +- : ipp Perl script tool : Reese Jones (Sandia) +- : eam_database and createatoms tools : Xiaowang Zhou (Sandia) +- : electron force field (eFF) : Andres Jaramillo-Botero and Julius Su (Caltech) +- : embedded ion method (EIM) potential : Xiaowang Zhou (Sandia) +- : COMB potential with charge equilibration : Tzu-Ray Shan (U Florida) +- : fix ave/correlate : Benoit Leblanc, Dave Rigby, \ + Paul Saxe (Materials Design) and Reese Jones (Sandia) +- : pair_style peri/lps : Mike Parks (Sandia) +- : fix msst : Lawrence Fried (LLNL), Evan Reed (LLNL, Stanford) +- : thermo_style custom tpcpu & spcpu keywords : Axel Kohlmeyer (Temple U) +- : fix rigid/nve, fix rigid/nvt : Tony Sheh and Trung Dac Nguyen (U Michigan) +- : public SVN & Git repositories for LAMMPS : \ + Axel Kohlmeyer (Temple U) and Bill Goldman (Sandia) +- : compute heat/flux : German Samolyuk (ORNL) and \ + Mario Pinto (Computational Research Lab, Pune, India) +- : pair_style yukawa/colloid : Randy Schunk (Sandia) +- : fix wall/colloid : Jeremy Lechman (Sandia) +2009 : fix imd for real-time viz and interactive MD : Axel Kohlmeyer (Temple Univ) +- : concentration-dependent EAM potential : \ + Alexander Stukowski (Technical University of Darmstadt) +- : parallel replica dymamics (PRD) : Mike Brown (Sandia) +- : min_style hftn : Todd Plantenga (Sandia) +- : fix atc : Reese Jones, Jon Zimmerman, Jeremy Templeton (Sandia) +- : dump cfg : Liang Wan (Chinese Academy of Sciences) +- : fix nvt with Nose/Hoover chains : Andy Ballard (U Maryland) +- : pair_style lj/cut/gpu, pair_style gayberne/gpu : Mike Brown (Sandia) +- : pair_style lj96/cut, bond_style table, angle_style table : Chuanfu Luo +- : fix langevin tally : Carolyn Phillips (U Michigan) +- : compute heat/flux for Green-Kubo : Reese Jones (Sandia), \ + Philip Howell (Siemens), Vikas Varsney (AFRL) +- : region cone : Pim Schravendijk +- : pair_style born/coul/long : Ahmed Ismail (Sandia) +- : fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan) +- : fix box/relax : Aidan Thompson and David Olmsted (Sandia) +- : ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT) +- : compute cna/atom : Liang Wan (Chinese Academy of Sciences) +2008 : Tersoff/ZBL potential : Dave Farrell (Northwestern U) +- : peridynamics : Mike Parks (Sandia) +- : fix smd for steered MD : Axel Kohlmeyer (U Penn) +- : GROMACS pair potentials : Mark Stevens (Sandia) +- : lmp2vmd tool : Axel Kohlmeyer (U Penn) +- : compute group/group : Naveen Michaud-Agrawal (Johns Hopkins U) +- : USER-CG-CMM package for coarse-graining : Axel Kohlmeyer (U Penn) +- : cosine/delta angle potential : Axel Kohlmeyer (U Penn) +- : VIM editor add-ons for LAMMPS input scripts : Gerolf Ziegenhain +- : pair_style lubricate : Randy Schunk (Sandia) +- : compute ackland/atom : Gerolf Ziegenhain +- : kspace_style ewald/n, pair_style lj/coul, pair_style buck/coul : \ + Pieter in 't Veld (Sandia) +- : AI-REBO bond-order potential : Ase Henry (MIT) +- : making LAMMPS a true "object" that can be instantiated \ + multiple times, e.g. as a library : Ben FrantzDale (RPI) +- : pymol_asphere viz tool : Mike Brown (Sandia) +2007 : NEMD SLLOD integration : Pieter in 't Veld (Sandia) +- : tensile and shear deformations : Pieter in 't Veld (Sandia) +- : GayBerne potential : Mike Brown (Sandia) +- : ellipsoidal particles : Mike Brown (Sandia) +- : colloid potentials : Pieter in 't Veld (Sandia) +- : fix heat : Paul Crozier and Ed Webb (Sandia) +- : neighbor multi and communicate multi : Pieter in 't Veld (Sandia) +- : MATLAB post-processing scripts : Arun Subramaniyan (Purdue) +- : triclinic (non-orthogonal) simulation domains : Pieter in 't Veld (Sandia) +- : thermo_extract tool: Vikas Varshney (Wright Patterson AFB) +- : fix ave/time and fix ave/spatial : Pieter in 't Veld (Sandia) +- : MEAM potential : Greg Wagner (Sandia) +- : optimized pair potentials for lj/cut, charmm/long, eam, morse : \ + James Fischer (High Performance Technologies), \ + David Richie and Vincent Natoli (Stone Ridge Technologies) +2006 : fix wall/lj126 : Mark Stevens (Sandia) +- : Stillinger-Weber and Tersoff potentials : \ + Aidan Thompson and Xiaowang Zhou (Sandia) +- : region prism : Pieter in 't Veld (Sandia) +- : fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U) +- : multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U) +- : OPLS dihedral potential: Mark Stevens (Sandia) +- : POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) +- : faster pair hybrid potential: James Fischer \ + (High Performance Technologies, Inc), Vincent Natoli and \ + David Richie (Stone Ridge Technology) +- : breakable bond quartic potential: Chris Lorenz and Mark Stevens (Sandia) +- : DCD and XTC dump styles: Naveen Michaud-Agrawal (Johns Hopkins U) +- : grain boundary orientation fix : Koenraad Janssens and \ + David Olmsted (Sandia) +- : pair_style lj/smooth potential : Craig Maloney (UCSB) +- : radius-of-gyration spring fix : Naveen Michaud-Agrawal \ + (Johns Hopkins U) and Paul Crozier (Sandia) +- : self spring fix : Naveen Michaud-Agrawal (Johns Hopkins U) +- : EAM CoAl and AlCu potentials : Kwang-Reoul Lee (KIST, Korea) +- : cosine/squared angle potential : Naveen Michaud-Agrawal (Johns Hopkins U) +- : helix dihedral potential : Naveen Michaud-Agrawal (Johns Hopkins U) and \ + Mark Stevens (Sandia) +- : Finnis/Sinclair EAM: Tim Lau (MIT) +- : dissipative particle dynamics (DPD) potentials: Kurt Smith (U Pitt) and \ + Frank van Swol (Sandia) +- : TIP4P potential (4-site water): Ahmed Ismail and \ + Amalie Frischknecht (Sandia) +2005 : uniaxial strain fix: Carsten Svaneborg (Max Planck Institute) +- : compressed dump files: Erik Luijten (U Illinois) +- : cylindrical indenter fix: Ravi Agrawal (Northwestern U) +- : electric field fix: Christina Payne (Vanderbilt U) +- : AMBER <-> LAMMPS tool: Keir Novik (Univ College London) and \ + Vikas Varshney (U Akron) +- : CHARMM <-> LAMMPS tool: Pieter in 't Veld and Paul Crozier (Sandia) +- : Morse bond potential: Jeff Greathouse (Sandia) +- : radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia) +- : force tables for long-range Coulombics: Paul Crozier (Sandia) +2004 : targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \ + Christian Burisch (Bochum University, Germany) +- : FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech) +- : lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \ + Andrey Kalinichev (Sandia) +- : parallel tempering: Mark Sears (Sandia) +earlier : granular force fields and BC: Leo Silbert & Gary Grest (Sandia) +- : multi-harmonic dihedral potential: Mathias Putz (Sandia) +- : embedded atom method (EAM) potential: Stephen Foiles (Sandia) +- : msi2lmp tool: Steve Lustig (Dupont), Mike Peachey & John Carpenter (Cray) +- : HTFN energy minimizer: Todd Plantenga (Sandia) +- : class 2 force fields: Eric Simon (Cray) +- : NVT/NPT integrators: Mark Stevens (Sandia) +- : rRESPA: Mark Stevens & Paul Crozier (Sandia) +- : Ewald and PPPM solvers: Roy Pollock (LLNL) : :tb(s=:,ca1=c) diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt new file mode 100644 index 0000000000000000000000000000000000000000..2bb7e25683be9bd90610193a3b265729b1eb9afa --- /dev/null +++ b/doc/src/Intro_features.txt @@ -0,0 +1,202 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS features :h3 + +LAMMPS is a classical molecular dynamics (MD) code with these general +classes of functionality: + +"General features"_#general +"Particle and model types"_#particle +"Interatomic potentials (force fields)"_#ff +"Atom creation"_#create +"Ensembles, constraints, and boundary conditions"_#ensemble +"Integrators"_#integrate +"Diagnostics"_#diag +"Output"_#output +"Multi-replica models"_#replica +"Pre- and post-processing"_#prepost +"Specialized features (beyond MD itself)"_#special :ul + +:line + +General features :h4,link(general) + + runs on a single processor or in parallel + distributed-memory message-passing parallelism (MPI) + spatial-decomposition of simulation domain for parallelism + open-source distribution + highly portable C++ + optional libraries used: MPI and single-processor FFT + GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features + easy to extend with new features and functionality + runs from an input script + syntax for defining and using variables and formulas + syntax for looping over runs and breaking out of loops + run one or multiple simulations simultaneously (in parallel) from one script + build as library, invoke LAMMPS thru library interface or provided Python wrapper + couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul + +Particle and model types :h4,link(particle) +("atom style"_atom_style.html command) + + atoms + coarse-grained particles (e.g. bead-spring polymers) + united-atom polymers or organic molecules + all-atom polymers, organic molecules, proteins, DNA + metals + granular materials + coarse-grained mesoscale models + finite-size spherical and ellipsoidal particles + finite-size line segment (2d) and triangle (3d) particles + point dipole particles + rigid collections of particles + hybrid combinations of these :ul + +Interatomic potentials (force fields) :h4,link(ff) +("pair style"_pair_style.html, "bond style"_bond_style.html, +"angle style"_angle_style.html, "dihedral style"_dihedral_style.html, +"improper style"_improper_style.html, "kspace style"_kspace_style.html +commands) + + pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ + Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated + charged pairwise potentials: Coulombic, point-dipole + manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ + embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ + REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic + long-range interactions for charge, point-dipoles, and LJ dispersion: \ + Ewald, Wolf, PPPM (similar to particle-mesh Ewald) + polarization models: "QEq"_fix_qeq.html, \ + "core/shell model"_Howto_coreshell.html, \ + "Drude dipole model"_Howto_drude.html + charge equilibration (QEq via dynamic, point, shielded, Slater methods) + coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO + mesoscopic potentials: granular, Peridynamics, SPH + electron force field (eFF, AWPMD) + bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ + quartic (breakable) + angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ + class 2 (COMPASS) + dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ + class 2 (COMPASS), OPLS + improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) + polymer potentials: all-atom, united-atom, bead-spring, breakable + water potentials: TIP3P, TIP4P, SPC + implicit solvent potentials: hydrodynamic lubrication, Debye + force-field compatibility with common CHARMM, AMBER, DREIDING, \ + OPLS, GROMACS, COMPASS options + access to "KIM archive"_http://openkim.org of potentials via \ + "pair kim"_pair_kim.html + hybrid potentials: multiple pair, bond, angle, dihedral, improper \ + potentials can be used in one simulation + overlaid potentials: superposition of multiple pair potentials :ul + +Atom creation :h4,link(create) +("read_data"_read_data.html, "lattice"_lattice.html, +"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, +"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) + + read in atom coords from files + create atoms on one or more lattices (e.g. grain boundaries) + delete geometric or logical groups of atoms (e.g. voids) + replicate existing atoms multiple times + displace atoms :ul + +Ensembles, constraints, and boundary conditions :h4,link(ensemble) +("fix"_fix.html command) + + 2d or 3d systems + orthogonal or non-orthogonal (triclinic symmetry) simulation domains + constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators + thermostatting options for groups and geometric regions of atoms + pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions + simulation box deformation (tensile and shear) + harmonic (umbrella) constraint forces + rigid body constraints + SHAKE bond and angle constraints + Monte Carlo bond breaking, formation, swapping + atom/molecule insertion and deletion + walls of various kinds + non-equilibrium molecular dynamics (NEMD) + variety of additional boundary conditions and constraints :ul + +Integrators :h4,link(integrate) +("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) + + velocity-Verlet integrator + Brownian dynamics + rigid body integration + energy minimization via conjugate gradient or steepest descent relaxation + rRESPA hierarchical timestepping + rerun command for post-processing of dump files :ul + +Diagnostics :h4,link(diag) + + see various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul + +Output :h4,link(output) +("dump"_dump.html, "restart"_restart.html commands) + + log file of thermodynamic info + text dump files of atom coords, velocities, other per-atom quantities + binary restart files + parallel I/O of dump and restart files + per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) + user-defined system-wide (log file) or per-atom (dump file) calculations + spatial and time averaging of per-atom quantities + time averaging of system-wide quantities + atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul + +Multi-replica models :h4,link(replica) + +"nudged elastic band"_neb.html +"parallel replica dynamics"_prd.html +"temperature accelerated dynamics"_tad.html +"parallel tempering"_temper.html :ul + +Pre- and post-processing :h4,link(prepost) + +A handful of pre- and post-processing tools are packaged with LAMMPS, +some of which can convert input and output files to/from formats used +by other codes; see the "Toos"_Tools.html doc page. :ulb,l + +Our group has also written and released a separate toolkit called +"Pizza.py"_pizza which provides tools for doing setup, analysis, +plotting, and visualization for LAMMPS simulations. Pizza.py is +written in "Python"_python and is available for download from "the +Pizza.py WWW site"_pizza. :l,ule + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(python,http://www.python.org) + +Specialized features :h4,link(special) + +LAMMPS can be built with optional packages which implement a variety +of additional capabilities. See the "Packages"_Packages.html doc +page for details. + +These are LAMMPS capabilities which you may not think of as typical +classical MD options: + +"static"_balance.html and "dynamic load-balancing"_fix_balance.html +"generalized aspherical particles"_Howto_body.html +"stochastic rotation dynamics (SRD)"_fix_srd.html +"real-time visualization and interactive MD"_fix_imd.html +calculate "virtual diffraction patterns"_compute_xrd.html +"atom-to-continuum coupling"_fix_atc.html with finite elements +coupled rigid body integration via the "POEMS"_fix_poems.html library +"QM/MM coupling"_fix_qmmm.html +Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html and "atom swapping"_fix_atom_swap.html +"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html +"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids +"Peridynamics mesoscale modeling"_pair_peri.html +"Lattice Boltzmann fluid"_fix_lb_fluid.html +"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics +"two-temperature electron model"_fix_ttm.html :ul diff --git a/doc/src/Intro_nonfeatures.txt b/doc/src/Intro_nonfeatures.txt new file mode 100644 index 0000000000000000000000000000000000000000..41f001fc8b675de6c1e3624b1695dd3bfc5ca96c --- /dev/null +++ b/doc/src/Intro_nonfeatures.txt @@ -0,0 +1,83 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS non-features :h3 + +LAMMPS is designed to be a fast, parallel engine for molecular +dynamics (MD) simulations. It provides only a modest amount of +functionality for setting up simulations and analyzing their output. + +Specifically, LAMMPS does not: + +run thru a GUI +build molecular systems +assign force-field coefficients automagically +perform sophisticated analyses of your MD simulation +visualize your MD simulation interactively +plot your output data :ul + +Here are suggestions on how to perform these tasks: + +GUI: LAMMPS can be built as a library and a Python wrapper that wraps +the library interface is provided. Thus, GUI interfaces can be +written in Python (or C or C++ if desired) that run LAMMPS and +visualize or plot its output. Examples of this are provided in the +python directory and described on the "Python"_Python.html doc +page. :ulb,l + +Builder: Several pre-processing tools are packaged with LAMMPS. Some +of them convert input files in formats produced by other MD codes such +as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them +are simple programs that will build simple molecular systems, such as +linear bead-spring polymer chains. The moltemplate program is a true +molecular builder that will generate complex molecular models. See +the "Tools"_Tools.html doc page for details on tools packaged with +LAMMPS. The "Pre/post processing +page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website +describes a variety of 3rd party tools for this task. :l + +Force-field assignment: The conversion tools described in the previous +bullet for CHARMM, AMBER, and Insight will also assign force field +coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER, +or Accelerys force field files. :l + +Simulation analyses: If you want to perform analyses on-the-fly as +your simulation runs, see the "compute"_compute.html and +"fix"_fix.html doc pages, which list commands that can be used in a +LAMMPS input script. Also see the "Modify"_Modify.html doc page for +info on how to add your own analysis code or algorithms to LAMMPS. +For post-processing, LAMMPS output such as "dump file +snapshots"_dump.html can be converted into formats used by other MD or +post-processing codes. Some post-processing tools packaged with +LAMMPS will do these conversions. Scripts provided with the {python} +tool in the tools directory can extract and massage data in dump files +to make it easier to import into other programs. See the +"Tools"_Tools.html doc page for details on these various options. :l + +Visualization: LAMMPS can produce JPG or PNG snapshot images +on-the-fly via its "dump image"_dump_image.html command. For +high-quality, interactive visualization there are many excellent and +free tools available. See the "Other Codes +page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for +visualization packages that can use LAMMPS output data. :l + +Plotting: See the next bullet about Pizza.py as well as the +"Python"_Python.html doc page for examples of plotting LAMMPS output. +Scripts provided with the {python} tool in the tools directory will +extract and massage data in log and dump files to make it easier to +analyze and plot. See the "Tools"_Tools.html doc page for more +discussion of the various tools. :l + +Pizza.py: Our group has also written a separate toolkit called +"Pizza.py"_http://pizza.sandia.gov which can do certain kinds of +setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS +simulations. It thus provides some functionality for several of the +above bullets. Pizza.py is written in "Python"_http://www.python.org +and is available for download from "this +page"_http://www.cs.sandia.gov/~sjplimp/download.html. :l,ule diff --git a/doc/src/Intro_opensource.txt b/doc/src/Intro_opensource.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0d57f7ce199b35ffa8abab06e9e0217b3a54304 --- /dev/null +++ b/doc/src/Intro_opensource.txt @@ -0,0 +1,44 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +LAMMPS open-source license :h3 + +LAMMPS is a freely-available open-source code, distributed under the +terms of the "GNU Public License"_gnu, which means you can use or +modify the code however you wish. + +LAMMPS comes with no warranty of any kind. As each source file states +in its header, it is a copyrighted code that is distributed free-of- +charge, under the terms of the "GNU Public License"_gnu (GPL). This +is often referred to as open-source distribution - see +"www.gnu.org"_gnuorg or "www.opensource.org"_opensource. The legal +text of the GPL is in the LICENSE file included in the LAMMPS +distribution. + +:link(gnu,http://www.gnu.org/copyleft/gpl.html) +:link(gnuorg,http://www.gnu.org) +:link(opensource,http://www.opensource.org) + +Here is a summary of what the GPL means for LAMMPS users: + +(1) Anyone is free to use, modify, or extend LAMMPS in any way they +choose, including for commercial purposes. + +(2) If you distribute a modified version of LAMMPS, it must remain +open-source, meaning you distribute it under the terms of the GPL. +You should clearly annotate such a code as a derivative version of +LAMMPS. + +(3) If you release any code that includes LAMMPS source code, then it +must also be open-sourced, meaning you distribute it under the terms +of the GPL. + +(4) If you give LAMMPS files to someone else, the GPL LICENSE file and +source file headers (including the copyright and GPL notices) should +remain part of the code. diff --git a/doc/src/Intro_overview.txt b/doc/src/Intro_overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..49c14bc5f06d463037d294d28873b43fdf6c7f14 --- /dev/null +++ b/doc/src/Intro_overview.txt @@ -0,0 +1,58 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Overview of LAMMPS :h3 + +LAMMPS is a classical molecular dynamics (MD) code that models +ensembles of particles in a liquid, solid, or gaseous state. It can +model atomic, polymeric, biological, solid-state (metals, ceramics, +oxides), granular, coarse-grained, or macroscopic systems using a +variety of interatomic potentials (force fields) and boundary +conditions. It can model 2d or 3d systems with only a few particles +up to millions or billions. + +LAMMPS can be built and run on a laptop or destop machine, but is +designed for parallel computers. It will run on any parallel machine +that supports the "MPI"_mpi message-passing library. This includes +shared-memory boxes and distributed-memory clusters and +supercomputers. + +:link(mpi,http://www-unix.mcs.anl.gov/mpi) + +LAMMPS is written in C++. Earlier versions were written in F77 and +F90. See the "History page"_http://lammps.sandia.gov/history.html of +the website for details. All versions can be downloaded from the +"LAMMPS website"_lws. + +LAMMPS is designed to be easy to modify or extend with new +capabilities, such as new force fields, atom types, boundary +conditions, or diagnostics. See the "Modify"_Modify.html doc page for +more details. + +In the most general sense, LAMMPS integrates Newton's equations of +motion for a collection of interacting particles. A single particle +can be an atom or molecule or electron, a coarse-grained cluster of +atoms, or a mesoscopic or macroscopic clump of material. The +interaction models that LAMMPS includes are mostly short-range in +nature; some long-range models are included as well. + +LAMMPS uses neighbor lists to keep track of nearby particles. The +lists are optimized for systems with particles that are repulsive at +short distances, so that the local density of particles never becomes +too large. This is in contrast to methods used for modeling plasmas +or gravitational bodies (e.g. galaxy formation). + +On parallel machines, LAMMPS uses spatial-decomposition techniques to +partition the simulation domain into small sub-domains of equal +computational cost, one of which is assigned to each processor. +Processors communicate and store "ghost" atom information for atoms +that border their sub-domain. + + + diff --git a/doc/src/Intro_website.txt b/doc/src/Intro_website.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8af94157ceb9545be2c6ddd22bcb928115b63d8 --- /dev/null +++ b/doc/src/Intro_website.txt @@ -0,0 +1,42 @@ +"Higher level section"_Intro.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Additional website links :h3 + +The "LAMMPS website"_lws has a variety of additional info about +LAMMPS, beyond what is in this manual. Some of the other pages in +this Intr are included in this list. + +"Brief intro and recently added significant features"_lws +"List of features"_http://lammps.sandia.gov/features.html +"List of non-features"_http://lammps.sandia.gov/non_features.html +"Recent bug fixes and new features"_http://lammps.sandia.gov/bug.html :ul + +"Download info"_http://lammps.sandia.gov/download.html +"GitHub site"_https://github.com/lammps/lammps +"SourceForge site"_https://sourceforge.net/projects/lammps +"LAMMPS open-source license"_http://lammps.sandia.gov/open_source.html :ul + +"Glossary of MD terms relevant to LAMMPS"_http://lammps.sandia.gov/glossary.html +"LAMMPS highlights with images"_http://lammps.sandia.gov/pictures.html +"LAMMPS highlights with movies"_http://lammps.sandia.gov/movies.html +"Mail list"_http://lammps.sandia.gov/mail.html +"Workshops"_http://lammps.sandia.gov/workshops.html +"Tutorials"_http://lammps.sandia.gov/tutorials.html +"Developer guide"_http://lammps.sandia.gov/Developer.pdf :ul + +"Pre- and post-processing tools for LAMMPS"_http://lammps.sandia.gov/prepost.html +"Other software usable with LAMMPS"_http://lammps.sandia.gov/offsite.html +"Viz tools usable with LAMMPS"_http://lammps.sandia.gov/viz.html :ul + +"Benchmark performance"_http://lammps.sandia.gov/bench.html +"Publications that have cited LAMMPS"_http://lammps.sandia.gov/papers.html +"Authors of LAMMPS"_http://lammps.sandia.gov/authors.html +"History of LAMMPS development"_http://lammps.sandia.gov/history.html +"Funding for LAMMPS"_http://lammps.sandia.gov/funding.html :ul diff --git a/doc/src/JPG/pair_body_rounded.jpg b/doc/src/JPG/pair_body_rounded.jpg new file mode 100644 index 0000000000000000000000000000000000000000..cd745c44e27e96585be021b3dcca342f686e15e9 Binary files /dev/null and b/doc/src/JPG/pair_body_rounded.jpg differ diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 6b2c7daac7d682c05469e44db60b9e0aad02f5c5..a5e8b63640be29f7212d66e1d6b42ceb66747a41 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -14,90 +14,53 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html#comm) :line -LAMMPS Documentation :c,h1 -11 May 2018 version :c,h2 - -Version info: :h3 - -The LAMMPS "version" is the date when it was released, such as 1 May -2010. LAMMPS is updated continuously. Whenever we fix a bug or add a -feature, we release it immediately, and post a notice on "this page of -the WWW site"_bug. Every 2-4 months one of the incremental releases -is subjected to more thorough testing and labeled as a {stable} version. - -Each dated copy of LAMMPS contains all the -features and bug-fixes up to and including that version date. The -version date is printed to the screen and logfile every time you run -LAMMPS. It is also in the file src/version.h and in the LAMMPS -directory name created when you unpack a tarball, and at the top of -the first page of the manual (this page). - -If you browse the HTML doc pages on the LAMMPS WWW site, they always -describe the most current [development] version of LAMMPS. :ulb,l - -If you browse the HTML doc pages included in your tarball, they -describe the version you have. :l +

-The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated -about once per month. This is because it is large, and we don't want -it to be part of every patch. :l +LAMMPS Documentation :c,h1 +2 Aug 2018 version :c,h2 -There is also a "Developer.pdf"_Developer.pdf file in the doc -directory, which describes the internal structure and algorithms of -LAMMPS. :l -:ule +"What is a LAMMPS version?"_Manual_version.html LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. -LAMMPS is a classical molecular dynamics simulation code designed to -run efficiently on parallel computers. It was developed at Sandia -National Laboratories, a US Department of Energy facility, with -funding from the DOE. It is an open-source code, distributed freely -under the terms of the GNU Public License (GPL). +LAMMPS is a classical molecular dynamics simulation code with a focus +on materials modeling. It was designed to run efficiently on parallel +computers. It was developed originally at Sandia National +Laboratories, a US Department of Energy facility. The majority of +funding for LAMMPS has come from the US Department of Energy (DOE). +LAMMPS is an open-source code, distributed freely under the terms of +the GNU Public License (GPL). + +The "LAMMPS website"_lws has a variety of information about the code. +It includes links to an on-line version of this manual, a "mail +list"_http://lammps.sandia.gov/mail.html where users can post +questions, and a "GitHub site"https://github.com/lammps/lammps where +all LAMMPS development is coordinated. -The current core group of LAMMPS developers is at Sandia National -Labs and Temple University: +:line -"Steve Plimpton"_sjp, sjplimp at sandia.gov :ulb,l -Aidan Thompson, athomps at sandia.gov :l -Stan Moore, stamoor at sandia.gov :l -"Axel Kohlmeyer"_ako, akohlmey at gmail.com :l -:ule +"PDF file"_Manual.pdf of the entire manual, generated by +"htmldoc"_http://freecode.com/projects/htmldoc -Past core developers include Paul Crozier, Ray Shan and Mark Stevens, -all at Sandia. The [LAMMPS home page] at -"http://lammps.sandia.gov"_http://lammps.sandia.gov has more information -about the code and its uses. Interaction with external LAMMPS developers, -bug reports and feature requests are mainly coordinated through the -"LAMMPS project on GitHub."_https://github.com/lammps/lammps -The lammps.org domain, currently hosting "public continuous integration -testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux -RPM and Windows installer packages"_http://packages.lammps.org is located -at Temple University and managed by Richard Berger, -richard.berger at temple.edu. +The content for this manual is part of the LAMMPS distribution. +You can build a local copy of the Manual as HTML pages or a PDF file, +by following the steps on the "this page"_Build_manual.html. -:link(bug,http://lammps.sandia.gov/bug.html) -:link(sjp,http://www.sandia.gov/~sjplimp) -:link(ako,http://goo.gl/1wk0) +There is also a "Developer.pdf"_Developer.pdf document which gives +a brief description of the basic code structure of LAMMPS. :line -The LAMMPS documentation is organized into the following sections. If -you find errors or omissions in this manual or have suggestions for -useful information to add, please send an email to the developers so -we can improve the LAMMPS documentation. +This manual is organized into the following sections. Once you are familiar with LAMMPS, you may want to bookmark "this -page"_Section_commands.html#comm at Section_commands.html#comm since -it gives quick access to documentation for all LAMMPS commands. - -"PDF file"_Manual.pdf of the entire manual, generated by -"htmldoc"_http://freecode.com/projects/htmldoc +page"_Commands.html since it gives quick access to a doc page for +every LAMMPS command. -"Introduction"_Section_intro.html :olb,l - 1.1 "What is LAMMPS"_intro_1 :ulb,b - 1.2 "LAMMPS features"_intro_2 :b - 1.3 "LAMMPS non-features"_intro_3 :b - 1.4 "Open source distribution"_intro_4 :b - 1.5 "Acknowledgments and citations"_intro_5 :ule,b +"Introduction"_Intro.html :olb,l "Getting started"_Section_start.html :l 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b 2.2 "Making LAMMPS"_start_2 :b @@ -161,96 +116,17 @@ END_RST --> 2.6 "Command-line options"_start_6 :b 2.7 "Screen output"_start_7 :b 2.8 "Tips for users of previous versions"_start_8 :ule,b -"Commands"_Section_commands.html :l - 3.1 "LAMMPS input script"_cmd_1 :ulb,b - 3.2 "Parsing rules"_cmd_2 :b - 3.3 "Input script structure"_cmd_3 :b - 3.4 "Commands listed by category"_cmd_4 :b - 3.5 "Commands listed alphabetically"_cmd_5 :ule,b -"Packages"_Section_packages.html :l - 4.1 "Standard packages"_pkg_1 :ulb,b - 4.2 "User packages"_pkg_2 :ule,b -"Accelerating LAMMPS performance"_Section_accelerate.html :l - 5.1 "Measuring performance"_acc_1 :ulb,b - 5.2 "Algorithms and code options to boost performace"_acc_2 :b - 5.3 "Accelerator packages with optimized styles"_acc_3 :b - 5.3.1 "GPU package"_accelerate_gpu.html :b - 5.3.2 "USER-INTEL package"_accelerate_intel.html :b - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b - 5.3.4 "USER-OMP package"_accelerate_omp.html :b - 5.3.5 "OPT package"_accelerate_opt.html :b - 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b -"How-to discussions"_Section_howto.html :l - 6.1 "Restarting a simulation"_howto_1 :ulb,b - 6.2 "2d simulations"_howto_2 :b - 6.3 "CHARMM and AMBER force fields"_howto_3 :b - 6.4 "Running multiple simulations from one input script"_howto_4 :b - 6.5 "Multi-replica simulations"_howto_5 :b - 6.6 "Granular models"_howto_6 :b - 6.7 "TIP3P water model"_howto_7 :b - 6.8 "TIP4P water model"_howto_8 :b - 6.9 "SPC water model"_howto_9 :b - 6.10 "Coupling LAMMPS to other codes"_howto_10 :b - 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b - 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b - 6.13 "NEMD simulations"_howto_13 :b - 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b - 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b - 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b - 6.17 "Walls"_howto_17 :b - 6.18 "Elastic constants"_howto_18 :b - 6.19 "Library interface to LAMMPS"_howto_19 :b - 6.20 "Calculating thermal conductivity"_howto_20 :b - 6.21 "Calculating viscosity"_howto_21 :b - 6.22 "Calculating a diffusion coefficient"_howto_22 :b - 6.23 "Using chunks to calculate system properties"_howto_23 :b - 6.24 "Setting parameters for pppm/disp"_howto_24 :b - 6.25 "Polarizable models"_howto_25 :b - 6.26 "Adiabatic core/shell model"_howto_26 :b - 6.27 "Drude induced dipoles"_howto_27 :ule,b -"Example problems"_Section_example.html :l -"Performance & scalability"_Section_perf.html :l -"Additional tools"_Section_tools.html :l -"Modifying & extending LAMMPS"_Section_modify.html :l - 10.1 "Atom styles"_mod_1 :ulb,b - 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b - 10.3 "Compute styles"_mod_3 :b - 10.4 "Dump styles"_mod_4 :b - 10.5 "Dump custom output options"_mod_5 :b - 10.6 "Fix styles"_mod_6 :b - 10.7 "Input script commands"_mod_7 :b - 10.8 "Kspace computations"_mod_8 :b - 10.9 "Minimization styles"_mod_9 :b - 10.10 "Pairwise potentials"_mod_10 :b - 10.11 "Region styles"_mod_11 :b - 10.12 "Body styles"_mod_12 :b - 10.13 "Thermodynamic output options"_mod_13 :b - 10.14 "Variable options"_mod_14 :b - 10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b -"Python interface"_Section_python.html :l - 11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b - 11.2 "Overview of using Python from a LAMMPS script"_py_2 :b - 11.3 "Building LAMMPS as a shared library"_py_3 :b - 11.4 "Installing the Python wrapper into Python"_py_4 :b - 11.5 "Extending Python with MPI to run in parallel"_py_5 :b - 11.6 "Testing the Python-LAMMPS interface"_py_6 :b - 11.7 "Using LAMMPS from Python"_py_7 :b - 11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b -"Errors"_Section_errors.html :l - 12.1 "Common problems"_err_1 :ulb,b - 12.2 "Reporting bugs"_err_2 :b - 12.3 "Error & warning messages"_err_3 :ule,b -"Future and history"_Section_history.html :l - 13.1 "Coming attractions"_hist_1 :ulb,b - 13.2 "Past versions"_hist_2 :ule,b +"Commands"_Commands.html :l +"Optional packages"_Packages.html :l +"Accelerate performance"_Speed.html :l +"How-to discussions"_Howto.html :l +"Example scripts"_Examples.html :l +"Auxiliary tools"_Tools.html :l +"Modify & extend LAMMPS"_Modify.html :l +"Use Python with LAMMPS"_Python.html :l +"Errors"_Errors.html :l :ole -:link(intro_1,Section_intro.html#intro_1) -:link(intro_2,Section_intro.html#intro_2) -:link(intro_3,Section_intro.html#intro_3) -:link(intro_4,Section_intro.html#intro_4) -:link(intro_5,Section_intro.html#intro_5) - :link(start_1,Section_start.html#start_1) :link(start_2,Section_start.html#start_2) :link(start_3,Section_start.html#start_3) @@ -260,77 +136,6 @@ END_RST --> :link(start_7,Section_start.html#start_7) :link(start_8,Section_start.html#start_8) -:link(cmd_1,Section_commands.html#cmd_1) -:link(cmd_2,Section_commands.html#cmd_2) -:link(cmd_3,Section_commands.html#cmd_3) -:link(cmd_4,Section_commands.html#cmd_4) -:link(cmd_5,Section_commands.html#cmd_5) - -:link(pkg_1,Section_packages.html#pkg_1) -:link(pkg_2,Section_packages.html#pkg_2) - -:link(acc_1,Section_accelerate.html#acc_1) -:link(acc_2,Section_accelerate.html#acc_2) -:link(acc_3,Section_accelerate.html#acc_3) -:link(acc_4,Section_accelerate.html#acc_4) - -:link(howto_1,Section_howto.html#howto_1) -:link(howto_2,Section_howto.html#howto_2) -:link(howto_3,Section_howto.html#howto_3) -:link(howto_4,Section_howto.html#howto_4) -:link(howto_5,Section_howto.html#howto_5) -:link(howto_6,Section_howto.html#howto_6) -:link(howto_7,Section_howto.html#howto_7) -:link(howto_8,Section_howto.html#howto_8) -:link(howto_9,Section_howto.html#howto_9) -:link(howto_10,Section_howto.html#howto_10) -:link(howto_11,Section_howto.html#howto_11) -:link(howto_12,Section_howto.html#howto_12) -:link(howto_13,Section_howto.html#howto_13) -:link(howto_14,Section_howto.html#howto_14) -:link(howto_15,Section_howto.html#howto_15) -:link(howto_16,Section_howto.html#howto_16) -:link(howto_17,Section_howto.html#howto_17) -:link(howto_18,Section_howto.html#howto_18) -:link(howto_19,Section_howto.html#howto_19) -:link(howto_20,Section_howto.html#howto_20) -:link(howto_21,Section_howto.html#howto_21) -:link(howto_22,Section_howto.html#howto_22) -:link(howto_23,Section_howto.html#howto_23) -:link(howto_24,Section_howto.html#howto_24) -:link(howto_25,Section_howto.html#howto_25) -:link(howto_26,Section_howto.html#howto_26) -:link(howto_27,Section_howto.html#howto_27) - -:link(mod_1,Section_modify.html#mod_1) -:link(mod_2,Section_modify.html#mod_2) -:link(mod_3,Section_modify.html#mod_3) -:link(mod_4,Section_modify.html#mod_4) -:link(mod_5,Section_modify.html#mod_5) -:link(mod_6,Section_modify.html#mod_6) -:link(mod_7,Section_modify.html#mod_7) -:link(mod_8,Section_modify.html#mod_8) -:link(mod_9,Section_modify.html#mod_9) -:link(mod_10,Section_modify.html#mod_10) -:link(mod_11,Section_modify.html#mod_11) -:link(mod_12,Section_modify.html#mod_12) -:link(mod_13,Section_modify.html#mod_13) -:link(mod_14,Section_modify.html#mod_14) -:link(mod_15,Section_modify.html#mod_15) - -:link(py_1,Section_python.html#py_1) -:link(py_2,Section_python.html#py_2) -:link(py_3,Section_python.html#py_3) -:link(py_4,Section_python.html#py_4) -:link(py_5,Section_python.html#py_5) -:link(py_6,Section_python.html#py_6) - -:link(err_1,Section_errors.html#err_1) -:link(err_2,Section_errors.html#err_2) -:link(err_3,Section_errors.html#err_3) - -:link(hist_1,Section_history.html#hist_1) -:link(hist_2,Section_history.html#hist_2) diff --git a/doc/src/Manual_version.txt b/doc/src/Manual_version.txt new file mode 100644 index 0000000000000000000000000000000000000000..8583eabf865afc3b9b9aeaae76d3acb34028fc85 --- /dev/null +++ b/doc/src/Manual_version.txt @@ -0,0 +1,33 @@ +"Higher level section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +What does a LAMMPS version mean: :h3 + +The LAMMPS "version" is the date when it was released, such as 1 May +2014. LAMMPS is updated continuously. Whenever we fix a bug or add a +feature, we release it in the next {patch} release, which are +typically made every couple of weeks. Info on patch releases are on +"this website page"_http://lammps.sandia.gov/bug.html. Every few +months, the latest patch release is subjected to more thorough testing +and labeled as a {stable} version. + +Each version of LAMMPS contains all the features and bug-fixes up to +and including its version date. + +The version date is printed to the screen and logfile every time you +run LAMMPS. It is also in the file src/version.h and in the LAMMPS +directory name created when you unpack a tarball. And it is on the +first page of the "manual"_Manual.html. + +If you browse the HTML doc pages on the LAMMPS WWW site, they always +describe the most current patch release of LAMMPS. :ulb,l + +If you browse the HTML doc pages included in your tarball, they +describe the version you have, which may be older. :l,ule + diff --git a/doc/src/Modify.txt b/doc/src/Modify.txt new file mode 100644 index 0000000000000000000000000000000000000000..f828bd5d74db99ceb5c0dfffd93062d93228ef4c --- /dev/null +++ b/doc/src/Modify.txt @@ -0,0 +1,76 @@ +"Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Python.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Modify & extend LAMMPS :h2 + +LAMMPS is designed in a modular fashion so as to be easy to modify and +extend with new functionality. In fact, about 95% of its source code +is add-on files. These doc pages give basic instructions on how to do +this. + +If you add a new feature to LAMMPS and think it will be of interest to +general users, we encourage you to submit it for inclusion in LAMMPS +as a pull request on our "GitHub +site"_https://github.com/lammps/lammps, after reading the "Modify +contribute"_Modify_contribute.html doc page. + + + + + +"Overview"_Modify_overview.html +"Submitting new features for inclusion in LAMMPS"_Modify_contribute.html :all(b) + +"Atom styles"_Modify_atom.html +"Pair styles"_Modify_pair.html +"Bond, angle, dihedral, improper styles"_Modify_bond.html +"Compute styles"_Modify_compute.html +"Fix styles"_Modify_fix.html +"Input script command styles"_Modify_command.html :all(b) + +"Dump styles"_Modify_dump.html +"Kspace styles"_Modify_kspace.html +"Minimization styles"_Modify_min.html +"Region styles"_Modify_region.html +"Body styles"_Modify_body.html :all(b) + +"Thermodynamic output options"_Modify_thermo.html +"Variable options"_Modify_variable.html :all(b) + + diff --git a/doc/src/Modify_atom.txt b/doc/src/Modify_atom.txt new file mode 100644 index 0000000000000000000000000000000000000000..60c7dccb29a38e4c628752f87c58a84532eb7c24 --- /dev/null +++ b/doc/src/Modify_atom.txt @@ -0,0 +1,90 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Atom styles :h3 + +Classes that define an "atom style"_atom_style.html are derived from +the AtomVec class and managed by the Atom class. The atom style +determines what attributes are associated with an atom. A new atom +style can be created if one of the existing atom styles does not +define all the attributes you need to store and communicate with +atoms. + +Atom_vec_atomic.cpp is a simple example of an atom style. + +Here is a brief description of methods you define in your new derived +class. See atom_vec.h for details. + +init: one time setup (optional) +grow: re-allocate atom arrays to longer lengths (required) +grow_reset: make array pointers in Atom and AtomVec classes consistent (required) +copy: copy info for one atom to another atom's array locations (required) +pack_comm: store an atom's info in a buffer communicated every timestep (required) +pack_comm_vel: add velocity info to communication buffer (required) +pack_comm_hybrid: store extra info unique to this atom style (optional) +unpack_comm: retrieve an atom's info from the buffer (required) +unpack_comm_vel: also retrieve velocity info (required) +unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) +pack_reverse: store an atom's info in a buffer communicating partial forces (required) +pack_reverse_hybrid: store extra info unique to this atom style (optional) +unpack_reverse: retrieve an atom's info from the buffer (required) +unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) +pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) +pack_border_vel: add velocity info to buffer (required) +pack_border_hybrid: store extra info unique to this atom style (optional) +unpack_border: retrieve an atom's info from the buffer (required) +unpack_border_vel: also retrieve velocity info (required) +unpack_border_hybrid: retrieve extra info unique to this atom style (optional) +pack_exchange: store all an atom's info to migrate to another processor (required) +unpack_exchange: retrieve an atom's info from the buffer (required) +size_restart: number of restart quantities associated with proc's atoms (required) +pack_restart: pack atom quantities into a buffer (required) +unpack_restart: unpack atom quantities from a buffer (required) +create_atom: create an individual atom of this style (required) +data_atom: parse an atom line from the data file (required) +data_atom_hybrid: parse additional atom info unique to this atom style (optional) +data_vel: parse one line of velocity information from data file (optional) +data_vel_hybrid: parse additional velocity data unique to this atom style (optional) +memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) + +The constructor of the derived class sets values for several variables +that you must set when defining a new atom style, which are documented +in atom_vec.h. New atom arrays are defined in atom.cpp. Search for +the word "customize" and you will find locations you will need to +modify. + +NOTE: It is possible to add some attributes, such as a molecule ID, to +atom styles that do not have them via the "fix +property/atom"_fix_property_atom.html command. This command also +allows new custom attributes consisting of extra integer or +floating-point values to be added to atoms. See the "fix +property/atom"_fix_property_atom.html doc page for examples of cases +where this is useful and details on how to initialize, access, and +output the custom values. + +New "pair styles"_pair_style.html, "fixes"_fix.html, or +"computes"_compute.html can be added to LAMMPS, as discussed below. +The code for these classes can use the per-atom properties defined by +fix property/atom. The Atom class has a find_custom() method that is +useful in this context: + +int index = atom->find_custom(char *name, int &flag); :pre + +The "name" of a custom attribute, as specified in the "fix +property/atom"_fix_property_atom.html command, is checked to verify +that it exists and its index is returned. The method also sets flag = +0/1 depending on whether it is an integer or floating-point attribute. +The vector of values associated with the attribute can then be +accessed using the returned index as + +int *ivector = atom->ivector\[index\]; +double *dvector = atom->dvector\[index\]; :pre + +Ivector or dvector are vectors of length Nlocal = # of owned atoms, +which store the attributes of individual atoms. diff --git a/doc/src/Modify_body.txt b/doc/src/Modify_body.txt new file mode 100644 index 0000000000000000000000000000000000000000..0114ae10c885c2cbd78cd1d2067ad2751ac997fd --- /dev/null +++ b/doc/src/Modify_body.txt @@ -0,0 +1,34 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Body styles :h3 + +Classes that define body particles are derived from the Body class. +Body particles can represent complex entities, such as surface meshes +of discrete points, collections of sub-particles, deformable objects, +etc. + +See the "Howto body"_Howto_body.html doc page for an overview of using +body particles and the various body styles LAMMPS supports. New +styles can be created to add new kinds of body particles to LAMMPS. + +Body_nparticle.cpp is an example of a body particle that is treated as +a rigid body containing N sub-particles. + +Here is a brief description of methods you define in your new derived +class. See body.h for details. + +data_body: process a line from the Bodies section of a data file +noutrow: number of sub-particles output is generated for +noutcol: number of values per-sub-particle output is generated for +output: output values for the Mth sub-particle +pack_comm_body: body attributes to communicate every timestep +unpack_comm_body: unpacking of those attributes +pack_border_body: body attributes to communicate when reneighboring is done +unpack_border_body: unpacking of those attributes :tb(s=:) diff --git a/doc/src/Modify_bond.txt b/doc/src/Modify_bond.txt new file mode 100644 index 0000000000000000000000000000000000000000..7ceea3f910121c4191b27cd0aaa8256e421281e3 --- /dev/null +++ b/doc/src/Modify_bond.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Bond, angle, dihedral, improper styles :h3 + +Classes that compute molecular interactions are derived from the Bond, +Angle, Dihedral, and Improper classes. New styles can be created to +add new potentials to LAMMPS. + +Bond_harmonic.cpp is the simplest example of a bond style. Ditto for +the harmonic forms of the angle, dihedral, and improper style +commands. + +Here is a brief description of common methods you define in your +new derived class. See bond.h, angle.h, dihedral.h, and improper.h +for details and specific additional methods. + +init: check if all coefficients are set, calls {init_style} (optional) +init_style: check if style specific conditions are met (optional) +compute: compute the molecular interactions (required) +settings: apply global settings for all types (optional) +coeff: set coefficients for one type (required) +equilibrium_distance: length of bond, used by SHAKE (required, bond only) +equilibrium_angle: opening of angle, used by SHAKE (required, angle only) +write & read_restart: writes/reads coeffs to restart files (required) +single: force and energy of a single bond or angle (required, bond or angle only) +memory_usage: tally memory allocated by the style (optional) :tb(s=:) diff --git a/doc/src/Modify_command.txt b/doc/src/Modify_command.txt new file mode 100644 index 0000000000000000000000000000000000000000..4576f6c8067684ca95b94b7ae022ec0df6166f76 --- /dev/null +++ b/doc/src/Modify_command.txt @@ -0,0 +1,27 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Input script command style :h3 + +New commands can be added to LAMMPS input scripts by adding new +classes that have a "command" method. For example, the create_atoms, +read_data, velocity, and run commands are all implemented in this +fashion. When such a command is encountered in the LAMMPS input +script, LAMMPS simply creates a class with the corresponding name, +invokes the "command" method of the class, and passes it the arguments +from the input script. The command method can perform whatever +operations it wishes on LAMMPS data structures. + +The single method your new class must define is as follows: + +command: operations performed by the new command :tb(s=:) + +Of course, the new class can define other methods and variables as +needed. + diff --git a/doc/src/Modify_compute.txt b/doc/src/Modify_compute.txt new file mode 100644 index 0000000000000000000000000000000000000000..2f6481dbd5be934fd8dcfa7f1abed50bd57cc3c3 --- /dev/null +++ b/doc/src/Modify_compute.txt @@ -0,0 +1,49 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Compute styles :h3 + +Classes that compute scalar and vector quantities like temperature +and the pressure tensor, as well as classes that compute per-atom +quantities like kinetic energy and the centro-symmetry parameter +are derived from the Compute class. New styles can be created +to add new calculations to LAMMPS. + +Compute_temp.cpp is a simple example of computing a scalar +temperature. Compute_ke_atom.cpp is a simple example of computing +per-atom kinetic energy. + +Here is a brief description of methods you define in your new derived +class. See compute.h for details. + +init: perform one time setup (required) +init_list: neighbor list setup, if needed (optional) +compute_scalar: compute a scalar quantity (optional) +compute_vector: compute a vector of quantities (optional) +compute_peratom: compute one or more quantities per atom (optional) +compute_local: compute one or more quantities per processor (optional) +pack_comm: pack a buffer with items to communicate (optional) +unpack_comm: unpack the buffer (optional) +pack_reverse: pack a buffer with items to reverse communicate (optional) +unpack_reverse: unpack the buffer (optional) +remove_bias: remove velocity bias from one atom (optional) +remove_bias_all: remove velocity bias from all atoms in group (optional) +restore_bias: restore velocity bias for one atom after remove_bias (optional) +restore_bias_all: same as before, but for all atoms in group (optional) +pair_tally_callback: callback function for {tally}-style computes (optional). +memory_usage: tally memory usage (optional) :tb(s=:) + +Tally-style computes are a special case, as their computation is done +in two stages: the callback function is registered with the pair style +and then called from the Pair::ev_tally() function, which is called for +each pair after force and energy has been computed for this pair. Then +the tallied values are retrieved with the standard compute_scalar or +compute_vector or compute_peratom methods. The USER-TALLY package +provides {examples}_compute_tally.html for utilizing this mechanism. + diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt new file mode 100644 index 0000000000000000000000000000000000000000..ef9fe6a7174eed7d41a74908b49b21e8ecfa6f6d --- /dev/null +++ b/doc/src/Modify_contribute.txt @@ -0,0 +1,211 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Submitting new features for inclusion in LAMMPS :h3 + +We encourage users to submit new features or modifications for LAMMPS +to "the core developers"_http://lammps.sandia.gov/authors.html so they +can be added to the LAMMPS distribution. The preferred way to manage +and coordinate this is as of Fall 2016 via the LAMMPS project on +"GitHub"_https://github.com/lammps/lammps. An alternative is to +contact the LAMMPS developers or the indicated developer of a package +or feature directly and send in your contribution via e-mail. + +For any larger modifications or programming project, you are +encouraged to contact the LAMMPS developers ahead of time, in order to +discuss implementation strategies and coding guidelines, that will +make it easier to integrate your contribution and result in less work +for everybody involved. You are also encouraged to search through the +list of "open issues on +GitHub"_https://github.com/lammps/lammps/issues and submit a new issue +for a planned feature, so you would not duplicate the work of others +(and possibly get scooped by them) or have your work duplicated by +others. + +How quickly your contribution will be integrated depends largely on +how much effort it will cause to integrate and test it, how much it +requires changes to the core codebase, and of how much interest it is +to the larger LAMMPS community. Please see below for a checklist of +typical requirements. Once you have prepared everything, see the +"Howto github"_Howto_github.html doc page for instructions on how to +submit your changes or new files through a GitHub pull request. If you +prefer to submit patches or full files, you should first make certain, +that your code works correctly with the latest patch-level version of +LAMMPS and contains all bugfixes from it. Then create a gzipped tar +file of all changed or added files or a corresponding patch file using +'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip +compression, as this works well on all platforms. + +If the new features/files are broadly useful we may add them as core +files to LAMMPS or as part of a "standard +package"_Section_start.html#start_3. Else we will add them as a +user-contributed file or package. Examples of user packages are in +src sub-directories that start with USER. The USER-MISC package is +simply a collection of (mostly) unrelated single files, which is the +simplest way to have your contribution quickly added to the LAMMPS +distribution. You can see a list of the both standard and user +packages by typing "make package" in the LAMMPS src directory. + +Note that by providing us files to release, you are agreeing to make +them open-source, i.e. we can release them under the terms of the GPL, +used as a license for the rest of LAMMPS. See the "Open +source"_http://lammps.sandia.gov/open_source.html page on the LAMMPS +website for details. + +With user packages and files, all we are really providing (aside from +the fame and fortune that accompanies having your name in the source +code and on the "Authors page"_http://lammps.sandia.gov/authors.html +of the "LAMMPS WWW site"_lws), is a means for you to distribute your +work to the LAMMPS user community, and a mechanism for others to +easily try out your new feature. This may help you find bugs or make +contact with new collaborators. Note that you're also implicitly +agreeing to support your code which means answer questions, fix bugs, +and maintain it if LAMMPS changes in some way that breaks it (an +unusual event). + +NOTE: If you prefer to actively develop and support your add-on +feature yourself, then you may wish to make it available for download +from your own website, as a user package that LAMMPS users can add to +their copy of LAMMPS. See the "Offsite LAMMPS packages and +tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web +site for examples of groups that do this. We are happy to advertise +your package and web site from that page. Simply email the +"developers"_http://lammps.sandia.gov/authors.html with info about +your package and we will post it there. + +The previous sections of this doc page describe how to add new "style" +files of various kinds to LAMMPS. Packages are simply collections of +one or more new class files which are invoked as a new style within a +LAMMPS input script. If designed correctly, these additions typically +do not require changes to the main core of LAMMPS; they are simply +add-on files. If you think your new feature requires non-trivial +changes in core LAMMPS files, you'll need to "communicate with the +developers"_http://lammps.sandia.gov/authors.html, since we may or may +not want to make those changes. An example of a trivial change is +making a parent-class method "virtual" when you derive a new child +class from it. + +Here is a checklist of steps you need to follow to submit a single file +or user package for our consideration. Following these steps will save +both you and us time. See existing files in packages in the src dir for +examples. If you are uncertain, please ask. + +All source files you provide must compile with the most current +version of LAMMPS with multiple configurations. In particular you +need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG +set in addition to the default -DLAMMPS_SMALLBIG setting. Your code +will need to work correctly in serial and in parallel using MPI. :ulb,l + +For consistency with the rest of LAMMPS and especially, if you want +your contribution(s) to be added to main LAMMPS code or one of its +standard packages, it needs to be written in a style compatible with +other LAMMPS source files. This means: 2-character indentation per +level, [no tabs], no lines over 80 characters. I/O is done via +the C-style stdio library, class header files should not import any +system headers outside , STL containers should be avoided +in headers, and forward declarations used where possible or needed. +All added code should be placed into the LAMMPS_NS namespace or a +sub-namespace; global or static variables should be avoided, as they +conflict with the modular nature of LAMMPS and the C++ class structure. +Header files must [not] import namespaces with {using}. +This all is so the developers can more easily understand, integrate, +and maintain your contribution and reduce conflicts with other parts +of LAMMPS. This basically means that the code accesses data +structures, performs its operations, and is formatted similar to other +LAMMPS source files, including the use of the error class for error +and warning messages. :l + +If you want your contribution to be added as a user-contributed +feature, and it's a single file (actually a *.cpp and *.h file) it can +rapidly be added to the USER-MISC directory. Send us the one-line +entry to add to the USER-MISC/README file in that dir, along with the +2 source files. You can do this multiple times if you wish to +contribute several individual features. :l + +If you want your contribution to be added as a user-contribution and +it is several related features, it is probably best to make it a user +package directory with a name like USER-FOO. In addition to your new +files, the directory should contain a README text file. The README +should contain your name and contact information and a brief +description of what your new package does. If your files depend on +other LAMMPS style files also being installed (e.g. because your file +is a derived class from the other LAMMPS class), then an Install.sh +file is also needed to check for those dependencies. See other README +and Install.sh files in other USER directories as examples. Send us a +tarball of this USER-FOO directory. :l + +Your new source files need to have the LAMMPS copyright, GPL notice, +and your name and email address at the top, like other +user-contributed LAMMPS source files. They need to create a class +that is inside the LAMMPS namespace. If the file is for one of the + +USER packages, including USER-MISC, then we are not as picky about the +coding style (see above). I.e. the files do not need to be in the +same stylistic format and syntax as other LAMMPS files, though that +would be nice for developers as well as users who try to read your +code. :l + +You [must] also create a [documentation] file for each new command or +style you are adding to LAMMPS. For simplicity and convenience, the +documentation of groups of closely related commands or styles may be +combined into a single file. This will be one file for a single-file +feature. For a package, it might be several files. These are simple +text files with a specific markup language, that are then auto-converted +to HTML and PDF. The tools for this conversion are included in the +source distribution, and the translation can be as simple as doing +"make html pdf" in the doc folder. +Thus the documentation source files must be in the same format and +style as other *.txt files in the lammps/doc/src directory for similar +commands and styles; use one or more of them as a starting point. +A description of the markup can also be found in +lammps/doc/utils/txt2html/README.html +As appropriate, the text files can include links to equations +(see doc/Eqs/*.tex for examples, we auto-create the associated JPG +files), or figures (see doc/JPG for examples), or even additional PDF +files with further details (see doc/PDF for examples). The doc page +should also include literature citations as appropriate; see the +bottom of doc/fix_nh.txt for examples and the earlier part of the same +file for how to format the cite itself. The "Restrictions" section of +the doc page should indicate that your command is only available if +LAMMPS is built with the appropriate USER-MISC or USER-FOO package. +See other user package doc files for examples of how to do this. The +prerequisite for building the HTML format files are Python 3.x and +virtualenv, the requirement for generating the PDF format manual +is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least +"make html" and carefully inspect and proofread the resulting HTML format +doc page before submitting your code. :l + +For a new package (or even a single command) you should include one or +more example scripts demonstrating its use. These should run in no +more than a couple minutes, even on a single processor, and not require +large data files as input. See directories under examples/USER for +examples of input scripts other users provided for their packages. +These example inputs are also required for validating memory accesses +and testing for memory leaks with valgrind :l + +If there is a paper of yours describing your feature (either the +algorithm/science behind the feature itself, or its initial usage, or +its implementation in LAMMPS), you can add the citation to the *.cpp +source file. See src/USER-EFF/atom_vec_electron.cpp for an example. +A LaTeX citation is stored in a variable at the top of the file and a +single line of code that references the variable is added to the +constructor of the class. Whenever a user invokes your feature from +their input script, this will cause LAMMPS to output the citation to a +log.cite file and prompt the user to examine the file. Note that you +should only use this for a paper you or your group authored. +E.g. adding a cite in the code for a paper by Nose and Hoover if you +write a fix that implements their integrator is not the intended +usage. That kind of citation should just be in the doc page you +provide. :l +:ule + +Finally, as a general rule-of-thumb, the more clear and +self-explanatory you make your documentation and README files, and the +easier you make it for people to get started, e.g. by providing example +scripts, the more likely it is that users will try out your new feature. diff --git a/doc/src/Modify_dump.txt b/doc/src/Modify_dump.txt new file mode 100644 index 0000000000000000000000000000000000000000..cfe96f5d3d0bc25402b73beef55261f8e7679eb1 --- /dev/null +++ b/doc/src/Modify_dump.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Dump styles :h3 + +Classes that dump per-atom info to files are derived from the Dump +class. To dump new quantities or in a new format, a new derived dump +class can be added, but it is typically simpler to modify the +DumpCustom class contained in the dump_custom.cpp file. + +Dump_atom.cpp is a simple example of a derived dump class. + +Here is a brief description of methods you define in your new derived +class. See dump.h for details. + +write_header: write the header section of a snapshot of atoms +count: count the number of lines a processor will output +pack: pack a proc's output data into a buffer +write_data: write a proc's data to a file :tb(s=:) + +See the "dump"_dump.html command and its {custom} style for a list of +keywords for atom information that can already be dumped by +DumpCustom. It includes options to dump per-atom info from Compute +classes, so adding a new derived Compute class is one way to calculate +new quantities to dump. + +Note that new keywords for atom properties are not typically +added to the "dump custom"_dump.html command. Instead they are added +to the "compute property/atom"_compute_property_atom.html command. diff --git a/doc/src/Modify_fix.txt b/doc/src/Modify_fix.txt new file mode 100644 index 0000000000000000000000000000000000000000..b095ebc4b5fa8b549fbfb411c2558e5c6bb14c4d --- /dev/null +++ b/doc/src/Modify_fix.txt @@ -0,0 +1,107 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Fix styles :h3 + +In LAMMPS, a "fix" is any operation that is computed during +timestepping that alters some property of the system. Essentially +everything that happens during a simulation besides force computation, +neighbor list construction, and output, is a "fix". This includes +time integration (update of coordinates and velocities), force +constraints or boundary conditions (SHAKE or walls), and diagnostics +(compute a diffusion coefficient). New styles can be created to add +new options to LAMMPS. + +Fix_setforce.cpp is a simple example of setting forces on atoms to +prescribed values. There are dozens of fix options already in LAMMPS; +choose one as a template that is similar to what you want to +implement. + +Here is a brief description of methods you can define in your new +derived class. See fix.h for details. + +setmask: determines when the fix is called during the timestep (required) +init: initialization before a run (optional) +setup_pre_exchange: called before atom exchange in setup (optional) +setup_pre_force: called before force computation in setup (optional) +setup: called immediately before the 1st timestep and after forces are computed (optional) +min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) +min_setup: like setup, but for minimizations instead of MD runs (optional) +initial_integrate: called at very beginning of each timestep (optional) +pre_exchange: called before atom exchange on re-neighboring steps (optional) +pre_neighbor: called before neighbor list build (optional) +pre_force: called before pair & molecular forces are computed (optional) +post_force: called after pair & molecular forces are computed and communicated (optional) +final_integrate: called at end of each timestep (optional) +end_of_step: called at very end of timestep (optional) +write_restart: dumps fix info to restart file (optional) +restart: uses info from restart file to re-initialize the fix (optional) +grow_arrays: allocate memory for atom-based arrays used by fix (optional) +copy_arrays: copy atom info when an atom migrates to a new processor (optional) +pack_exchange: store atom's data in a buffer (optional) +unpack_exchange: retrieve atom's data from a buffer (optional) +pack_restart: store atom's data for writing to restart file (optional) +unpack_restart: retrieve atom's data from a restart file buffer (optional) +size_restart: size of atom's data (optional) +maxsize_restart: max size of atom's data (optional) +setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) +initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) +post_integrate_respa: called after the first half integration step is done in rRESPA (optional) +pre_force_respa: same as pre_force, but for rRESPA (optional) +post_force_respa: same as post_force, but for rRESPA (optional) +final_integrate_respa: same as final_integrate, but for rRESPA (optional) +min_pre_force: called after pair & molecular forces are computed in minimizer (optional) +min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) +min_store: store extra data for linesearch based minimization on a LIFO stack (optional) +min_pushstore: push the minimization LIFO stack one element down (optional) +min_popstore: pop the minimization LIFO stack one element up (optional) +min_clearstore: clear minimization LIFO stack (optional) +min_step: reset or move forward on line search minimization (optional) +min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) +max_alpha: report maximum allowed step size during linesearch minimization (optional) +pack_comm: pack a buffer to communicate a per-atom quantity (optional) +unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) +pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) +unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) +dof: report number of degrees of freedom {removed} by this fix during MD (optional) +compute_scalar: return a global scalar property that the fix computes (optional) +compute_vector: return a component of a vector property that the fix computes (optional) +compute_array: return a component of an array property that the fix computes (optional) +deform: called when the box size is changed (optional) +reset_target: called when a change of the target temperature is requested during a run (optional) +reset_dt: is called when a change of the time step is requested during a run (optional) +modify_param: called when a fix_modify request is executed (optional) +memory_usage: report memory used by fix (optional) +thermo: compute quantities for thermodynamic output (optional) :tb(s=:) + +Typically, only a small fraction of these methods are defined for a +particular fix. Setmask is mandatory, as it determines when the fix +will be invoked during the timestep. Fixes that perform time +integration ({nve}, {nvt}, {npt}) implement initial_integrate() and +final_integrate() to perform velocity Verlet updates. Fixes that +constrain forces implement post_force(). + +Fixes that perform diagnostics typically implement end_of_step(). For +an end_of_step fix, one of your fix arguments must be the variable +"nevery" which is used to determine when to call the fix and you must +set this variable in the constructor of your fix. By convention, this +is the first argument the fix defines (after the ID, group-ID, style). + +If the fix needs to store information for each atom that persists from +timestep to timestep, it can manage that memory and migrate the info +with the atoms as they move from processors to processor by +implementing the grow_arrays, copy_arrays, pack_exchange, and +unpack_exchange methods. Similarly, the pack_restart and +unpack_restart methods can be implemented to store information about +the fix in restart files. If you wish an integrator or force +constraint fix to work with rRESPA (see the "run_style"_run_style.html +command), the initial_integrate, post_force_integrate, and +final_integrate_respa methods can be implemented. The thermo method +enables a fix to contribute values to thermodynamic output, as printed +quantities and/or to be summed to the potential energy of the system. diff --git a/doc/src/Modify_kspace.txt b/doc/src/Modify_kspace.txt new file mode 100644 index 0000000000000000000000000000000000000000..d5f018411d8d280d679b7a7940403b1658a20726 --- /dev/null +++ b/doc/src/Modify_kspace.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Kspace styles :h3 + +Classes that compute long-range Coulombic interactions via K-space +representations (Ewald, PPPM) are derived from the KSpace class. New +styles can be created to add new K-space options to LAMMPS. + +Ewald.cpp is an example of computing K-space interactions. + +Here is a brief description of methods you define in your new derived +class. See kspace.h for details. + +init: initialize the calculation before a run +setup: computation before the 1st timestep of a run +compute: every-timestep computation +memory_usage: tally of memory usage :tb(s=:) + diff --git a/doc/src/Modify_min.txt b/doc/src/Modify_min.txt new file mode 100644 index 0000000000000000000000000000000000000000..8252a576f3b01b7d58461a5bf200c0ddc1405c19 --- /dev/null +++ b/doc/src/Modify_min.txt @@ -0,0 +1,23 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Minimization styles :h3 + +Classes that perform energy minimization derived from the Min class. +New styles can be created to add new minimization algorithms to +LAMMPS. + +Min_cg.cpp is an example of conjugate gradient minimization. + +Here is a brief description of methods you define in your new derived +class. See min.h for details. + +init: initialize the minimization before a run +run: perform the minimization +memory_usage: tally of memory usage :tb(s=:) diff --git a/doc/src/Modify_overview.txt b/doc/src/Modify_overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..cf94b40281417805515700d697dc84cbd476fc38 --- /dev/null +++ b/doc/src/Modify_overview.txt @@ -0,0 +1,101 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Overview :h3 + +The best way to add a new feature to LAMMPS is to find a similar +featureand look at the corresponding source and header files to figure +out what it does. You will need some knowledge of C++ to be able to +understand the hi-level structure of LAMMPS and its class +organization, but functions (class methods) that do actual +computations are written in vanilla C-style code and operate on simple +C-style data structures (vectors and arrays). + +Most of the new features described on the "Modify"_Modify.html doc +page require you to write a new C++ derived class (except for +exceptions described below, where you can make small edits to existing +files). Creating a new class requires 2 files, a source code file +(*.cpp) and a header file (*.h). The derived class must provide +certain methods to work as a new option. Depending on how different +your new feature is compared to existing features, you can either +derive from the base class itself, or from a derived class that +already exists. Enabling LAMMPS to invoke the new class is as simple +as putting the two source files in the src dir and re-building LAMMPS. + +The advantage of C++ and its object-orientation is that all the code +and variables needed to define the new feature are in the 2 files you +write, and thus shouldn't make the rest of LAMMPS more complex or +cause side-effect bugs. + +Here is a concrete example. Suppose you write 2 files pair_foo.cpp +and pair_foo.h that define a new class PairFoo that computes pairwise +potentials described in the classic 1997 "paper"_#Foo by Foo, et al. +If you wish to invoke those potentials in a LAMMPS input script with a +command like + +pair_style foo 0.1 3.5 :pre + +then your pair_foo.h file should be structured as follows: + +#ifdef PAIR_CLASS +PairStyle(foo,PairFoo) +#else +... +(class definition for PairFoo) +... +#endif :pre + +where "foo" is the style keyword in the pair_style command, and +PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h +files. + +When you re-build LAMMPS, your new pairwise potential becomes part of +the executable and can be invoked with a pair_style command like the +example above. Arguments like 0.1 and 3.5 can be defined and +processed by your new class. + +As illustrated by this pairwise example, many kinds of options are +referred to in the LAMMPS documentation as the "style" of a particular +command. + +The "Modify page"_Modify.html lists all the common styles in LAMMPS, +and discusses the header file for the base class that these styles are +derived from. Public variables in that file are ones used and set by +the derived classes which are also used by the base class. Sometimes +they are also used by the rest of LAMMPS. Virtual functions in the +base class header file which are set = 0 are ones you must define in +your new derived class to give it the functionality LAMMPS expects. +Virtual functions that are not set to 0 are functions you can +optionally define. + +Additionally, new output options can be added directly to the +thermo.cpp, dump_custom.cpp, and variable.cpp files. These are also +listed on the "Modify page"_Modify.html. + +Here are additional guidelines for modifying LAMMPS and adding new +functionality: + +Think about whether what you want to do would be better as a pre- or +post-processing step. Many computations are more easily and more +quickly done that way. :ulb,l + +Don't do anything within the timestepping of a run that isn't +parallel. E.g. don't accumulate a bunch of data on a single processor +and analyze it. You run the risk of seriously degrading the parallel +efficiency. :l + +If your new feature reads arguments or writes output, make sure you +follow the unit conventions discussed by the "units"_units.html +command. :l +:ule + +:line + +:link(Foo) +[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt new file mode 100644 index 0000000000000000000000000000000000000000..0ebf2daa30baab30e377cb5df9cae40d5e0f5a36 --- /dev/null +++ b/doc/src/Modify_pair.txt @@ -0,0 +1,33 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Pair styles :h3 + +Classes that compute pairwise interactions are derived from the Pair +class. In LAMMPS, pairwise calculation include manybody potentials +such as EAM or Tersoff where particles interact without a static bond +topology. New styles can be created to add new pair potentials to +LAMMPS. + +Pair_lj_cut.cpp is a simple example of a Pair class, though it +includes some optional methods to enable its use with rRESPA. + +Here is a brief description of the class methods in pair.h: + +compute: workhorse routine that computes pairwise interactions +settings: reads the input script line with arguments you define +coeff: set coefficients for one i,j type pair +init_one: perform initialization for one i,j type pair +init_style: initialization specific to this pair style +write & read_restart: write/read i,j pair coeffs to restart files +write & read_restart_settings: write/read global settings to restart files +single: force and energy of a single pairwise interaction between 2 atoms +compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) + +The inner/middle/outer routines are optional. diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt new file mode 100644 index 0000000000000000000000000000000000000000..cdf192323ac50a8f5d771a4ea80822ec2bc6d3bf --- /dev/null +++ b/doc/src/Modify_region.txt @@ -0,0 +1,25 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Region styles :h3 + +Classes that define geometric regions are derived from the Region +class. Regions are used elsewhere in LAMMPS to group atoms, delete +atoms to create a void, insert atoms in a specified region, etc. New +styles can be created to add new region shapes to LAMMPS. + +Region_sphere.cpp is an example of a spherical region. + +Here is a brief description of methods you define in your new derived +class. See region.h for details. + +inside: determine whether a point is in the region +surface_interior: determine if a point is within a cutoff distance inside of surc +surface_exterior: determine if a point is within a cutoff distance outside of surf +shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/src/Modify_thermo.txt b/doc/src/Modify_thermo.txt new file mode 100644 index 0000000000000000000000000000000000000000..1772bae87a185846f941e0b540d8df2a904a1208 --- /dev/null +++ b/doc/src/Modify_thermo.txt @@ -0,0 +1,35 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Thermodynamic output options :h3 + +There is one class that computes and prints thermodynamic information +to the screen and log file; see the file thermo.cpp. + +There are two styles defined in thermo.cpp: "one" and "multi". There +is also a flexible "custom" style which allows the user to explicitly +list keywords for quantities to print when thermodynamic info is +output. See the "thermo_style"_thermo_style.html command for a list +of defined quantities. + +The thermo styles (one, multi, etc) are simply lists of keywords. +Adding a new style thus only requires defining a new list of keywords. +Search for the word "customize" with references to "thermo style" in +thermo.cpp to see the two locations where code will need to be added. + +New keywords can also be added to thermo.cpp to compute new quantities +for output. Search for the word "customize" with references to +"keyword" in thermo.cpp to see the several locations where code will +need to be added. + +Note that the "thermo_style custom"_thermo.html command already allows +for thermo output of quantities calculated by "fixes"_fix.html, +"computes"_compute.html, and "variables"_variable.html. Thus, it may +be simpler to compute what you wish via one of those constructs, than +by adding a new keyword to the thermo command. diff --git a/doc/src/Modify_variable.txt b/doc/src/Modify_variable.txt new file mode 100644 index 0000000000000000000000000000000000000000..b163272f3ebc225522467d08fe144b725dc22a27 --- /dev/null +++ b/doc/src/Modify_variable.txt @@ -0,0 +1,46 @@ +"Higher level section"_Modify.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Variable options :h3 + +There is one class that computes and stores "variable"_variable.html +information in LAMMPS; see the file variable.cpp. The value +associated with a variable can be periodically printed to the screen +via the "print"_print.html, "fix print"_fix_print.html, or +"thermo_style custom"_thermo_style.html commands. Variables of style +"equal" can compute complex equations that involve the following types +of arguments: + +thermo keywords = ke, vol, atoms, ... +other variables = v_a, v_myvar, ... +math functions = div(x,y), mult(x,y), add(x,y), ... +group functions = mass(group), xcm(group,x), ... +atom values = x\[123\], y\[3\], vx\[34\], ... +compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre + +Adding keywords for the "thermo_style custom"_thermo_style.html +command (which can then be accessed by variables) is discussed on the +"Modify thermo"_Modify_thermo.html doc page. + +Adding a new math function of one or two arguments can be done by +editing one section of the Variable::evaluate() method. Search for +the word "customize" to find the appropriate location. + +Adding a new group function can be done by editing one section of the +Variable::evaluate() method. Search for the word "customize" to find +the appropriate location. You may need to add a new method to the +Group class as well (see the group.cpp file). + +Accessing a new atom-based vector can be done by editing one section +of the Variable::evaluate() method. Search for the word "customize" +to find the appropriate location. + +Adding new "compute styles"_compute.html (whose calculated values can +then be accessed by variables) is discussed on the "Modify +compute"_Modify_compute.html doc page. diff --git a/doc/src/Packages.txt b/doc/src/Packages.txt new file mode 100644 index 0000000000000000000000000000000000000000..a7f45a99b7fa8f3d33e3c8d2e771f069139a0249 --- /dev/null +++ b/doc/src/Packages.txt @@ -0,0 +1,39 @@ +"Previous Section"_Commands.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Speed.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Optional packages :h2 + +This section gives an overview of the optional packages that extend +LAMMPS functionality. Packages are groups of files that enable a +specific set of features. For example, force fields for molecular +systems or rigid-body constraint are in packages. You can see the +list of all packages and "make" commands to manage them by typing +"make package" from within the src directory of the LAMMPS +distribution. "Section 2.3"_Section_start.html#start_3 gives general +info on how to install and un-install packages as part of the LAMMPS +build process. + + + + + +"Standard packages"_Packages_standard.html +"User packages"_Packages_user.html +"Details on each package"_Packages_details.html :ul + + diff --git a/doc/src/Section_packages.txt b/doc/src/Packages_details.txt similarity index 84% rename from doc/src/Section_packages.txt rename to doc/src/Packages_details.txt index e9387fe35fb41758089081bed202e832029c25df..eb92fe4dc4c27506cf41b250f7a3dce49e159941 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Packages_details.txt @@ -1,159 +1,96 @@ -"Previous Section"_Section_commands.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_accelerate.html :c +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -4. Packages :h2 - -This section gives an overview of the optional packages that extend -LAMMPS functionality with instructions on how to build LAMMPS with -each of them. Packages are groups of files that enable a specific set -of features. For example, force fields for molecular systems or -granular systems are in packages. You can see the list of all -packages and "make" commands to manage them by typing "make package" -from within the src directory of the LAMMPS distribution. "Section -2.3"_Section_start.html#start_3 gives general info on how to install -and un-install packages as part of the LAMMPS build process. - -There are two kinds of packages in LAMMPS, standard and user packages: - -"Table of standard packages"_#table_standard -"Table of user packages"_#table_user :ul - -Either of these kinds of packages may work as is, may require some -additional code compiled located in the lib folder, or may require -an external library to be downloaded, compiled, installed, and LAMMPS -configured to know about its location and additional compiler flags. -You can often do the build of the internal or external libraries -in one step by typing "make lib-name args='...'" from the src dir, -with appropriate arguments included in args='...'. If you just type -"make lib-name" you should see a help message about supported flags -and some examples. For more details about this, please study the -tables below and the sections about the individual packages. - -Standard packages are supported by the LAMMPS developers and are -written in a syntax and style consistent with the rest of LAMMPS. -This means the developers will answer questions about them, debug and -fix them if necessary, and keep them compatible with future changes to -LAMMPS. - -User packages have been contributed by users, and begin with the -"user" prefix. If they are a single command (single file), they are -typically in the user-misc package. User packages don't necessarily -meet the requirements of the standard packages. This means the -developers will try to keep things working and usually can answer -technical questions about compiling the package. If you have problems -using a feature provided in a user package, you may need to contact -the contributor directly to get help. Information on how to submit -additions you make to LAMMPS as single files or as a standard or user -package are given in "this section"_Section_modify.html#mod_15 of the -manual. - -Following the next two tables is a sub-section for each package. It -lists authors (if applicable) and summarizes the package contents. It -has specific instructions on how to install the package, including (if -necessary) downloading or building any extra library it requires. It -also gives links to documentation, example scripts, and -pictures/movies (if available) that illustrate use of the package. +:link(lc,Commands_all.html) + +:line + +Package details :h3 + +Here is a brief description of all the standard and user packages in +LAMMPS. It lists authors (if applicable) and summarizes the package +contents. It has specific instructions on how to install the package, +including, if necessary, info on how to download or build any extra +library it requires. It also gives links to documentation, example +scripts, and pictures/movies (if available) that illustrate use of the +package. NOTE: To see the complete list of commands a package adds to LAMMPS, -just look at the files in its src directory, e.g. "ls src/GRANULAR". -Files with names that start with fix, compute, atom, pair, bond, -angle, etc correspond to commands with the same style names. - -In these two tables, the "Example" column is a sub-directory in the -examples directory of the distribution which has an input script that -uses the package. E.g. "peptide" refers to the examples/peptide -directory; USER/atc refers to the examples/USER/atc directory. The -"Library" column indicates whether an extra library is needed to build -and use the package: - -dash = no library -sys = system library: you likely have it on your machine -int = internal library: provided with LAMMPS, but you may need to build it -ext = external library: you will need to download and install it on your machine :ul - -:line -:line - -[Standard packages] :link(table_standard),p - -Package, Description, Doc page, Example, Library -"ASPHERE"_#ASPHERE, aspherical particle models, "Section 6.6.14"_Section_howto.html#howto_14, ellipse, - -"BODY"_#BODY, body-style particles, "body"_body.html, body, - -"CLASS2"_#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - -"COLLOID"_#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - -"COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys -"CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - -"DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - -"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int -"GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, - -"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext -"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - -"LATTE"_#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext -"MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - -"MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - -"MEAM"_#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int -"MISC"_#MISC, miscellanous single-file commands, -, -, - -"MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - -"MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - -"MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext -"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - -"POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int -"PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys -"QEQ"_#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - -"REAX"_#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int -"REPLICA"_#REPLICA, multi-replica methods, "Section 6.6.5"_Section_howto.html#howto_5, tad, - -"RIGID"_#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - -"SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - -"SNAP"_#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - -"SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - -"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) - -[USER packages] :link(table_user),p - -Package, Description, Doc page, Example, Library -"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int -"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - -"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - -"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - -"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int -"USER-DIFFRACTION"_#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - -"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - -"USER-DRUDE"_#USER-DRUDE, Drude oscillators, "tutorial"_tutorial_drude.html, USER/drude, - -"USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - -"USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - -"USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext -"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - -"USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - -"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - -"USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - -"USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - -"USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - -"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - -"USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext -"USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext -"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - -"USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - -"USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext -"USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - -"USER-QUIP"_#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext -"USER-REAXC"_#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - -"USER-SMD"_#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext -"USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - -"USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - -"USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - -"USER-UEF"_#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - -"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) +you can examine the files in its src directory, e.g. "ls +src/GRANULAR". Files with names that start with fix, compute, atom, +pair, bond, angle, etc correspond to commands with the same style name +as contained in the file name. + +"ASPHERE"_#ASPHERE, +"BODY"_#BODY, +"CLASS2"_#CLASS2, +"COLLOID"_#COLLOID, +"COMPRESS"_#COMPRESS, +"CORESHELL"_#CORESHELL, +"DIPOLE"_#DIPOLE, +"GPU"_#GPU, +"GRANULAR"_#GRANULAR, +"KIM"_#KIM, +"KOKKOS"_#KOKKOS, +"KSPACE"_#KSPACE, +"LATTE"_#LATTE, +"MANYBODY"_#MANYBODY, +"MC"_#MC, +"MEAM"_#MEAM, +"MISC"_#MISC, +"MOLECULE"_#MOLECULE, +"MPIIO"_#MPIIO, +"MSCG"_#MSCG, +"OPT"_#OPT, +"PERI"_#PERI, +"POEMS"_#POEMS, +"PYTHON"_#PYTHON, +"QEQ"_#QEQ, +"REAX"_#REAX, +"REPLICA"_#REPLICA, +"RIGID"_#RIGID, +"SHOCK"_#SHOCK, +"SNAP"_#SNAP, +"SPIN"_#SPIN, +"SRD"_#SRD, +"VORONOI"_#VORONOI :tb(c=6,ea=c) + +"USER-ATC"_#USER-ATC, +"USER-AWPMD"_#USER-AWPMD, +"USER-BOCS"_#USER-BOCS, +"USER-CGDNA"_#USER-CGDNA, +"USER-CGSDK"_#USER-CGSDK, +"USER-COLVARS"_#USER-COLVARS, +"USER-DIFFRACTION"_#USER-DIFFRACTION, +"USER-DPD"_#USER-DPD, +"USER-DRUDE"_#USER-DRUDE, +"USER-EFF"_#USER-EFF, +"USER-FEP"_#USER-FEP, +"USER-H5MD"_#USER-H5MD, +"USER-INTEL"_#USER-INTEL, +"USER-LB"_#USER-LB, +"USER-MANIFOLD"_#USER-MANIFOLD, +"USER-MEAMC"_#USER-MEAMC, +"USER-MESO"_#USER-MESO, +"USER-MGPT"_#USER-MGPT, +"USER-MISC"_#USER-MISC, +"USER-MOFFF"_#USER-MOFFF, +"USER-MOLFILE"_#USER-MOLFILE, +"USER-NETCDF"_#USER-NETCDF, +"USER-OMP"_#USER-OMP, +"USER-PHONON"_#USER-PHONON, +"USER-QMMM"_#USER-QMMM, +"USER-QTB"_#USER-QTB, +"USER-QUIP"_#USER-QUIP, +"USER-REAXC"_#USER-REAXC, +"USER-SMD"_#USER-SMD, +"USER-SMTBQ"_#USER-SMTBQ, +"USER-SPH"_#USER-SPH, +"USER-TALLY"_#USER-TALLY, +"USER-UEF"_#USER-UEF, +"USER-VTK"_#USER-VTK :tb(c=6,ea=c) :line :line @@ -176,7 +113,7 @@ make machine :pre [Supporting info:] src/ASPHERE: filenames -> commands -"Section 6.14"_Section_howto.html#howto_14 +"Howto spherical"_Howto_spherical.html "pair_style gayberne"_pair_gayberne.html "pair_style resquared"_pair_resquared.html "doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf @@ -194,7 +131,8 @@ BODY package :link(BODY),h4 Body-style particles with internal structure. Computes, time-integration fixes, pair styles, as well as the body styles -themselves. See the "body"_body.html doc page for an overview. +themselves. See the "Howto body"_Howto_body.html doc page for an +overview. [Install or un-install:] @@ -207,10 +145,10 @@ make machine :pre [Supporting info:] src/BODY filenames -> commands -"body"_body.html +"Howto_body"_Howto_body.html "atom_style body"_atom_style.html "fix nve/body"_fix_nve_body.html -"pair_style body"_pair_body.html +"pair_style body/nparticle"_pair_body_nparticle.html examples/body :ul :line @@ -322,9 +260,9 @@ Compute and pair styles that implement the adiabatic core/shell model for polarizability. The pair styles augment Born, Buckingham, and Lennard-Jones styles with core/shell capabilities. The "compute temp/cs"_compute_temp_cs.html command calculates the temperature of a -system with core/shell particles. See "Section -6.26"_Section_howto.html#howto_26 for an overview of how to use this -package. +system with core/shell particles. See the "Howto +coreshell"_Howto_coreshell.html doc page for an overview of how to use +this package. [Author:] Hendrik Heenen (Technical U of Munich). @@ -339,8 +277,8 @@ make machine :pre [Supporting info:] src/CORESHELL: filenames -> commands -"Section 6.26"_Section_howto.html#howto_26 -"Section 6.25"_Section_howto.html#howto_25 +"Howto coreshell"_Howto_coreshell.html +"Howto polarizable"_Howto_polarizable.html "compute temp/cs"_compute_temp_cs.html "pair_style born/coul/long/cs"_pair_cs.html "pair_style buck/coul/long/cs"_pair_cs.html @@ -380,14 +318,14 @@ GPU package :link(GPU),h4 [Contents:] Dozens of pair styles and a version of the PPPM long-range Coulombic -solver optimized for GPUs. All such styles have a "gpu" as a -suffix in their style name. The GPU code can be compiled with either -CUDA or OpenCL, however the OpenCL variants are no longer actively -maintained and only the CUDA versions are regularly tested. -"Section 5.3.1"_accelerate_gpu.html gives details of what -hardware and GPU software is required on your system, -and details on how to build and use this package. Its styles can be -invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line +solver optimized for GPUs. All such styles have a "gpu" as a suffix +in their style name. The GPU code can be compiled with either CUDA or +OpenCL, however the OpenCL variants are no longer actively maintained +and only the CUDA versions are regularly tested. The "Speed +gpu"_Speed_gpu.html doc page gives details of what hardware and GPU +software is required on your system, and details on how to build and +use this package. Its styles can be invoked at run time via the "-sf +gpu" or "-suffix gpu" "command-line switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS package, which has GPU-enabled styles. @@ -453,12 +391,12 @@ GPU library. src/GPU: filenames -> commands src/GPU/README lib/gpu/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.1"_accelerate_gpu.html +"Speed packages"_Speed_packages.html +"Speed gpu"_Speed_gpu.html.html "Section 2.6 -sf gpu"_Section_start.html#start_6 "Section 2.6 -pk gpu"_Section_start.html#start_6 "package gpu"_package.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (g) +"Commands all"_Commands_all.html pages (pair,kspace) for styles followed by (g) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -482,7 +420,7 @@ make machine :pre [Supporting info:] src/GRANULAR: filenames -> commands -"Section 6.6"_Section_howto.html#howto_6, +"Howto granular"_Howto_granular.html "fix pour"_fix_pour.html "fix wall/gran"_fix_wall_gran.html "pair_style gran/hooke"_pair_gran.html @@ -549,8 +487,8 @@ See the list of all KIM models here: https://openkim.org/kim-items/models/by-model-drivers See the list of example KIM models included by default here: -https://openkim.org/kim-api in the "What is in the KIM API source -package?" section +https://openkim.org/kim-api on the "What is in the KIM API source +package?" page. You can then install/un-install the package and build LAMMPS in the usual manner: @@ -579,10 +517,10 @@ Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their -style name. "Section 5.3.3"_accelerate_kokkos.html gives details of -what hardware and software is required on your system, and how to -build and use this package. Its styles can be invoked at run time via -the "-sf kk" or "-suffix kk" "command-line +style name. The "Speed kokkos"_Speed_kokkos.html doc page gives +details of what hardware and software is required on your system, and +how to build and use this package. Its styles can be invoked at run +time via the "-sf kk" or "-suffix kk" "command-line switches"_Section_start.html#start_6. Also see the "GPU"_#GPU, "OPT"_#OPT, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which have styles optimized for CPUs, KNLs, and GPUs. @@ -649,13 +587,13 @@ make machine :pre src/KOKKOS: filenames -> commands src/KOKKOS/README lib/kokkos/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.3"_accelerate_kokkos.html +"Speed packages"_Speed_packages.html +"Speed kokkos"_Speed_kokkos.html "Section 2.6 -k on ..."_Section_start.html#start_6 "Section 2.6 -sf kk"_Section_start.html#start_6 "Section 2.6 -pk kokkos"_Section_start.html#start_6 "package kokkos"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (k) +"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (k) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -689,11 +627,11 @@ make machine :pre src/KSPACE: filenames -> commands "kspace_style"_kspace_style.html "doc/PDF/kspace.pdf"_PDF/kspace.pdf -"Section 6.7"_Section_howto.html#howto_7 -"Section 6.8"_Section_howto.html#howto_8 -"Section 6.9"_Section_howto.html#howto_9 +"Howto tip3p"_Howto_tip3p.html +"Howto tip4p"_Howto_tip4p.html +"Howto spc"_Howto_spc.html "pair_style coul"_pair_coul.html -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 with "long" or "msm" in pair style name +"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name examples/peptide bench/in.rhodo :ul @@ -777,7 +715,7 @@ make machine :pre [Supporting info:] src/MANYBODY: filenames -> commands -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 +"Commands pair"_Commands_pair.html page examples/comb examples/eim examples/nb3d @@ -940,7 +878,7 @@ src/MOLECULE: filenames -> commands "improper_style"_improper_style.html "pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html "pair_style lj/charmm/coul/charmm"_pair_charmm.html -"Section 6.3"_Section_howto.html#howto_3 +"Howto bioFF"_Howto_bioFF.html examples/cmap examples/dreiding examples/micelle, @@ -1048,9 +986,9 @@ OPT package :link(OPT),h4 A handful of pair styles which are optimized for improved CPU performance on single or multiple cores. These include EAM, LJ, CHARMM, and Morse potentials. The styles have an "opt" suffix in -their style name. "Section 5.3.5"_accelerate_opt.html gives details -of how to build and use this package. Its styles can be invoked at -run time via the "-sf opt" or "-suffix opt" "command-line +their style name. The "Speed opt"_Speed_opt.html doc page gives +details of how to build and use this package. Its styles can be +invoked at run time via the "-sf opt" or "-suffix opt" "command-line switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS, "USER-INTEL"_#USER-INTEL, and "USER-OMP"_#USER-OMP packages, which have styles optimized for CPU performance. @@ -1076,10 +1014,10 @@ CCFLAGS: add -restrict for Intel compilers :ul [Supporting info:] src/OPT: filenames -> commands -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.5"_accelerate_opt.html +"Speed packages"_Speed_packages.html +"Speed opt"_Speed_opt.html "Section 2.6 -sf opt"_Section_start.html#start_6 -Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5 for pair styles followed by (t) +"Commands pair"_Commands_pair.html for styles followed by (t) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line @@ -1178,10 +1116,10 @@ PYTHON package :link(PYTHON),h4 A "python"_python.html command which allow you to execute Python code from a LAMMPS input script. The code can be in a separate file or -embedded in the input script itself. See "Section -11.2"_Section_python.html#py_2 for an overview of using Python from -LAMMPS in this manner and the entire section for other ways to use -LAMMPS and Python together. +embedded in the input script itself. See the "Python +call"_Python_call.html doc page for an overview of using Python from +LAMMPS in this manner and all the "Python"_Python.html doc pages for +other ways to use LAMMPS and Python together. [Install or un-install:] @@ -1202,7 +1140,7 @@ to Makefile.lammps) if the LAMMPS build fails. [Supporting info:] src/PYTHON: filenames -> commands -"Section 11"_Section_python.html +"Python call"_Python.html lib/python/README examples/python :ul @@ -1292,8 +1230,8 @@ REPLICA package :link(REPLICA),h4 [Contents:] A collection of multi-replica methods which can be used when running -multiple LAMMPS simulations (replicas). See "Section -6.5"_Section_howto.html#howto_5 for an overview of how to run +multiple LAMMPS simulations (replicas). See the "Howto +replica"_Howto_replica.html doc page for an overview of how to run multi-replica simulations in LAMMPS. Methods in the package include nudged elastic band (NEB), parallel replica dynamics (PRD), temperature accelerated dynamics (TAD), parallel tempering, and a @@ -1312,7 +1250,7 @@ make machine :pre [Supporting info:] src/REPLICA: filenames -> commands -"Section 6.5"_Section_howto.html#howto_5 +"Howto replica"_Howto_replica.html "neb"_neb.html "prd"_prd.html "tad"_tad.html @@ -1415,6 +1353,38 @@ examples/snap :ul :line +SPIN package :link(SPIN),h4 + +[Contents:] + +Model atomic magnetic spins classically, coupled to atoms moving in +the usual manner via MD. Various pair, fix, and compute styles. + +[Author:] Julian Tranchida (Sandia). + +[Install or un-install:] + +make yes-spin +make machine :pre + +make no-spin +make machine :pre + +[Supporting info:] + +src/SPIN: filenames -> commands +"Howto spin"_Howto_spin.html +"pair_style spin/dmi"_pair_spin_dmi.html +"pair_style spin/exchange"_pair_spin_exchange.html +"pair_style spin/magelec"_pair_spin_magelec.html +"pair_style spin/neel"_pair_spin_neel.html +"fix nve/spin"_fix_nve_spin.html +"fix precession/spin"_fix_precession_spin.html +"compute spin"_compute_spin.html +examples/SPIN :ul + +:line + SRD package :link(SRD),h4 [Contents:] @@ -1862,10 +1832,10 @@ USER-DRUDE package :link(USER-DRUDE),h4 [Contents:] Fixes, pair styles, and a compute to simulate thermalized Drude -oscillators as a model of polarization. See "Section -6.27"_Section_howto.html#howto_27 for an overview of how to use the -package. There are auxiliary tools for using this package in -tools/drude. +oscillators as a model of polarization. See the "Howto +drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages +for an overview of how to use the package. There are auxiliary tools +for using this package in tools/drude. [Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien Devemy (CNRS), and Agilio Padua (U Blaise Pascal). @@ -1881,8 +1851,9 @@ make machine :pre [Supporting info:] src/USER-DRUDE: filenames -> commands -"Section 6.27"_Section_howto.html#howto_27 -"Section 6.25"_Section_howto.html#howto_25 +"Howto drude"_Howto_drude.html +"Howto drude2"_Howto_drude2.html +"Howto polarizable"_Howto_polarizable.html src/USER-DRUDE/README "fix drude"_fix_drude.html "fix drude/transform/*"_fix_drude_transform.html @@ -2033,8 +2004,8 @@ USER-INTEL package :link(USER-INTEL),h4 Dozens of pair, fix, bond, angle, dihedral, improper, and kspace styles which are optimized for Intel CPUs and KNLs (Knights Landing). -All of them have an "intel" in their style name. "Section -5.3.2"_accelerate_intel.html gives details of what hardware and +All of them have an "intel" in their style name. The "Speed +intel"_Speed_intel.html doc page gives details of what hardware and compilers are required on your system, and how to build and use this package. Its styles can be invoked at run time via the "-sf intel" or "-suffix intel" "command-line switches"_Section_start.html#start_6. @@ -2084,7 +2055,7 @@ hardware target, to produce a separate executable. You should also typically install the USER-OMP package, as it can be used in tandem with the USER-INTEL package to good effect, as -explained in "Section 5.3.2"_accelerate_intel.html. +explained on the "Speed intel"_Speed_intel.html doc page. make yes-user-intel yes-user-omp make machine :pre @@ -2096,12 +2067,12 @@ make machine :pre src/USER-INTEL: filenames -> commands src/USER-INTEL/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.2"_accelerate_gpu.html +"Speed packages"_Speed_packages.html +"Speed intel"_Speed_intel.html "Section 2.6 -sf intel"_Section_start.html#start_6 "Section 2.6 -pk intel"_Section_start.html#start_6 "package intel"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (i) +"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (i) src/USER-INTEL/TEST "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul @@ -2222,7 +2193,7 @@ make machine :pre src/USER-MANIFOLD: filenames -> commands src/USER-MANIFOLD/README -"doc/manifolds"_manifolds.html +"Howto manifold"_Howto_manifold.html "fix manifoldforce"_fix_manifoldforce.html "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html @@ -2443,10 +2414,10 @@ USER-OMP package :link(USER-OMP),h4 Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and kspace styles which are altered to enable threading on many-core CPUs via OpenMP directives. All of them have an "omp" in their style name. -"Section 5.3.4"_accelerate_omp.html gives details of what hardware and -compilers are required on your system, and how to build and use this -package. Its styles can be invoked at run time via the "-sf omp" or -"-suffix omp" "command-line switches"_Section_start.html#start_6. +The "Speed omp"_Speed_omp.html doc page gives details of what hardware +and compilers are required on your system, and how to build and use +this package. Its styles can be invoked at run time via the "-sf omp" +or "-suffix omp" "command-line switches"_Section_start.html#start_6. Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-INTEL"_#USER-INTEL packages, which have styles optimized for CPUs. @@ -2481,12 +2452,12 @@ LINKFLAGS: add -fopenmp :ul src/USER-OMP: filenames -> commands src/USER-OMP/README -"Section 5.3"_Section_accelerate.html#acc_3 -"Section 5.3.4"_accelerate_omp.html +"Speed packages"_Speed_packages.html +"Speed omp"_Speed_omp.html "Section 2.6 -sf omp"_Section_start.html#start_6 "Section 2.6 -pk omp"_Section_start.html#start_6 "package omp"_package.html -Styles sections of "Section 3.5"_Section_commands.html#cmd_5 for styles followed by (o) +"Commands all"_Commands_all.html pages (fix,compute,pair,etc) for styles followed by (o) "Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul :line diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt new file mode 100644 index 0000000000000000000000000000000000000000..7e6434560244abfce710c182af2c4fb6cad31da6 --- /dev/null +++ b/doc/src/Packages_standard.txt @@ -0,0 +1,65 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Standard packages :h3 + +This is the list of standard packages in LAMMPS. The link for each +package name gives more details. + +Standard packages are supported by the LAMMPS developers and are +written in a syntax and style consistent with the rest of LAMMPS. +This means the developers will answer questions about them, debug and +fix them if necessary, and keep them compatible with future changes to +LAMMPS. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +dash = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"ASPHERE"_Packages_details.html#ASPHERE, aspherical particle models, "Howto spherical"_Howto_spherical.html, ellipse, - +"BODY"_Packages_details.html#BODY, body-style particles, "Howto body"_Howto_body.html, body, - +"CLASS2"_Packages_details.html#CLASS2, class 2 force fields, "pair_style lj/class2"_pair_class2.html, -, - +"COLLOID"_Packages_details.html#COLLOID, colloidal particles, "atom_style colloid"_atom_style.html, colloid, - +"COMPRESS"_Packages_details.html#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys +"CORESHELL"_Packages_details.html#CORESHELL, adiabatic core/shell model, "Howto coreshell"_Howto_coreshell.html, coreshell, - +"DIPOLE"_Packages_details.html#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - +"GPU"_Packages_details.html#GPU, GPU-enabled styles, "Section gpu"_Speed_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int +"GRANULAR"_Packages_details.html#GRANULAR, granular systems, "Howto granular"_Howto_granular.html, pour, - +"KIM"_Packages_details.html#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext +"KOKKOS"_Packages_details.html#KOKKOS, Kokkos-enabled styles, "Speed kokkos"_Speed_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"KSPACE"_Packages_details.html#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - +"LATTE"_Packages_details.html#LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext +"MANYBODY"_Packages_details.html#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - +"MC"_Packages_details.html#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - +"MEAM"_Packages_details.html#MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int +"MISC"_Packages_details.html#MISC, miscellanous single-file commands, -, -, - +"MOLECULE"_Packages_details.html#MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, - +"MPIIO"_Packages_details.html#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - +"MSCG"_Packages_details.html#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext +"OPT"_Packages_details.html#OPT, optimized pair styles, "Speed opt"_Speed_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"PERI"_Packages_details.html#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - +"POEMS"_Packages_details.html#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int +"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys +"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, - +"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int +"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, - +"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, - +"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - +"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, - +"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - +"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt new file mode 100644 index 0000000000000000000000000000000000000000..c8728148f9c1a83f0c900524e3b49bc586101aa6 --- /dev/null +++ b/doc/src/Packages_user.txt @@ -0,0 +1,74 @@ +"Higher level section"_Packages.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +User packages :h3 + +This is a list of user packages in LAMMPS. The link for each package +name gives more details. + +User packages have been contributed by users, and begin with the +"user" prefix. If a contribution is a single command (single file), +it is typically in the user-misc package. User packages don't +necessarily meet the requirements of the "standard +packages"_Packages_standard.html. This means the developers will try +to keep things working and usually can answer technical questions +about compiling the package. If you have problems using a specific +feature provided in a user package, you may need to contact the +contributor directly to get help. Information on how to submit +additions you make to LAMMPS as single files or as a standard or user +package is explained on the "Modify contribute"_Modify_contribute.html +doc page. + +The "Example" column is a sub-directory in the examples directory of +the distribution which has an input script that uses the package. +E.g. "peptide" refers to the examples/peptide directory; USER/atc +refers to the examples/USER/atc directory. The "Library" column +indicates whether an extra library is needed to build and use the +package: + +dash = no library +sys = system library: you likely have it on your machine +int = internal library: provided with LAMMPS, but you may need to build it +ext = external library: you will need to download and install it on your machine :ul + +Package, Description, Doc page, Example, Library +"USER-ATC"_Packages_details.html#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int +"USER-AWPMD"_Packages_details.html#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-BOCS"_Packages_details.html#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, - +"USER-CGDNA"_Packages_details.html#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, - +"USER-CGSDK"_Packages_details.html#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, - +"USER-COLVARS"_Packages_details.html#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int +"USER-DIFFRACTION"_Packages_details.html#USER-DIFFRACTION, virtual x-ray and electron diffraction,"compute xrd"_compute_xrd.html, USER/diffraction, - +"USER-DPD"_Packages_details.html#USER-DPD, reactive dissipative particle dynamics, src/USER-DPD/README, USER/dpd, - +"USER-DRUDE"_Packages_details.html#USER-DRUDE, Drude oscillators, "Howto drude"_Howto_drude.html, USER/drude, - +"USER-EFF"_Packages_details.html#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - +"USER-FEP"_Packages_details.html#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - +"USER-H5MD"_Packages_details.html#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext +"USER-INTEL"_Packages_details.html#USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"USER-LB"_Packages_details.html#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - +"USER-MANIFOLD"_Packages_details.html#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - +"USER-MEAMC"_Packages_details.html#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - +"USER-MESO"_Packages_details.html#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, - +"USER-MGPT"_Packages_details.html#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - +"USER-MISC"_Packages_details.html#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - +"USER-MOFFF"_Packages_details.html#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, - +"USER-MOLFILE"_Packages_details.html#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext +"USER-NETCDF"_Packages_details.html#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext +"USER-OMP"_Packages_details.html#USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - +"USER-PHONON"_Packages_details.html#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - +"USER-QMMM"_Packages_details.html#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext +"USER-QTB"_Packages_details.html#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - +"USER-QUIP"_Packages_details.html#USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext +"USER-REAXC"_Packages_details.html#USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, - +"USER-SMD"_Packages_details.html#USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext +"USER-SMTBQ"_Packages_details.html#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - +"USER-SPH"_Packages_details.html#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - +"USER-TALLY"_Packages_details.html#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - +"USER-UEF"_Packages_details.html#USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, - +"USER-VTK"_Packages_details.html#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) diff --git a/doc/src/Python.txt b/doc/src/Python.txt new file mode 100644 index 0000000000000000000000000000000000000000..2c9c6872bbf21e5704088b46752603f7349cd3e6 --- /dev/null +++ b/doc/src/Python.txt @@ -0,0 +1,79 @@ +"Previous Section"_Modify.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Errors.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Use Python with LAMMPS :h2 + +These doc pages describe various ways that LAMMPS and Python can be +used together. + + + + + +"Overview of Python and LAMMPS"_Python_overview.html :all(b) + +"Run LAMMPS from Python"_Python_run.html +"Build LAMMPS as a shared library"_Python_shlib.html +"Install LAMMPS in Python"_Python_install.html +"Extend Python to run in parallel"_Python_mpi.html +"Test the Python/LAMMPS interface"_Python_test.html +"Python library interface"_Python_library.html +"PyLammps interface"_Python_pylammps.html +"Example Python scripts that use LAMMPS"_Python_examples.html :all(b) + +"Call Python from a LAMMPS input script"_Python_call.html :all(b) + + + +If you're not familiar with "Python"_http://www.python.org, it's a +powerful scripting and programming language which can do most +everything that lower-level languages like C or C++ can do in fewer +lines of code. The only drawback is slower execution speed. Python +is also easy to use as a "glue" language to drive a program through +its library interface, or to hook multiple pieces of software +together, such as a simulation code plus a visualization tool, or to +run a coupled multiscale or multiphysics model. + +See the "Howto_couple"_Howto_couple.html doc page for more ideas about +coupling LAMMPS to other codes. See the "Howto +library"_Howto_library.html doc page for a description of the LAMMPS +library interface provided in src/library.h and src/library.h. That +interface is exposed to Python either when calling LAMMPS from Python +or when calling Python from a LAMMPS input script and then calling +back to LAMMPS from Python code. The library interface is designed to +be easy to add funcionality to. Thus the Python interface to LAMMPS +is also easy to extend as well. + +If you create interesting Python scripts that run LAMMPS or +interesting Python functions that can be called from a LAMMPS input +script, that you think would be genearlly useful, please post them as +a pull request to our "GitHub site"_https://github.com/lammps/lammps, +and they can be added to the LAMMPS distribution or webpage. diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt new file mode 100644 index 0000000000000000000000000000000000000000..621f1fe2410f7f7d58e193466481cc3cd19a4578 --- /dev/null +++ b/doc/src/Python_call.txt @@ -0,0 +1,85 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Call Python from a LAMMPS input script :h3 + +LAMMPS has several commands which can be used to invoke Python +code directly from an input script: + +"python"_python.html +"variable python"_variable.html +"fix python/invoke"_fix_python_invoke.html +"pair_style python"_pair_python.html :ul + +The "python"_python.html command which can be used to define and +execute a Python function that you write the code for. The Python +function can also be assigned to a LAMMPS python-style variable via +the "variable"_variable.html command. Each time the variable is +evaluated, either in the LAMMPS input script itself, or by another +LAMMPS command that uses the variable, this will trigger the Python +function to be invoked. + +The Python code for the function can be included directly in the input +script or in an auxiliary file. The function can have arguments which +are mapped to LAMMPS variables (also defined in the input script) and +it can return a value to a LAMMPS variable. This is thus a mechanism +for your input script to pass information to a piece of Python code, +ask Python to execute the code, and return information to your input +script. + +Note that a Python function can be arbitrarily complex. It can import +other Python modules, instantiate Python classes, call other Python +functions, etc. The Python code that you provide can contain more +code than the single function. It can contain other functions or +Python classes, as well as global variables or other mechanisms for +storing state between calls from LAMMPS to the function. + +The Python function you provide can consist of "pure" Python code that +only performs operations provided by standard Python. However, the +Python function can also "call back" to LAMMPS through its +Python-wrapped library interface, in the manner described in the +"Python run"_Python_run.html doc page. This means it can issue LAMMPS +input script commands or query and set internal LAMMPS state. As an +example, this can be useful in an input script to create a more +complex loop with branching logic, than can be created using the +simple looping and branching logic enabled by the "next"_next.html and +"if"_if.html commands. + +See the "python"_python.html doc page and the "variable"_variable.html +doc page for its python-style variables for more info, including +examples of Python code you can write for both pure Python operations +and callbacks to LAMMPS. + +The "fix python/invoke"_fix_python_invoke.html command can execute +Python code at selected timesteps during a simulation run. + +The "pair_style python"_pair_python command allows you to define +pairwise potentials as python code which encodes a single pairwise +interaction. This is useful for rapid-developement and debugging of a +new potential. + +To use any of these commands, you only need to build LAMMPS with the +PYTHON package installed: + +make yes-python +make machine :pre + +Note that this will link LAMMPS with the Python library on your +system, which typically requires several auxiliary system libraries to +also be linked. The list of these libraries and the paths to find +them are specified in the lib/python/Makefile.lammps file. You need +to insure that file contains the correct information for your version +of Python and your machine to successfully build LAMMPS. See the +lib/python/README file for more info. + +If you want to write Python code with callbacks to LAMMPS, then you +must also follow the steps overviewed in the "Python +run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared +library and insure that Python can find the python/lammps.py file and +the shared library. diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt new file mode 100644 index 0000000000000000000000000000000000000000..46e5fee2b97da5d4f46644883434729c6e5406ad --- /dev/null +++ b/doc/src/Python_examples.txt @@ -0,0 +1,81 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Example Python scripts that use LAMMPS :h3 + +These are the Python scripts included as demos in the python/examples +directory of the LAMMPS distribution, to illustrate the kinds of +things that are possible when Python wraps LAMMPS. If you create your +own scripts, send them to us and we can include them in the LAMMPS +distribution. + +trivial.py, read/run a LAMMPS input script thru Python, +demo.py, invoke various LAMMPS library interface routines, +simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, +split.py, same as simple.py but running in parallel on a subset of procs, +gui.py, GUI go/stop/temperature-slider to control LAMMPS, +plot.py, real-time temperature plot with GnuPlot via Pizza.py, +viz_tool.py, real-time viz via some viz package, +vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) + +:line + +For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" +with "gl" or "atomeye" or "pymol" or "vmd", depending on what +visualization package you have installed. + +Note that for GL, you need to be able to run the Pizza.py GL tool, +which is included in the pizza sub-directory. See the "Pizza.py doc +pages"_pizza for more info: + +:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) + +Note that for AtomEye, you need version 3, and there is a line in the +scripts that specifies the path and name of the executable. See the +AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: + +http://mt.seas.upenn.edu/Archive/Graphics/A +http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre + +:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) +:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) + +The latter link is to AtomEye 3 which has the scriping +capability needed by these Python scripts. + +Note that for PyMol, you need to have built and installed the +open-source version of PyMol in your Python, so that you can import it +from a Python script. See the PyMol WWW pages "here"_pymolhome or +"here"_pymolopen for more details: + +http://www.pymol.org +http://sourceforge.net/scm/?type=svn&group_id=4546 :pre + +:link(pymolhome,http://www.pymol.org) +:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) + +The latter link is to the open-source version. + +Note that for VMD, you need a fairly current version (1.8.7 works for +me) and there are some lines in the pizza/vmd.py script for 4 PIZZA +variables that have to match the VMD installation on your system. + +:line + +See the python/README file for instructions on how to run them and the +source code for individual scripts for comments about what they do. + +Here are screenshots of the vizplotgui_tool.py script in action for +different visualization package options. Click to see larger images: + +:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) +:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) +:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) +:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) + diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt new file mode 100644 index 0000000000000000000000000000000000000000..6591360ae2535935f0c9e88e8bf6bc2c830f6cb0 --- /dev/null +++ b/doc/src/Python_install.txt @@ -0,0 +1,74 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Installing LAMMPS in Python :h3 + +For Python to invoke LAMMPS, there are 2 files it needs to know about: + +python/lammps.py +src/liblammps.so :ul + +Lammps.py is the Python wrapper on the LAMMPS library interface. +Liblammps.so is the shared LAMMPS library that Python loads, as +described above. + +You can insure Python can find these files in one of two ways: + +set two environment variables +run the python/install.py script :ul + +If you set the paths to these files as environment variables, you only +have to do it once. For the csh or tcsh shells, add something like +this to your ~/.cshrc file, one line for each of the two files: + +setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python +setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre + +If you use the python/install.py script, you need to invoke it every +time you rebuild LAMMPS (as a shared library) or make changes to the +python/lammps.py file. + +You can invoke install.py from the python directory as + +% python install.py \[libdir\] \[pydir\] :pre + +The optional libdir is where to copy the LAMMPS shared library to; the +default is /usr/local/lib. The optional pydir is where to copy the +lammps.py file to; the default is the site-packages directory of the +version of Python that is running the install script. + +Note that libdir must be a location that is in your default +LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a +location that Python looks in by default for imported modules, like +its site-packages dir. If you want to copy these files to +non-standard locations, such as within your own user space, you will +need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables +accordingly, as above. + +If the install.py script does not allow you to copy files into system +directories, prefix the python command with "sudo". If you do this, +make sure that the Python that root runs is the same as the Python you +run. E.g. you may need to do something like + +% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre + +You can also invoke install.py from the make command in the src +directory as + +% make install-python :pre + +In this mode you cannot append optional arguments. Again, you may +need to prefix this with "sudo". In this mode you cannot control +which Python is invoked by root. + +Note that if you want Python to be able to load different versions of +the LAMMPS shared library (see "this section"_#py_5 below), you will +need to manually copy files like liblammps_g++.so into the appropriate +system directory. This is not needed if you set the LD_LIBRARY_PATH +environment variable as described above. diff --git a/doc/src/Python_library.txt b/doc/src/Python_library.txt new file mode 100644 index 0000000000000000000000000000000000000000..8d0c724a45992294f7860612e5042387efc150ec --- /dev/null +++ b/doc/src/Python_library.txt @@ -0,0 +1,256 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Python library interface :h3 + +As described previously, the Python interface to LAMMPS consists of a +Python "lammps" module, the source code for which is in +python/lammps.py, which creates a "lammps" object, with a set of +methods that can be invoked on that object. The sample Python code +below assumes you have first imported the "lammps" module in your +Python script, as follows: + +from lammps import lammps :pre + +These are the methods defined by the lammps module. If you look at +the files src/library.cpp and src/library.h you will see they +correspond one-to-one with calls you can make to the LAMMPS library +from a C++ or C or Fortran program, and which are described on the +"Howto library"_Howto_library.html doc page. + +The python/examples directory has Python scripts which show how Python +can run LAMMPS, grab data, change it, and put it back into LAMMPS. + +lmp = lammps() # create a LAMMPS object using the default liblammps.so library + # 4 optional args are allowed: name, cmdargs, ptr, comm +lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object +lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later +lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library +lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre + +lmp.close() # destroy a LAMMPS object :pre + +version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre + +lmp.file(file) # run an entire input script, file = "in.lj" +lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" +lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] +lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre + +size = lmp.extract_setting(name) # return data type info :pre + +xlo = lmp.extract_global(name,type) # extract a global quantity + # name = "boxxlo", "nlocal", etc + # type = 0 = int + # 1 = double :pre + +boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre + +coords = lmp.extract_atom(name,type) # extract a per-atom quantity + # name = "x", "type", etc + # type = 0 = vector of ints + # 1 = array of ints + # 2 = vector of doubles + # 3 = array of doubles :pre + +eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute +v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix + # id = ID of compute or fix + # style = 0 = global data + # 1 = per-atom data + # 2 = local data + # type = 0 = scalar + # 1 = vector + # 2 = array + # i,j = indices of value in global vector or array :pre + +var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable + # name = name of variable + # group = group ID (ignored for equal-style variables) + # flag = 0 = equal-style variable + # 1 = atom-style variable :pre + +value = lmp.get_thermo(name) # return current value of a thermo keyword +natoms = lmp.get_natoms() # total # of atoms as int :pre + +flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful +lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre + +data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID + # name = "x", "charge", "type", etc +data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) +data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID + # name = "x", "charge", "type", etc + # count = # of per-atom values, 1 or 3, etc :pre +lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre + +lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre + +:line + +The lines + +from lammps import lammps +lmp = lammps() :pre + +create an instance of LAMMPS, wrapped in a Python class by the lammps +Python module, and return an instance of the Python class as lmp. It +is used to make all subsequent calls to the LAMMPS library. + +Additional arguments to lammps() can be used to tell Python the name +of the shared library to load or to pass arguments to the LAMMPS +instance, the same as if LAMMPS were launched from a command-line +prompt. + +If the ptr argument is set like this: + +lmp = lammps(ptr=lmpptr) :pre + +then lmpptr must be an argument passed to Python via the LAMMPS +"python"_python.html command, when it is used to define a Python +function that is invoked by the LAMMPS input script. This mode of +calling Python from LAMMPS is described in the "Python +call"_Python_call.html doc page. The variable lmpptr refers to the +instance of LAMMPS that called the embedded Python interpreter. Using +it as an argument to lammps() allows the returned Python class +instance "lmp" to make calls to that instance of LAMMPS. See the +"python"_python.html command doc page for examples using this syntax. + +Note that you can create multiple LAMMPS objects in your Python +script, and coordinate and run multiple simulations, e.g. + +from lammps import lammps +lmp1 = lammps() +lmp2 = lammps() +lmp1.file("in.file1") +lmp2.file("in.file2") :pre + +The file(), command(), commands_list(), commands_string() methods +allow an input script, a single command, or multiple commands to be +invoked. + +The extract_setting(), extract_global(), extract_box(), +extract_atom(), extract_compute(), extract_fix(), and +extract_variable() methods return values or pointers to data +structures internal to LAMMPS. + +For extract_global() see the src/library.cpp file for the list of +valid names. New names could easily be added. A double or integer is +returned. You need to specify the appropriate data type via the type +argument. + +For extract_atom(), a pointer to internal LAMMPS atom-based data is +returned, which you can use via normal Python subscripting. See the +extract() method in the src/atom.cpp file for a list of valid names. +Again, new names could easily be added if the property you want is not +listed. A pointer to a vector of doubles or integers, or a pointer to +an array of doubles (double **) or integers (int **) is returned. You +need to specify the appropriate data type via the type argument. + +For extract_compute() and extract_fix(), the global, per-atom, or +local data calculated by the compute or fix can be accessed. What is +returned depends on whether the compute or fix calculates a scalar or +vector or array. For a scalar, a single double value is returned. If +the compute or fix calculates a vector or array, a pointer to the +internal LAMMPS data is returned, which you can use via normal Python +subscripting. The one exception is that for a fix that calculates a +global vector or array, a single double value from the vector or array +is returned, indexed by I (vector) or I and J (array). I,J are +zero-based indices. The I,J arguments can be left out if not needed. +See the "Howto output"_Howto_output.html doc page for a discussion of +global, per-atom, and local data, and of scalar, vector, and array +data types. See the doc pages for individual "computes"_compute.html +and "fixes"_fix.html for a description of what they calculate and +store. + +For extract_variable(), an "equal-style or atom-style +variable"_variable.html is evaluated and its result returned. + +For equal-style variables a single double value is returned and the +group argument is ignored. For atom-style variables, a vector of +doubles is returned, one value per atom, which you can use via normal +Python subscripting. The values will be zero for atoms not in the +specified group. + +The get_thermo() method returns returns the current value of a thermo +keyword as a float. + +The get_natoms() method returns the total number of atoms in the +simulation, as an int. + +The set_variable() methosd sets an existing string-style variable to a +new string value, so that subsequent LAMMPS commands can access the +variable. + +The reset_box() emthods resets the size and shape of the simulation +box, e.g. as part of restoring a previously extracted and saved state +of a simulation. + +The gather methods collect peratom info of the requested type (atom +coords, atom types, forces, etc) from all processors, and returns the +same vector of values to each callling processor. The scatter +functions do the inverse. They distribute a vector of peratom values, +passed by all calling processors, to invididual atoms, which may be +owned by different processos. + +Note that the data returned by the gather methods, +e.g. gather_atoms("x"), is different from the data structure returned +by extract_atom("x") in four ways. (1) Gather_atoms() returns a +vector which you index as x\[i\]; extract_atom() returns an array +which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms +by atom ID while extract_atom() does not. (3) Gather_atoms() returns +a list of all atoms in the simulation; extract_atoms() returns just +the atoms local to each processor. (4) Finally, the gather_atoms() +data structure is a copy of the atom coords stored internally in +LAMMPS, whereas extract_atom() returns an array that effectively +points directly to the internal data. This means you can change +values inside LAMMPS from Python by assigning a new values to the +extract_atom() array. To do this with the gather_atoms() vector, you +need to change values in the vector, then invoke the scatter_atoms() +method. + +For the scatter methods, the array of coordinates passed to must be a +ctypes vector of ints or doubles, allocated and initialized something +like this: + +from ctypes import * +natoms = lmp.get_natoms() +n3 = 3*natoms +x = (n3*c_double)() +x\[0\] = x coord of atom with ID 1 +x\[1\] = y coord of atom with ID 1 +x\[2\] = z coord of atom with ID 1 +x\[3\] = x coord of atom with ID 2 +... +x\[n3-1\] = z coord of atom with ID natoms +lmp.scatter_atoms("x",1,3,x) :pre + +Alternatively, you can just change values in the vector returned by +the gather methods, since they are also ctypes vectors. + +:line + +As noted above, these Python class methods correspond one-to-one with +the functions in the LAMMPS library interface in src/library.cpp and +library.h. This means you can extend the Python wrapper via the +following steps: + +Add a new interface function to src/library.cpp and +src/library.h. :ulb,l + +Rebuild LAMMPS as a shared library. :l + +Add a wrapper method to python/lammps.py for this interface +function. :l + +You should now be able to invoke the new interface function from a +Python script. :l +:ule diff --git a/doc/src/Python_mpi.txt b/doc/src/Python_mpi.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e0a2ce3198fd79bb98d1bf24fe0e60675de72ce --- /dev/null +++ b/doc/src/Python_mpi.txt @@ -0,0 +1,67 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Extending Python to run in parallel :h3 + +If you wish to run LAMMPS in parallel from Python, you need to extend +your Python with an interface to MPI. This also allows you to +make MPI calls directly from Python in your script, if you desire. + +We recommend use of mpi4py: + +"PyPar"_https://github.com/daleroberts/pypar :ul + +As of version 2.0.0 it allows passing a custom MPI communicator to +the LAMMPS constructor, which means one can easily run one or more +LAMMPS instances on subsets of the total MPI ranks. + +To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it +and from its main directory, type + +python setup.py build +sudo python setup.py install :pre + +Again, the "sudo" is only needed if required to copy mpi4py files into +your Python distribution's site-packages directory. To install with +user privilege into the user local directory type + +python setup.py install --user :pre + +If you have successfully installed mpi4py, you should be able to run +Python and type + +from mpi4py import MPI :pre + +without error. You should also be able to run python in parallel +on a simple test script + +% mpirun -np 4 python test.py :pre + +where test.py contains the lines + +from mpi4py import MPI +comm = MPI.COMM_WORLD +print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre + +and see one line of output for each processor you run on. + +NOTE: To use mpi4py and LAMMPS in parallel from Python, you must +insure both are using the same version of MPI. If you only have one +MPI installed on your system, this is not an issue, but it can be if +you have multiple MPIs. Your LAMMPS build is explicit about which MPI +it is using, since you specify the details in your lo-level +src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find +information about the MPI it uses to build against. And it tries to +load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find +the MPI library that LAMMPS is using. If you have problems running +both mpi4py and LAMMPS together, this is an issue you may need to +address, e.g. by moving other MPI installations so that mpi4py finds +the right one. + + diff --git a/doc/src/Python_overview.txt b/doc/src/Python_overview.txt new file mode 100644 index 0000000000000000000000000000000000000000..a5d6a469ffdaffddfe5347e1c5ecaec0be5257cb --- /dev/null +++ b/doc/src/Python_overview.txt @@ -0,0 +1,35 @@ +"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Tools.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands.html#comm) + +:line + +Overview of Python and LAMMPS :h3 + +LAMMPS can work together with Python in three ways. First, Python can +wrap LAMMPS through the its "library interface"_Howto_library.html, so +that a Python script can create one or more instances of LAMMPS and +launch one or more simulations. In Python lingo, this is "extending" +Python with LAMMPS. + +Second, a lower-level Python interface can be used indirectly through +provided PyLammps and IPyLammps wrapper classes, written in Python. +These wrappers try to simplify the usage of LAMMPS in Python by +providing an object-based interface to common LAMMPS functionality. +They also reduces the amount of code necessary to parameterize LAMMPS +scripts through Python and make variables and computes directly +accessible. + +Third, LAMMPS can use the Python interpreter, so that a LAMMPS +input script can invoke Python code directly, and pass information +back-and-forth between the input script and Python functions you +write. This Python code can also callback to LAMMPS to query or change +its attributes. In Python lingo, this is "embedding" Python in +LAMMPS. When used in this mode, Python can perform operations that +the simple LAMMPS input script syntax cannot. + + diff --git a/doc/src/Python_pylammps.txt b/doc/src/Python_pylammps.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7baa93e2e69154b20fdc2f7f4666f500f2d6a02 --- /dev/null +++ b/doc/src/Python_pylammps.txt @@ -0,0 +1,14 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +PyLammps interface :h3 + +PyLammps is a Python wrapper class which can be created on its own or +use an existing lammps Python object. It has its own "Howto +pylammps"_Howto_pylammps.html doc page. diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt new file mode 100644 index 0000000000000000000000000000000000000000..a94dc07f2d7368ec8086fc1535337ed3c245f82f --- /dev/null +++ b/doc/src/Python_run.txt @@ -0,0 +1,40 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Run LAMMPS from Python :h3 + +The LAMMPS distribution includes a python directory with all you need +to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS +library interface, with one wrapper function per LAMMPS library +function. This file makes it is possible to do the following either +from a Python script, or interactively from a Python prompt: create +one or more instances of LAMMPS, invoke LAMMPS commands or give it an +input script, run LAMMPS incrementally, extract LAMMPS results, an +modify internal LAMMPS variables. From a Python script you can do +this in serial or parallel. Running Python interactively in parallel +does not generally work, unless you have a version of Python that +extends Python to enable multiple instances of Python to read what you +type. + +To do all of this, you must first build LAMMPS as a shared library, +then insure that your Python can find the python/lammps.py file and +the shared library. + +Two advantages of using Python to run LAMMPS are how concise the +language is, and that it can be run interactively, enabling rapid +development and debugging. If you use it to mostly invoke costly +operations within LAMMPS, such as running a simulation for a +reasonable number of timesteps, then the overhead cost of invoking +LAMMPS thru Python will be negligible. + +The Python wrapper for LAMMPS uses the "ctypes" package in Python, +which auto-generates the interface code needed between Python and a +set of C-style library functions. Ctypes is part of standard Python +for versions 2.5 and later. You can check which version of Python you +have by simply typing "python" at a shell prompt. diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a921e4025cde5cc1376c603a4beb2cf5c4c58fb --- /dev/null +++ b/doc/src/Python_shlib.txt @@ -0,0 +1,34 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Build LAMMPS as a shared library :h3 + +Instructions on how to build LAMMPS as a shared library are given in +"Section 2.4"_Section_start.html#start_4. A shared library is one +that is dynamically loadable, which is what Python requires to wrap +LAMMPS. On Linux this is a library file that ends in ".so", not ".a". + +From the src directory, type + +make foo mode=shlib :pre + +where foo is the machine target name, such as mpi or serial. +This should create the file liblammps_foo.so in the src directory, as +well as a soft link liblammps.so, which is what the Python wrapper will +load by default. Note that if you are building multiple machine +versions of the shared library, the soft link is always set to the +most recently built version. + +NOTE: If you are building LAMMPS with an MPI or FFT library or other +auxiliary libraries (used by various packages), then all of these +extra libraries must also be shared libraries. If the LAMMPS +shared-library build fails with an error complaining about this, see +"Section 2.4"_Section_start.html#start_4 for more details. + +Also include CMake info on this diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a05d5c4680df053cd563f5e09d017e64fe4bb1f --- /dev/null +++ b/doc/src/Python_test.txt @@ -0,0 +1,131 @@ +"Higher level section"_Python.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Test the Python/LAMMPS interface :h3 + +To test if LAMMPS is callable from Python, launch Python interactively +and type: + +>>> from lammps import lammps +>>> lmp = lammps() :pre + +If you get no errors, you're ready to use LAMMPS from Python. If the +2nd command fails, the most common error to see is + +OSError: Could not load LAMMPS dynamic library :pre + +which means Python was unable to load the LAMMPS shared library. This +typically occurs if the system can't find the LAMMPS shared library or +one of the auxiliary shared libraries it depends on, or if something +about the library is incompatible with your Python. The error message +should give you an indication of what went wrong. + +You can also test the load directly in Python as follows, without +first importing from the lammps.py file: + +>>> from ctypes import CDLL +>>> CDLL("liblammps.so") :pre + +If an error occurs, carefully go thru the steps in "Section +2.4"_Section_start.html#start_4 and above about building a shared +library and about insuring Python can find the necessary two files +it needs. + +[Test LAMMPS and Python in serial:] :h4 + +To run a LAMMPS test in serial, type these lines into Python +interactively from the bench directory: + +>>> from lammps import lammps +>>> lmp = lammps() +>>> lmp.file("in.lj") :pre + +Or put the same lines in the file test.py and run it as + +% python test.py :pre + +Either way, you should see the results of running the in.lj benchmark +on a single processor appear on the screen, the same as if you had +typed something like: + +lmp_g++ -in in.lj :pre + +[Test LAMMPS and Python in parallel:] :h4 + +To run LAMMPS in parallel, assuming you have installed the +"PyPar"_https://github.com/daleroberts/pypar package as discussed +above, create a test.py file containing these lines: + +import pypar +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp +pypar.finalize() :pre + +To run LAMMPS in parallel, assuming you have installed the +"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed +above, create a test.py file containing these lines: + +from mpi4py import MPI +from lammps import lammps +lmp = lammps() +lmp.file("in.lj") +me = MPI.COMM_WORLD.Get_rank() +nprocs = MPI.COMM_WORLD.Get_size() +print "Proc %d out of %d procs has" % (me,nprocs),lmp +MPI.Finalize() :pre + +You can either script in parallel as: + +% mpirun -np 4 python test.py :pre + +and you should see the same output as if you had typed + +% mpirun -np 4 lmp_g++ -in in.lj :pre + +Note that if you leave out the 3 lines from test.py that specify PyPar +commands you will instantiate and run LAMMPS independently on each of +the P processors specified in the mpirun command. In this case you +should get 4 sets of output, each showing that a LAMMPS run was made +on a single processor, instead of one set of output showing that +LAMMPS ran on 4 processors. If the 1-processor outputs occur, it +means that PyPar is not working correctly. + +Also note that once you import the PyPar module, PyPar initializes MPI +for you, and you can use MPI calls directly in your Python script, as +described in the PyPar documentation. The last line of your Python +script should be pypar.finalize(), to insure MPI is shut down +correctly. + +[Running Python scripts:] :h4 + +Note that any Python script (not just for LAMMPS) can be invoked in +one of several ways: + +% python foo.script +% python -i foo.script +% foo.script :pre + +The last command requires that the first line of the script be +something like this: + +#!/usr/local/bin/python +#!/usr/local/bin/python -i :pre + +where the path points to where you have Python installed, and that you +have made the script file executable: + +% chmod +x foo.script :pre + +Without the "-i" flag, Python will exit when the script finishes. +With the "-i" flag, you will be left in the Python interpreter when +the script finishes, so you can type subsequent commands. As +mentioned above, you can only run Python interactively when running +Python on a single processor, not in parallel. diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt deleted file mode 100644 index d5cbf77a84e2881a7cfd2f23d6cd94d98031cfec..0000000000000000000000000000000000000000 --- a/doc/src/Section_accelerate.txt +++ /dev/null @@ -1,391 +0,0 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_howto.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -5. Accelerating LAMMPS performance :h2 - -This section describes various methods for improving LAMMPS -performance for different classes of problems running on different -kinds of machines. - -There are two thrusts to the discussion that follows. The -first is using code options that implement alternate algorithms -that can speed-up a simulation. The second is to use one -of the several accelerator packages provided with LAMMPS that -contain code optimized for certain kinds of hardware, including -multi-core CPUs, GPUs, and Intel Xeon Phi coprocessors. - -5.1 "Measuring performance"_#acc_1 :ulb,l -5.2 "Algorithms and code options to boost performace"_#acc_2 :l -5.3 "Accelerator packages with optimized styles"_#acc_3 :l - 5.3.1 "GPU package"_accelerate_gpu.html :l - 5.3.2 "USER-INTEL package"_accelerate_intel.html :l - 5.3.3 "KOKKOS package"_accelerate_kokkos.html :l - 5.3.4 "USER-OMP package"_accelerate_omp.html :l - 5.3.5 "OPT package"_accelerate_opt.html :l -5.4 "Comparison of various accelerator packages"_#acc_4 :l -:ule - -The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS -web site gives performance results for the various accelerator -packages discussed in Section 5.2, for several of the standard LAMMPS -benchmark problems, as a function of problem size and number of -compute nodes, on different hardware platforms. - -:line -:line - -5.1 Measuring performance :h3,link(acc_1) - -Before trying to make your simulation run faster, you should -understand how it currently performs and where the bottlenecks are. - -The best way to do this is run the your system (actual number of -atoms) for a modest number of timesteps (say 100 steps) on several -different processor counts, including a single processor if possible. -Do this for an equilibrium version of your system, so that the -100-step timings are representative of a much longer run. There is -typically no need to run for 1000s of timesteps to get accurate -timings; you can simply extrapolate from short runs. - -For the set of runs, look at the timing data printed to the screen and -log file at the end of each LAMMPS run. "This -section"_Section_start.html#start_7 of the manual has an overview. - -Running on one (or a few processors) should give a good estimate of -the serial performance and what portions of the timestep are taking -the most time. Running the same problem on a few different processor -counts should give an estimate of parallel scalability. I.e. if the -simulation runs 16x faster on 16 processors, its 100% parallel -efficient; if it runs 8x faster on 16 processors, it's 50% efficient. - -The most important data to look at in the timing info is the timing -breakdown and relative percentages. For example, trying different -options for speeding up the long-range solvers will have little impact -if they only consume 10% of the run time. If the pairwise time is -dominating, you may want to look at GPU or OMP versions of the pair -style, as discussed below. Comparing how the percentages change as -you increase the processor count gives you a sense of how different -operations within the timestep are scaling. Note that if you are -running with a Kspace solver, there is additional output on the -breakdown of the Kspace time. For PPPM, this includes the fraction -spent on FFTs, which can be communication intensive. - -Another important detail in the timing info are the histograms of -atoms counts and neighbor counts. If these vary widely across -processors, you have a load-imbalance issue. This often results in -inaccurate relative timing data, because processors have to wait when -communication occurs for other processors to catch up. Thus the -reported times for "Communication" or "Other" may be higher than they -really are, due to load-imbalance. If this is an issue, you can -uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile -LAMMPS, to obtain synchronized timings. - -:line - -5.2 General strategies :h3,link(acc_2) - -NOTE: this section 5.2 is still a work in progress - -Here is a list of general ideas for improving simulation performance. -Most of them are only applicable to certain models and certain -bottlenecks in the current performance, so let the timing data you -generate be your guide. It is hard, if not impossible, to predict how -much difference these options will make, since it is a function of -problem size, number of processors used, and your machine. There is -no substitute for identifying performance bottlenecks, and trying out -various options. - -rRESPA -2-FFT PPPM -Staggered PPPM -single vs double PPPM -partial charge PPPM -verlet/split run style -processor command for proc layout and numa layout -load-balancing: balance and fix balance :ul - -2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses -2 FFTs instead of the 4 FFTs used by the default {ik differentiation} -PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to -achieve the same accuracy as 4-FFT PPPM. For problems where the FFT -cost is the performance bottleneck (typically large problems running -on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. - -Staggered PPPM performs calculations using two different meshes, one -shifted slightly with respect to the other. This can reduce force -aliasing errors and increase the accuracy of the method, but also -doubles the amount of work required. For high relative accuracy, using -staggered PPPM allows one to half the mesh size in each dimension as -compared to regular PPPM, which can give around a 4x speedup in the -kspace time. However, for low relative accuracy, using staggered PPPM -gives little benefit and can be up to 2x slower in the kspace -time. For example, the rhodopsin benchmark was run on a single -processor, and results for kspace time vs. relative accuracy for the -different methods are shown in the figure below. For this system, -staggered PPPM (using ik differentiation) becomes useful when using a -relative accuracy of slightly greater than 1e-5 and above. - -:c,image(JPG/rhodo_staggered.jpg) - -NOTE: Using staggered PPPM may not give the same increase in accuracy -of energy and pressure as it does in forces, so some caution must be -used if energy and/or pressure are quantities of interest, such as -when using a barostat. - -:line - -5.3 Packages with optimized styles :h3,link(acc_3) - -Accelerated versions of various "pair_style"_pair_style.html, -"fixes"_fix.html, "computes"_compute.html, and other commands have -been added to LAMMPS, which will typically run faster than the -standard non-accelerated versions. Some require appropriate hardware -to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. - -All of these commands are in packages provided with LAMMPS. An -overview of packages is give in "Section -packages"_Section_packages.html. - -These are the accelerator packages -currently in LAMMPS, either as standard or user packages: - -"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support -"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi -"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading -"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations -"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:) - - - -Inverting this list, LAMMPS currently has acceleration support for -three kinds of hardware, via the listed packages: - -Many-core CPUs : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html, "USER-OMP"_accelerate_omp.html, "OPT"_accelerate_opt.html packages -NVIDIA GPUs : "GPU"_accelerate_gpu.html, "KOKKOS"_accelerate_kokkos.html packages -Intel Phi : "USER-INTEL"_accelerate_intel.html, "KOKKOS"_accelerate_kokkos.html packages :tb(s=:) - -Which package is fastest for your hardware may depend on the size -problem you are running and what commands (accelerated and -non-accelerated) are invoked by your input script. While these doc -pages include performance guidelines, there is no substitute for -trying out the different packages appropriate to your hardware. - -Any accelerated style has the same name as the corresponding standard -style, except that a suffix is appended. Otherwise, the syntax for -the command that uses the style is identical, their functionality is -the same, and the numerical results it produces should also be the -same, except for precision and round-off effects. - -For example, all of these styles are accelerated variants of the -Lennard-Jones "pair_style lj/cut"_pair_lj.html: - -"pair_style lj/cut/gpu"_pair_lj.html -"pair_style lj/cut/intel"_pair_lj.html -"pair_style lj/cut/kk"_pair_lj.html -"pair_style lj/cut/omp"_pair_lj.html -"pair_style lj/cut/opt"_pair_lj.html :ul - -To see what accelerate styles are currently available, see -"Section 3.5"_Section_commands.html#cmd_5 of the manual. The -doc pages for individual commands (e.g. "pair lj/cut"_pair_lj.html or -"fix nve"_fix_nve.html) also list any accelerated variants available -for that style. - -To use an accelerator package in LAMMPS, and one or more of the styles -it provides, follow these general steps. Details vary from package to -package and are explained in the individual accelerator doc pages, -listed above: - -build the accelerator library | - only for GPU package | -install the accelerator package | - make yes-opt, make yes-user-intel, etc | -add compile/link flags to Makefile.machine in src/MAKE | - only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | -re-build LAMMPS | - make machine | -prepare and test a regular LAMMPS simulation | - lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | -enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, | - only needed for KOKKOS package | -set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, | - only if defaults need to be changed | -use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu -:tb(c=2,s=|) - -Note that the first 4 steps can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual, and its use is -illustrated in the individual accelerator sections. Typically these -steps only need to be done once, to create an executable that uses one -or more accelerator packages. - -The last 4 steps can all be done from the command-line when LAMMPS is -launched, without changing your input script, as illustrated in the -individual accelerator sections. Or you can add -"package"_package.html and "suffix"_suffix.html commands to your input -script. - -NOTE: With a few exceptions, you can build a single LAMMPS executable -with all its accelerator packages installed. Note however that the -USER-INTEL and KOKKOS packages require you to choose one of their -hardware options when building for a specific platform. I.e. CPU or -Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi -option for the KOKKOS package. - -These are the exceptions. You cannot build a single executable with: - -both the USER-INTEL Phi and KOKKOS Phi options -the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul - -See the examples/accelerate/README and make.list files for sample -Make.py commands that build LAMMPS with any or all of the accelerator -packages. As an example, here is a command that builds with all the -GPU related packages installed (GPU, KOKKOS with Cuda), including -settings to build the needed auxiliary GPU libraries for Kepler GPUs: - -Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ - -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre - -The examples/accelerate directory also has input scripts that can be -used with all of the accelerator packages. See its README file for -details. - -Likewise, the bench directory has FERMI and KEPLER and PHI -sub-directories with Make.py commands and input scripts for using all -the accelerator packages on various machines. See the README files in -those dirs. - -As mentioned above, the "Benchmark -page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives -performance results for the various accelerator packages for several -of the standard LAMMPS benchmark problems, as a function of problem -size and number of compute nodes, on different hardware platforms. - -Here is a brief summary of what the various packages provide. Details -are in the individual accelerator sections. - -Styles with a "gpu" suffix are part of the GPU package, and can be run -on NVIDIA GPUs. The speed-up on a GPU depends on a variety of -factors, discussed in the accelerator sections. :ulb,l - -Styles with an "intel" suffix are part of the USER-INTEL -package. These styles support vectorized single and mixed precision -calculations, in addition to full double precision. In extreme cases, -this can provide speedups over 3.5x on CPUs. The package also -supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending -on the hardware configuration. :l - -Styles with a "kk" suffix are part of the KOKKOS package, and can be -run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel -Xeon Phi in "native" mode. The speed-up depends on a variety of -factors, as discussed on the KOKKOS accelerator page. :l - -Styles with an "omp" suffix are part of the USER-OMP package and allow -a pair-style to be run in multi-threaded mode using OpenMP. This can -be useful on nodes with high-core counts when using less MPI processes -than cores is advantageous, e.g. when running with PPPM so that FFTs -are run on fewer MPI processors or when the many MPI tasks would -overload the available bandwidth for communication. :l - -Styles with an "opt" suffix are part of the OPT package and typically -speed-up the pairwise calculations of your simulation by 5-25% on a -CPU. :l -:ule - -The individual accelerator package doc pages explain: - -what hardware and software the accelerated package requires -how to build LAMMPS with the accelerated package -how to run with the accelerated package either via command-line switches or modifying the input script -speed-ups to expect -guidelines for best performance -restrictions :ul - -:line - -5.4 Comparison of various accelerator packages :h3,link(acc_4) - -NOTE: this section still needs to be re-worked with additional KOKKOS -and USER-INTEL information. - -The next section compares and contrasts the various accelerator -options, since there are multiple ways to perform OpenMP threading, -run on GPUs, and run on Intel Xeon Phi coprocessors. - -All 3 of these packages accelerate a LAMMPS calculation using NVIDIA -hardware, but they do it in different ways. - -As a consequence, for a particular simulation on specific hardware, -one package may be faster than the other. We give guidelines below, -but the best way to determine which package is faster for your input -script is to try both of them on your machine. See the benchmarking -section below for examples where this has been done. - -[Guidelines for using each package optimally:] - -The GPU package allows you to assign multiple CPUs (cores) to a single -GPU (a common configuration for "hybrid" nodes that contain multicore -CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l - -The GPU package moves per-atom data (coordinates, forces) -back-and-forth between the CPU and GPU every timestep. The -KOKKOS/CUDA package only does this on timesteps when a CPU calculation -is required (e.g. to invoke a fix or compute that is non-GPU-ized). -Hence, if you can formulate your input script to only use GPU-ized -fixes and computes, and avoid doing I/O too often (thermo output, dump -file snapshots, restart files), then the data transfer cost of the -KOKKOS/CUDA package can be very low, causing it to run faster than the -GPU package. :l - -The GPU package is often faster than the KOKKOS/CUDA package, if the -number of atoms per GPU is smaller. The crossover point, in terms of -atoms/GPU at which the KOKKOS/CUDA package becomes faster depends -strongly on the pair style. For example, for a simple Lennard Jones -system the crossover (in single precision) is often about 50K-100K -atoms per GPU. When performing double precision calculations the -crossover point can be significantly smaller. :l - -Both packages compute bonded interactions (bonds, angles, etc) on the -CPU. If the GPU package is running with several MPI processes -assigned to one GPU, the cost of computing the bonded interactions is -spread across more CPUs and hence the GPU package can run faster. :l - -When using the GPU package with multiple CPUs assigned to one GPU, its -performance depends to some extent on high bandwidth between the CPUs -and the GPU. Hence its performance is affected if full 16 PCIe lanes -are not available for each GPU. In HPC environments this can be the -case if S2050/70 servers are used, where two devices generally share -one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide -full 16 lanes to each of the PCIe 2.0 16x slots. :l -:ule - -[Differences between the two packages:] - -The GPU package accelerates only pair force, neighbor list, and PPPM -calculations. :ulb,l - -The GPU package requires neighbor lists to be built on the CPU when using -exclusion lists, hybrid pair styles, or a triclinic simulation box. :l -:ule diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt deleted file mode 100644 index cc9757a88e8923e8bbcbb5aee8381c8488b9de55..0000000000000000000000000000000000000000 --- a/doc/src/Section_commands.txt +++ /dev/null @@ -1,1268 +0,0 @@ -"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -3. Commands :h2 - -This section describes how a LAMMPS input script is formatted and the -input script commands used to define a LAMMPS simulation. - -3.1 "LAMMPS input script"_#cmd_1 -3.2 "Parsing rules"_#cmd_2 -3.3 "Input script structure"_#cmd_3 -3.4 "Commands listed by category"_#cmd_4 -3.5 "Commands listed alphabetically"_#cmd_5 :all(b) - -:line -:line - -3.1 LAMMPS input script :link(cmd_1),h4 - -LAMMPS executes by reading commands from a input script (text file), -one line at a time. When the input script ends, LAMMPS exits. Each -command causes LAMMPS to take some action. It may set an internal -variable, read in a file, or run a simulation. Most commands have -default settings, which means you only need to use the command if you -wish to change the default. - -In many cases, the ordering of commands in an input script is not -important. However the following rules apply: - -(1) LAMMPS does not read your entire input script and then perform a -simulation with all the settings. Rather, the input script is read -one line at a time and each command takes effect when it is read. -Thus this sequence of commands: - -timestep 0.5 -run 100 -run 100 :pre - -does something different than this sequence: - -run 100 -timestep 0.5 -run 100 :pre - -In the first case, the specified timestep (0.5 fmsec) is used for two -simulations of 100 timesteps each. In the 2nd case, the default -timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 -fmsec timestep is used for the 2nd one. - -(2) Some commands are only valid when they follow other commands. For -example you cannot set the temperature of a group of atoms until atoms -have been defined and a group command is used to define which atoms -belong to the group. - -(3) Sometimes command B will use values that can be set by command A. -This means command A must precede command B in the input script if it -is to have the desired effect. For example, the -"read_data"_read_data.html command initializes the system by setting -up the simulation box and assigning atoms to processors. If default -values are not desired, the "processors"_processors.html and -"boundary"_boundary.html commands need to be used before read_data to -tell LAMMPS how to map processors to the simulation box. - -Many input script errors are detected by LAMMPS and an ERROR or -WARNING message is printed. "This section"_Section_errors.html gives -more information on what errors mean. The documentation for each -command lists restrictions on how the command can be used. - -:line - -3.2 Parsing rules :link(cmd_2),h4 - -Each non-blank line in the input script is treated as a command. -LAMMPS commands are case sensitive. Command names are lower-case, as -are specified command arguments. Upper case letters may be used in -file names or user-chosen ID strings. - -Here is how each line in the input script is parsed by LAMMPS: - -(1) If the last printable character on the line is a "&" character, -the command is assumed to continue on the next line. The next line is -concatenated to the previous line by removing the "&" character and -line break. This allows long commands to be continued across two or -more lines. See the discussion of triple quotes in (6) for how to -continue a command across multiple line without using "&" characters. - -(2) All characters from the first "#" character onward are treated as -comment and discarded. See an exception in (6). Note that a -comment after a trailing "&" character will prevent the command from -continuing on the next line. Also note that for multi-line commands a -single leading "#" will comment out the entire command. - -(3) The line is searched repeatedly for $ characters, which indicate -variables that are replaced with a text string. See an exception in -(6). - -If the $ is followed by curly brackets, then the variable name is the -text inside the curly brackets. If no curly brackets follow the $, -then the variable name is the single character immediately following -the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and -"x". - -How the variable is converted to a text string depends on what style -of variable it is; see the "variable"_variable.html doc page for details. -It can be a variable that stores multiple text strings, and return one -of them. The returned text string can be multiple "words" (space -separated) which will then be interpreted as multiple arguments in the -input command. The variable can also store a numeric formula which -will be evaluated and its numeric result returned as a string. - -As a special case, if the $ is followed by parenthesis, then the text -inside the parenthesis is treated as an "immediate" variable and -evaluated as an "equal-style variable"_variable.html. This is a way -to use numeric formulas in an input script without having to assign -them to variable names. For example, these 3 input script lines: - -variable X equal (xlo+xhi)/2+sqrt(v_area) -region 1 block $X 2 INF INF EDGE EDGE -variable X delete :pre - -can be replaced by - -region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre - -so that you do not have to define (or discard) a temporary variable X. - -Note that neither the curly-bracket or immediate form of variables can -contain nested $ characters for other variables to substitute for. -Thus you cannot do this: - -variable a equal 2 -variable b2 equal 4 -print "B2 = $\{b$a\}" :pre - -Nor can you specify this $($x-1.0) for an immediate variable, but -you could use $(v_x-1.0), since the latter is valid syntax for an -"equal-style variable"_variable.html. - -See the "variable"_variable.html command for more details of how -strings are assigned to variables and evaluated, and how they can be -used in input script commands. - -(4) The line is broken into "words" separated by whitespace (tabs, -spaces). Note that words can thus contain letters, digits, -underscores, or punctuation characters. - -(5) The first word is the command name. All successive words in the -line are arguments. - -(6) If you want text with spaces to be treated as a single argument, -it can be enclosed in either single or double or triple quotes. A -long single argument enclosed in single or double quotes can span -multiple lines if the "&" character is used, as described above. When -the lines are concatenated together (and the "&" characters and line -breaks removed), the text will become a single line. If you want -multiple lines of an argument to retain their line breaks, the text -can be enclosed in triple quotes, in which case "&" characters are not -needed. For example: - -print "Volume = $v" -print 'Volume = $v' -if "$\{steps\} > 1000" then quit -variable a string "red green blue & - purple orange cyan" -print """ -System volume = $v -System temperature = $t -""" :pre - -In each case, the single, double, or triple quotes are removed when -the single argument they enclose is stored internally. - -See the "dump modify format"_dump_modify.html, "print"_print.html, -"if"_if.html, and "python"_python.html commands for examples. - -A "#" or "$" character that is between quotes will not be treated as a -comment indicator in (2) or substituted for as a variable in (3). - -NOTE: If the argument is itself a command that requires a quoted -argument (e.g. using a "print"_print.html command as part of an -"if"_if.html or "run every"_run.html command), then single, double, or -triple quotes can be nested in the usual manner. See the doc pages -for those commands for examples. Only one of level of nesting is -allowed, but that should be sufficient for most use cases. - -:line - -3.3 Input script structure :h3,link(cmd_3) - -This section describes the structure of a typical LAMMPS input script. -The "examples" directory in the LAMMPS distribution contains many -sample input scripts; the corresponding problems are discussed in -"Section 7"_Section_example.html, and animated on the "LAMMPS -WWW Site"_lws. - -A LAMMPS input script typically has 4 parts: - -Initialization -Atom definition -Settings -Run a simulation :ol - -The last 2 parts can be repeated as many times as desired. I.e. run a -simulation, change some settings, run some more, etc. Each of the 4 -parts is now described in more detail. Remember that almost all the -commands need only be used if a non-default value is desired. - -(1) Initialization - -Set parameters that need to be defined before atoms are created or -read-in from a file. - -The relevant commands are "units"_units.html, -"dimension"_dimension.html, "newton"_newton.html, -"processors"_processors.html, "boundary"_boundary.html, -"atom_style"_atom_style.html, "atom_modify"_atom_modify.html. - -If force-field parameters appear in the files that will be read, these -commands tell LAMMPS what kinds of force fields are being used: -"pair_style"_pair_style.html, "bond_style"_bond_style.html, -"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, -"improper_style"_improper_style.html. - -(2) Atom definition - -There are 3 ways to define atoms in LAMMPS. Read them in from a data -or restart file via the "read_data"_read_data.html or -"read_restart"_read_restart.html commands. These files can contain -molecular topology information. Or create atoms on a lattice (with no -molecular topology), using these commands: "lattice"_lattice.html, -"region"_region.html, "create_box"_create_box.html, -"create_atoms"_create_atoms.html. The entire set of atoms can be -duplicated to make a larger simulation using the -"replicate"_replicate.html command. - -(3) Settings - -Once atoms and molecular topology are defined, a variety of settings -can be specified: force field coefficients, simulation parameters, -output options, etc. - -Force field coefficients are set by these commands (they can also be -set in the read-in files): "pair_coeff"_pair_coeff.html, -"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, -"dihedral_coeff"_dihedral_coeff.html, -"improper_coeff"_improper_coeff.html, -"kspace_style"_kspace_style.html, "dielectric"_dielectric.html, -"special_bonds"_special_bonds.html. - -Various simulation parameters are set by these commands: -"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, -"group"_group.html, "timestep"_timestep.html, -"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, -"min_style"_min_style.html, "min_modify"_min_modify.html. - -Fixes impose a variety of boundary conditions, time integration, and -diagnostic options. The "fix"_fix.html command comes in many flavors. - -Various computations can be specified for execution during a -simulation using the "compute"_compute.html, -"compute_modify"_compute_modify.html, and "variable"_variable.html -commands. - -Output options are set by the "thermo"_thermo.html, "dump"_dump.html, -and "restart"_restart.html commands. - -(4) Run a simulation - -A molecular dynamics simulation is run using the "run"_run.html -command. Energy minimization (molecular statics) is performed using -the "minimize"_minimize.html command. A parallel tempering -(replica-exchange) simulation can be run using the -"temper"_temper.html command. - -:line - -3.4 Commands listed by category :link(cmd_4),h4 - -This section lists core LAMMPS commands, grouped by category. -The "next section"_#cmd_5 lists all commands alphabetically. The -next section also includes (long) lists of style options for entries -that appear in the following categories as a single command (fix, -compute, pair, etc). Commands that are added by user packages are not -included in the categories here, but they are in the next section. - -Initialization: - -"newton"_newton.html, -"package"_package.html, -"processors"_processors.html, -"suffix"_suffix.html, -"units"_units.html - -Setup simulation box: - -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"create_box"_create_box.html, -"dimension"_dimension.html, -"lattice"_lattice.html, -"region"_region.html - -Setup atoms: - -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"displace_atoms"_displace_atoms.html, -"group"_group.html, -"mass"_mass.html, -"molecule"_molecule.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"replicate"_replicate.html, -"set"_set.html, -"velocity"_velocity.html - -Force fields: - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"special_bonds"_special_bonds.html - -Settings: - -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"info"_info.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"partition"_partition.html, -"reset_timestep"_reset_timestep.html, -"run_style"_run_style.html, -"timer"_timer.html, -"timestep"_timestep.html - -Operations within timestepping (fixes) and diagnostics (computes): - -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"uncompute"_uncompute.html, -"unfix"_unfix.html - -Output: - -"dump image"_dump_image.html, -"dump movie"_dump_image.html, -"dump"_dump.html, -"dump_modify"_dump_modify.html, -"restart"_restart.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"undump"_undump.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html - -Actions: - -"minimize"_minimize.html, -"neb"_neb.html, -"prd"_prd.html, -"rerun"_rerun.html, -"run"_run.html, -"tad"_tad.html, -"temper"_temper.html - -Input script control: - -"clear"_clear.html, -"echo"_echo.html, -"if"_if.html, -"include"_include.html, -"jump"_jump.html, -"label"_label.html, -"log"_log.html, -"next"_next.html, -"print"_print.html, -"python"_python.html, -"quit"_quit.html, -"shell"_shell.html, -"variable"_variable.html - -:line - -3.5 Individual commands :h3,link(cmd_5),link(comm) - -This section lists all LAMMPS commands alphabetically, with a separate -listing below of styles within certain commands. The "previous -section"_#cmd_4 lists the same commands, grouped by category. Note -that some style options for some commands are part of specific LAMMPS -packages, which means they cannot be used unless the package was -included when LAMMPS was built. Not all packages are included in a -default LAMMPS build. These dependencies are listed as Restrictions -in the command's documentation. - -"angle_coeff"_angle_coeff.html, -"angle_style"_angle_style.html, -"atom_modify"_atom_modify.html, -"atom_style"_atom_style.html, -"balance"_balance.html, -"bond_coeff"_bond_coeff.html, -"bond_style"_bond_style.html, -"bond_write"_bond_write.html, -"boundary"_boundary.html, -"box"_box.html, -"change_box"_change_box.html, -"clear"_clear.html, -"comm_modify"_comm_modify.html, -"comm_style"_comm_style.html, -"compute"_compute.html, -"compute_modify"_compute_modify.html, -"create_atoms"_create_atoms.html, -"create_bonds"_create_bonds.html, -"create_box"_create_box.html, -"delete_atoms"_delete_atoms.html, -"delete_bonds"_delete_bonds.html, -"dielectric"_dielectric.html, -"dihedral_coeff"_dihedral_coeff.html, -"dihedral_style"_dihedral_style.html, -"dimension"_dimension.html, -"displace_atoms"_displace_atoms.html, -"dump"_dump.html, -"dump image"_dump_image.html, -"dump_modify"_dump_modify.html, -"dump movie"_dump_image.html, -"echo"_echo.html, -"fix"_fix.html, -"fix_modify"_fix_modify.html, -"group"_group.html, -"if"_if.html, -"info"_info.html, -"improper_coeff"_improper_coeff.html, -"improper_style"_improper_style.html, -"include"_include.html, -"jump"_jump.html, -"kspace_modify"_kspace_modify.html, -"kspace_style"_kspace_style.html, -"label"_label.html, -"lattice"_lattice.html, -"log"_log.html, -"mass"_mass.html, -"minimize"_minimize.html, -"min_modify"_min_modify.html, -"min_style"_min_style.html, -"molecule"_molecule.html, -"neb"_neb.html, -"neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, -"newton"_newton.html, -"next"_next.html, -"package"_package.html, -"pair_coeff"_pair_coeff.html, -"pair_modify"_pair_modify.html, -"pair_style"_pair_style.html, -"pair_write"_pair_write.html, -"partition"_partition.html, -"prd"_prd.html, -"print"_print.html, -"processors"_processors.html, -"python"_python.html, -"quit"_quit.html, -"read_data"_read_data.html, -"read_dump"_read_dump.html, -"read_restart"_read_restart.html, -"region"_region.html, -"replicate"_replicate.html, -"rerun"_rerun.html, -"reset_ids"_reset_ids.html, -"reset_timestep"_reset_timestep.html, -"restart"_restart.html, -"run"_run.html, -"run_style"_run_style.html, -"set"_set.html, -"shell"_shell.html, -"special_bonds"_special_bonds.html, -"suffix"_suffix.html, -"tad"_tad.html, -"temper"_temper.html, -"thermo"_thermo.html, -"thermo_modify"_thermo_modify.html, -"thermo_style"_thermo_style.html, -"timer"_timer.html, -"timestep"_timestep.html, -"uncompute"_uncompute.html, -"undump"_undump.html, -"unfix"_unfix.html, -"units"_units.html, -"variable"_variable.html, -"velocity"_velocity.html, -"write_coeff"_write_coeff.html, -"write_data"_write_data.html, -"write_dump"_write_dump.html, -"write_restart"_write_restart.html :tb(c=6,ea=c) - -These are additional commands in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"dump netcdf"_dump_netcdf.html, -"dump netcdf/mpiio"_dump_netcdf.html, -"dump vtk"_dump_vtk.html, -"group2ndx"_group2ndx.html, -"ndx2group"_group2ndx.html, -"temper/grem"_temper_grem.html, -"temper/npt"_temper_npt.html :tb(c=3,ea=c) - -:line - -Fix styles :h3 - -See the "fix"_fix.html command for one-line descriptions of each style -or click on the style itself for a full description. Some of the -styles have accelerated versions, which can be used if LAMMPS is built -with the "appropriate accelerated package"_Section_accelerate.html. -This is indicated by additional letters in parenthesis: g = GPU, i = -USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. - -"adapt"_fix_adapt.html, -"addforce"_fix_addforce.html, -"append/atoms"_fix_append_atoms.html, -"atom/swap"_fix_atom_swap.html, -"aveforce"_fix_aveforce.html, -"ave/atom"_fix_ave_atom.html, -"ave/chunk"_fix_ave_chunk.html, -"ave/correlate"_fix_ave_correlate.html, -"ave/histo"_fix_ave_histo.html, -"ave/histo/weight"_fix_ave_histo.html, -"ave/time"_fix_ave_time.html, -"balance"_fix_balance.html, -"bond/break"_fix_bond_break.html, -"bond/create"_fix_bond_create.html, -"bond/swap"_fix_bond_swap.html, -"box/relax"_fix_box_relax.html, -"cmap"_fix_cmap.html, -"controller"_fix_controller.html, -"deform (k)"_fix_deform.html, -"deposit"_fix_deposit.html, -"drag"_fix_drag.html, -"dt/reset"_fix_dt_reset.html, -"efield"_fix_efield.html, -"ehex"_fix_ehex.html, -"enforce2d (k)"_fix_enforce2d.html, -"evaporate"_fix_evaporate.html, -"external"_fix_external.html, -"freeze"_fix_freeze.html, -"gcmc"_fix_gcmc.html, -"gld"_fix_gld.html, -"gravity (o)"_fix_gravity.html, -"halt"_fix_halt.html, -"heat"_fix_heat.html, -"indent"_fix_indent.html, -"latte"_fix_latte.html, -"langevin (k)"_fix_langevin.html, -"lineforce"_fix_lineforce.html, -"momentum (k)"_fix_momentum.html, -"move"_fix_move.html, -"mscg"_fix_mscg.html, -"msst"_fix_msst.html, -"neb"_fix_neb.html, -"nph (ko)"_fix_nh.html, -"nphug (o)"_fix_nphug.html, -"nph/asphere (o)"_fix_nph_asphere.html, -"nph/body"_fix_nph_body.html, -"nph/sphere (o)"_fix_nph_sphere.html, -"npt (kio)"_fix_nh.html, -"npt/asphere (o)"_fix_npt_asphere.html, -"npt/body"_fix_npt_body.html, -"npt/sphere (o)"_fix_npt_sphere.html, -"nve (kio)"_fix_nve.html, -"nve/asphere (i)"_fix_nve_asphere.html, -"nve/asphere/noforce"_fix_nve_asphere_noforce.html, -"nve/body"_fix_nve_body.html, -"nve/limit"_fix_nve_limit.html, -"nve/line"_fix_nve_line.html, -"nve/noforce"_fix_nve_noforce.html, -"nve/sphere (o)"_fix_nve_sphere.html, -"nve/tri"_fix_nve_tri.html, -"nvt (iko)"_fix_nh.html, -"nvt/asphere (o)"_fix_nvt_asphere.html, -"nvt/body"_fix_nvt_body.html, -"nvt/sllod (io)"_fix_nvt_sllod.html, -"nvt/sphere (o)"_fix_nvt_sphere.html, -"oneway"_fix_oneway.html, -"orient/bcc"_fix_orient.html, -"orient/fcc"_fix_orient.html, -"planeforce"_fix_planeforce.html, -"poems"_fix_poems.html, -"pour"_fix_pour.html, -"press/berendsen"_fix_press_berendsen.html, -"print"_fix_print.html, -"property/atom (k)"_fix_property_atom.html, -"python/invoke"_fix_python_invoke.html, -"python/move"_fix_python_move.html, -"qeq/comb (o)"_fix_qeq_comb.html, -"qeq/dynamic"_fix_qeq.html, -"qeq/fire"_fix_qeq.html, -"qeq/point"_fix_qeq.html, -"qeq/shielded"_fix_qeq.html, -"qeq/slater"_fix_qeq.html, -"rattle"_fix_shake.html, -"reax/bonds"_fix_reax_bonds.html, -"recenter"_fix_recenter.html, -"restrain"_fix_restrain.html, -"rigid (o)"_fix_rigid.html, -"rigid/nph (o)"_fix_rigid.html, -"rigid/npt (o)"_fix_rigid.html, -"rigid/nve (o)"_fix_rigid.html, -"rigid/nvt (o)"_fix_rigid.html, -"rigid/small (o)"_fix_rigid.html, -"rigid/small/nph"_fix_rigid.html, -"rigid/small/npt"_fix_rigid.html, -"rigid/small/nve"_fix_rigid.html, -"rigid/small/nvt"_fix_rigid.html, -"setforce (k)"_fix_setforce.html, -"shake"_fix_shake.html, -"spring"_fix_spring.html, -"spring/chunk"_fix_spring_chunk.html, -"spring/rg"_fix_spring_rg.html, -"spring/self"_fix_spring_self.html, -"srd"_fix_srd.html, -"store/force"_fix_store_force.html, -"store/state"_fix_store_state.html, -"temp/berendsen"_fix_temp_berendsen.html, -"temp/csld"_fix_temp_csvr.html, -"temp/csvr"_fix_temp_csvr.html, -"temp/rescale"_fix_temp_rescale.html, -"tfmc"_fix_tfmc.html, -"thermal/conductivity"_fix_thermal_conductivity.html, -"tmd"_fix_tmd.html, -"ttm"_fix_ttm.html, -"tune/kspace"_fix_tune_kspace.html, -"vector"_fix_vector.html, -"viscosity"_fix_viscosity.html, -"viscous"_fix_viscous.html, -"wall/colloid"_fix_wall.html, -"wall/gran"_fix_wall_gran.html, -"wall/gran/region"_fix_wall_gran_region.html, -"wall/harmonic"_fix_wall.html, -"wall/lj1043"_fix_wall.html, -"wall/lj126"_fix_wall.html, -"wall/lj93 (k)"_fix_wall.html, -"wall/piston"_fix_wall_piston.html, -"wall/reflect (k)"_fix_wall_reflect.html, -"wall/region"_fix_wall_region.html, -"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) - -These are additional fix styles in USER packages, which can be used if -"LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"adapt/fep"_fix_adapt_fep.html, -"addtorque"_fix_addtorque.html, -"atc"_fix_atc.html, -"ave/correlate/long"_fix_ave_correlate_long.html, -"bond/react"_fix_bond_react.html, -"colvars"_fix_colvars.html, -"dpd/energy (k)"_fix_dpd_energy.html, -"drude"_fix_drude.html, -"drude/transform/direct"_fix_drude_transform.html, -"drude/transform/reverse"_fix_drude_transform.html, -"edpd/source"_fix_dpd_source.html, -"eos/cv"_fix_eos_cv.html, -"eos/table"_fix_eos_table.html, -"eos/table/rx (k)"_fix_eos_table_rx.html, -"filter/corotate"_fix_filter_corotate.html, -"flow/gauss"_fix_flow_gauss.html, -"gle"_fix_gle.html, -"grem"_fix_grem.html, -"imd"_fix_imd.html, -"ipi"_fix_ipi.html, -"langevin/drude"_fix_langevin_drude.html, -"langevin/eff"_fix_langevin_eff.html, -"lb/fluid"_fix_lb_fluid.html, -"lb/momentum"_fix_lb_momentum.html, -"lb/pc"_fix_lb_pc.html, -"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, -"lb/viscous"_fix_lb_viscous.html, -"meso"_fix_meso.html, -"manifoldforce"_fix_manifoldforce.html, -"meso/stationary"_fix_meso_stationary.html, -"mvv/dpd"_fix_mvv_dpd.html, -"mvv/edpd"_fix_mvv_dpd.html, -"mvv/tdpd"_fix_mvv_dpd.html, -"nph/eff"_fix_nh_eff.html, -"npt/eff"_fix_nh_eff.html, -"npt/uef"_fix_nh_uef.html, -"nve/dot"_fix_nve_dot.html, -"nve/dotc/langevin"_fix_nve_dotc_langevin.html, -"nve/eff"_fix_nve_eff.html, -"nve/manifold/rattle"_fix_nve_manifold_rattle.html, -"nvk"_fix_nvk.html, -"nvt/eff"_fix_nh_eff.html, -"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, -"nvt/sllod/eff"_fix_nvt_sllod_eff.html, -"nvt/uef"_fix_nh_uef.html, -"phonon"_fix_phonon.html, -"pimd"_fix_pimd.html, -"qbmsst"_fix_qbmsst.html, -"qeq/reax (ko)"_fix_qeq_reax.html, -"qmmm"_fix_qmmm.html, -"qtb"_fix_qtb.html, -"reax/c/bonds (k)"_fix_reax_bonds.html, -"reax/c/species (k)"_fix_reaxc_species.html, -"rhok"_fix_rhok.html, -"rx (k)"_fix_rx.html, -"saed/vtk"_fix_saed_vtk.html, -"shardlow (k)"_fix_shardlow.html, -"smd"_fix_smd.html, -"smd/adjust/dt"_fix_smd_adjust_dt.html, -"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, -"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, -"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, -"smd/setvel"_fix_smd_setvel.html, -"smd/wall/surface"_fix_smd_wall_surface.html, -"tdpd/source"_fix_dpd_source.html, -"temp/rescale/eff"_fix_temp_rescale_eff.html, -"ti/spring"_fix_ti_spring.html, -"ttm/mod"_fix_ttm.html, -"wall/ees"_fix_wall_ees.html, -"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c) - -:line - -Compute styles :h3 - -See the "compute"_compute.html command for one-line descriptions of -each style or click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"aggregate/atom"_compute_cluster_atom.html, -"angle"_compute_angle.html, -"angle/local"_compute_angle_local.html, -"angmom/chunk"_compute_angmom_chunk.html, -"body/local"_compute_body_local.html, -"bond"_compute_bond.html, -"bond/local"_compute_bond_local.html, -"centro/atom"_compute_centro_atom.html, -"chunk/atom"_compute_chunk_atom.html, -"cluster/atom"_compute_cluster_atom.html, -"cna/atom"_compute_cna_atom.html, -"com"_compute_com.html, -"com/chunk"_compute_com_chunk.html, -"contact/atom"_compute_contact_atom.html, -"coord/atom"_compute_coord_atom.html, -"damage/atom"_compute_damage_atom.html, -"dihedral"_compute_dihedral.html, -"dihedral/local"_compute_dihedral_local.html, -"dilatation/atom"_compute_dilatation_atom.html, -"dipole/chunk"_compute_dipole_chunk.html, -"displace/atom"_compute_displace_atom.html, -"erotate/asphere"_compute_erotate_asphere.html, -"erotate/rigid"_compute_erotate_rigid.html, -"erotate/sphere"_compute_erotate_sphere.html, -"erotate/sphere/atom"_compute_erotate_sphere_atom.html, -"event/displace"_compute_event_displace.html, -"fragment/atom"_compute_cluster_atom.html, -"global/atom"_compute_global_atom.html, -"group/group"_compute_group_group.html, -"gyration"_compute_gyration.html, -"gyration/chunk"_compute_gyration_chunk.html, -"heat/flux"_compute_heat_flux.html, -"hexorder/atom"_compute_hexorder_atom.html, -"improper"_compute_improper.html, -"improper/local"_compute_improper_local.html, -"inertia/chunk"_compute_inertia_chunk.html, -"ke"_compute_ke.html, -"ke/atom"_compute_ke_atom.html, -"ke/rigid"_compute_ke_rigid.html, -"msd"_compute_msd.html, -"msd/chunk"_compute_msd_chunk.html, -"msd/nongauss"_compute_msd_nongauss.html, -"omega/chunk"_compute_omega_chunk.html, -"orientorder/atom"_compute_orientorder_atom.html, -"pair"_compute_pair.html, -"pair/local"_compute_pair_local.html, -"pe"_compute_pe.html, -"pe/atom"_compute_pe_atom.html, -"plasticity/atom"_compute_plasticity_atom.html, -"pressure"_compute_pressure.html, -"property/atom"_compute_property_atom.html, -"property/local"_compute_property_local.html, -"property/chunk"_compute_property_chunk.html, -"rdf"_compute_rdf.html, -"reduce"_compute_reduce.html, -"reduce/region"_compute_reduce.html, -"rigid/local"_compute_rigid_local.html, -"slice"_compute_slice.html, -"sna/atom"_compute_sna_atom.html, -"snad/atom"_compute_sna_atom.html, -"snav/atom"_compute_sna_atom.html, -"stress/atom"_compute_stress_atom.html, -"temp (k)"_compute_temp.html, -"temp/asphere"_compute_temp_asphere.html, -"temp/body"_compute_temp_body.html, -"temp/chunk"_compute_temp_chunk.html, -"temp/com"_compute_temp_com.html, -"temp/deform"_compute_temp_deform.html, -"temp/partial"_compute_temp_partial.html, -"temp/profile"_compute_temp_profile.html, -"temp/ramp"_compute_temp_ramp.html, -"temp/region"_compute_temp_region.html, -"temp/sphere"_compute_temp_sphere.html, -"ti"_compute_ti.html, -"torque/chunk"_compute_torque_chunk.html, -"vacf"_compute_vacf.html, -"vcm/chunk"_compute_vcm_chunk.html, -"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c) - -These are additional compute styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"ackland/atom"_compute_ackland_atom.html, -"basal/atom"_compute_basal_atom.html, -"cnp/atom"_compute_cnp_atom.html, -"dpd"_compute_dpd.html, -"dpd/atom"_compute_dpd_atom.html, -"edpd/temp/atom"_compute_edpd_temp_atom.html, -"fep"_compute_fep.html, -"force/tally"_compute_tally.html, -"heat/flux/tally"_compute_tally.html, -"ke/eff"_compute_ke_eff.html, -"ke/atom/eff"_compute_ke_atom_eff.html, -"meso/e/atom"_compute_meso_e_atom.html, -"meso/rho/atom"_compute_meso_rho_atom.html, -"meso/t/atom"_compute_meso_t_atom.html, -"pe/tally"_compute_tally.html, -"pe/mol/tally"_compute_tally.html, -"pressure/uef"_compute_pressure_uef.html, -"saed"_compute_saed.html, -"smd/contact/radius"_compute_smd_contact_radius.html, -"smd/damage"_compute_smd_damage.html, -"smd/hourglass/error"_compute_smd_hourglass_error.html, -"smd/internal/energy"_compute_smd_internal_energy.html, -"smd/plastic/strain"_compute_smd_plastic_strain.html, -"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, -"smd/rho"_compute_smd_rho.html, -"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, -"smd/tlsph/dt"_compute_smd_tlsph_dt.html, -"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, -"smd/tlsph/shape"_compute_smd_tlsph_shape.html, -"smd/tlsph/strain"_compute_smd_tlsph_strain.html, -"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph/stress"_compute_smd_tlsph_stress.html, -"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, -"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, -"smd/ulsph/strain"_compute_smd_ulsph_strain.html, -"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, -"smd/ulsph/stress"_compute_smd_ulsph_stress.html, -"smd/vol"_compute_smd_vol.html, -"stress/tally"_compute_tally.html, -"tdpd/cc/atom"_compute_tdpd_cc_atom.html, -"temp/drude"_compute_temp_drude.html, -"temp/eff"_compute_temp_eff.html, -"temp/deform/eff"_compute_temp_deform_eff.html, -"temp/region/eff"_compute_temp_region_eff.html, -"temp/rotate"_compute_temp_rotate.html, -"temp/uef"_compute_temp_uef.html, -"xrd"_compute_xrd.html :tb(c=6,ea=c) - -:line - -Pair_style potentials :h3 - -See the "pair_style"_pair_style.html command for an overview of pair -potentials. Click on the style itself for a full description. Many -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"none"_pair_none.html, -"zero"_pair_zero.html, -"hybrid"_pair_hybrid.html, -"hybrid/overlay (k)"_pair_hybrid.html, -"adp (o)"_pair_adp.html, -"airebo (oi)"_pair_airebo.html, -"airebo/morse (oi)"_pair_airebo.html, -"beck (go)"_pair_beck.html, -"body"_pair_body.html, -"bop"_pair_bop.html, -"born (go)"_pair_born.html, -"born/coul/dsf"_pair_born.html, -"born/coul/dsf/cs"_pair_born.html, -"born/coul/long (go)"_pair_born.html, -"born/coul/long/cs"_pair_born.html, -"born/coul/msm (o)"_pair_born.html, -"born/coul/wolf (go)"_pair_born.html, -"born/coul/wolf/cs"_pair_born.html, -"brownian (o)"_pair_brownian.html, -"brownian/poly (o)"_pair_brownian.html, -"buck (giko)"_pair_buck.html, -"buck/coul/cut (giko)"_pair_buck.html, -"buck/coul/long (giko)"_pair_buck.html, -"buck/coul/long/cs"_pair_buck.html, -"buck/coul/msm (o)"_pair_buck.html, -"buck/long/coul/long (o)"_pair_buck_long.html, -"colloid (go)"_pair_colloid.html, -"comb (o)"_pair_comb.html, -"comb3"_pair_comb.html, -"coul/cut (gko)"_pair_coul.html, -"coul/debye (gko)"_pair_coul.html, -"coul/dsf (gko)"_pair_coul.html, -"coul/long (gko)"_pair_coul.html, -"coul/long/cs"_pair_coul.html, -"coul/msm"_pair_coul.html, -"coul/streitz"_pair_coul.html, -"coul/wolf (ko)"_pair_coul.html, -"coul/wolf/cs"_pair_coul.html, -"dpd (gio)"_pair_dpd.html, -"dpd/tstat (go)"_pair_dpd.html, -"dsmc"_pair_dsmc.html, -"eam (gikot)"_pair_eam.html, -"eam/alloy (gikot)"_pair_eam.html, -"eam/fs (gikot)"_pair_eam.html, -"eim (o)"_pair_eim.html, -"gauss (go)"_pair_gauss.html, -"gayberne (gio)"_pair_gayberne.html, -"gran/hertz/history (o)"_pair_gran.html, -"gran/hooke (o)"_pair_gran.html, -"gran/hooke/history (o)"_pair_gran.html, -"gw"_pair_gw.html, -"gw/zbl"_pair_gw.html, -"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, -"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, -"kim"_pair_kim.html, -"lcbop"_pair_lcbop.html, -"line/lj"_pair_line_lj.html, -"lj/charmm/coul/charmm (iko)"_pair_charmm.html, -"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, -"lj/charmm/coul/long (giko)"_pair_charmm.html, -"lj/charmm/coul/msm"_pair_charmm.html, -"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, -"lj/charmmfsw/coul/long"_pair_charmm.html, -"lj/class2 (gko)"_pair_class2.html, -"lj/class2/coul/cut (ko)"_pair_class2.html, -"lj/class2/coul/long (gko)"_pair_class2.html, -"lj/cubic (go)"_pair_lj_cubic.html, -"lj/cut (gikot)"_pair_lj.html, -"lj/cut/coul/cut (gko)"_pair_lj.html, -"lj/cut/coul/debye (gko)"_pair_lj.html, -"lj/cut/coul/dsf (gko)"_pair_lj.html, -"lj/cut/coul/long (gikot)"_pair_lj.html, -"lj/cut/coul/long/cs"_pair_lj.html, -"lj/cut/coul/msm (go)"_pair_lj.html, -"lj/cut/coul/wolf (o)"_pair_lj.html, -"lj/cut/dipole/cut (go)"_pair_dipole.html, -"lj/cut/dipole/long"_pair_dipole.html, -"lj/cut/tip4p/cut (o)"_pair_lj.html, -"lj/cut/tip4p/long (ot)"_pair_lj.html, -"lj/expand (gko)"_pair_lj_expand.html, -"lj/gromacs (gko)"_pair_gromacs.html, -"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, -"lj/long/coul/long (io)"_pair_lj_long.html, -"lj/long/dipole/long"_pair_dipole.html, -"lj/long/tip4p/long"_pair_lj_long.html, -"lj/smooth (o)"_pair_lj_smooth.html, -"lj/smooth/linear (o)"_pair_lj_smooth_linear.html, -"lj96/cut (go)"_pair_lj96.html, -"lubricate (o)"_pair_lubricate.html, -"lubricate/poly (o)"_pair_lubricate.html, -"lubricateU"_pair_lubricateU.html, -"lubricateU/poly"_pair_lubricateU.html, -"meam"_pair_meam.html, -"mie/cut (o)"_pair_mie.html, -"morse (gkot)"_pair_morse.html, -"nb3b/harmonic (o)"_pair_nb3b_harmonic.html, -"nm/cut (o)"_pair_nm.html, -"nm/cut/coul/cut (o)"_pair_nm.html, -"nm/cut/coul/long (o)"_pair_nm.html, -"peri/eps"_pair_peri.html, -"peri/lps (o)"_pair_peri.html, -"peri/pmb (o)"_pair_peri.html, -"peri/ves"_pair_peri.html, -"polymorphic"_pair_polymorphic.html, -"python"_pair_python.html, -"reax"_pair_reax.html, -"rebo (oi)"_pair_airebo.html, -"resquared (go)"_pair_resquared.html, -"snap (k)"_pair_snap.html, -"soft (go)"_pair_soft.html, -"sw (giko)"_pair_sw.html, -"table (gko)"_pair_table.html, -"tersoff (giko)"_pair_tersoff.html, -"tersoff/mod (gko)"_pair_tersoff_mod.html, -"tersoff/mod/c (o)"_pair_tersoff_mod.html, -"tersoff/zbl (gko)"_pair_tersoff_zbl.html, -"tip4p/cut (o)"_pair_coul.html, -"tip4p/long (o)"_pair_coul.html, -"tri/lj"_pair_tri_lj.html, -"ufm (got)"_pair_ufm.html, -"vashishta (ko)"_pair_vashishta.html, -"vashishta/table (o)"_pair_vashishta.html, -"yukawa (gok)"_pair_yukawa.html, -"yukawa/colloid (go)"_pair_yukawa_colloid.html, -"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c) - -These are additional pair styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"agni (o)"_pair_agni.html, -"awpmd/cut"_pair_awpmd.html, -"buck/mdf"_pair_mdf.html, -"coul/cut/soft (o)"_pair_lj_soft.html, -"coul/diel (o)"_pair_coul_diel.html, -"coul/long/soft (o)"_pair_lj_soft.html, -"coul/shield"_pair_coul_shield.html, -"dpd/fdt"_pair_dpd_fdt.html, -"dpd/fdt/energy (k)"_pair_dpd_fdt.html, -"eam/cd (o)"_pair_eam.html, -"edip (o)"_pair_edip.html, -"edip/multi"_pair_edip.html, -"edpd"_pair_meso.html, -"eff/cut"_pair_eff.html, -"exp6/rx (k)"_pair_exp6_rx.html, -"extep"_pair_extep.html, -"gauss/cut"_pair_gauss.html, -"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html, -"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, -"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, -"lennard/mdf"_pair_mdf.html, -"list"_pair_list.html, -"lj/charmm/coul/long/soft (o)"_pair_charmm.html, -"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, -"lj/cut/dipole/sf (go)"_pair_dipole.html, -"lj/cut/soft (o)"_pair_lj_soft.html, -"lj/cut/thole/long (o)"_pair_thole.html, -"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, -"lj/mdf"_pair_mdf.html, -"lj/sdk (gko)"_pair_sdk.html, -"lj/sdk/coul/long (go)"_pair_sdk.html, -"lj/sdk/coul/msm (o)"_pair_sdk.html, -"mdpd"_pair_meso.html, -"mdpd/rhosum"_pair_meso.html, -"meam/c"_pair_meam.html, -"meam/spline (o)"_pair_meam_spline.html, -"meam/sw/spline"_pair_meam_sw_spline.html, -"mgpt"_pair_mgpt.html, -"momb"_pair_momb.html, -"morse/smooth/linear"_pair_morse.html, -"morse/soft"_pair_morse.html, -"multi/lucy"_pair_multi_lucy.html, -"multi/lucy/rx (k)"_pair_multi_lucy_rx.html, -"oxdna/coaxstk"_pair_oxdna.html, -"oxdna/excv"_pair_oxdna.html, -"oxdna/hbond"_pair_oxdna.html, -"oxdna/stk"_pair_oxdna.html, -"oxdna/xstk"_pair_oxdna.html, -"oxdna2/coaxstk"_pair_oxdna2.html, -"oxdna2/dh"_pair_oxdna2.html, -"oxdna2/excv"_pair_oxdna2.html, -"oxdna2/stk"_pair_oxdna2.html, -"quip"_pair_quip.html, -"reax/c (ko)"_pair_reaxc.html, -"smd/hertz"_pair_smd_hertz.html, -"smd/tlsph"_pair_smd_tlsph.html, -"smd/triangulated/surface"_pair_smd_triangulated_surface.html, -"smd/ulsph"_pair_smd_ulsph.html, -"smtbq"_pair_smtbq.html, -"snap (k)"_pair_snap.html, -"sph/heatconduction"_pair_sph_heatconduction.html, -"sph/idealgas"_pair_sph_idealgas.html, -"sph/lj"_pair_sph_lj.html, -"sph/rhosum"_pair_sph_rhosum.html, -"sph/taitwater"_pair_sph_taitwater.html, -"sph/taitwater/morris"_pair_sph_taitwater_morris.html, -"srp"_pair_srp.html, -"table/rx (k)"_pair_table_rx.html, -"tdpd"_pair_meso.html, -"tersoff/table (o)"_pair_tersoff.html, -"thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) - -:line - -Bond_style potentials :h3 - -See the "bond_style"_bond_style.html command for an overview of bond -potentials. Click on the style itself for a full description. Some -of the styles have accelerated versions, which can be used if LAMMPS -is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = -KOKKOS, o = USER-OMP, t = OPT. - -"none"_bond_none.html, -"zero"_bond_zero.html, -"hybrid"_bond_hybrid.html, -"class2 (ko)"_bond_class2.html, -"fene (iko)"_bond_fene.html, -"fene/expand (o)"_bond_fene_expand.html, -"gromos (o)"_bond_gromos.html, -"harmonic (ko)"_bond_harmonic.html, -"morse (o)"_bond_morse.html, -"nonlinear (o)"_bond_nonlinear.html, -"quartic (o)"_bond_quartic.html, -"table (o)"_bond_table.html :tb(c=4,ea=c) - -These are additional bond styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"harmonic/shift (o)"_bond_harmonic_shift.html, -"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, -"oxdna/fene"_bond_oxdna.html, -"oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c) - -:line - -Angle_style potentials :h3 - -See the "angle_style"_angle_style.html command for an overview of -angle potentials. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_angle_none.html, -"zero"_angle_zero.html, -"hybrid"_angle_hybrid.html, -"charmm (ko)"_angle_charmm.html, -"class2 (ko)"_angle_class2.html, -"cosine (o)"_angle_cosine.html, -"cosine/delta (o)"_angle_cosine_delta.html, -"cosine/periodic (o)"_angle_cosine_periodic.html, -"cosine/squared (o)"_angle_cosine_squared.html, -"harmonic (iko)"_angle_harmonic.html, -"table (o)"_angle_table.html :tb(c=4,ea=c) - -These are additional angle styles in USER packages, which can be used -if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift (o)"_angle_cosine_shift.html, -"cosine/shift/exp (o)"_angle_cosine_shift_exp.html, -"dipole (o)"_angle_dipole.html, -"fourier (o)"_angle_fourier.html, -"fourier/simple (o)"_angle_fourier_simple.html, -"quartic (o)"_angle_quartic.html, -"sdk"_angle_sdk.html :tb(c=4,ea=c) - -:line - -Dihedral_style potentials :h3 - -See the "dihedral_style"_dihedral_style.html command for an overview -of dihedral potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_dihedral_none.html, -"zero"_dihedral_zero.html, -"hybrid"_dihedral_hybrid.html, -"charmm (iko)"_dihedral_charmm.html, -"charmmfsw"_dihedral_charmm.html, -"class2 (ko)"_dihedral_class2.html, -"harmonic (io)"_dihedral_harmonic.html, -"helix (o)"_dihedral_helix.html, -"multi/harmonic (o)"_dihedral_multi_harmonic.html, -"opls (iko)"_dihedral_opls.html :tb(c=4,ea=c) - -These are additional dihedral styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, -"fourier (io)"_dihedral_fourier.html, -"nharmonic (o)"_dihedral_nharmonic.html, -"quadratic (o)"_dihedral_quadratic.html, -"spherical (o)"_dihedral_spherical.html, -"table (o)"_dihedral_table.html, -"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c) - -:line - -Improper_style potentials :h3 - -See the "improper_style"_improper_style.html command for an overview -of improper potentials. Click on the style itself for a full -description. Some of the styles have accelerated versions, which can -be used if LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"none"_improper_none.html, -"zero"_improper_zero.html, -"hybrid"_improper_hybrid.html, -"class2 (ko)"_improper_class2.html, -"cvff (io)"_improper_cvff.html, -"harmonic (iko)"_improper_harmonic.html, -"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) - -These are additional improper styles in USER packages, which can be -used if "LAMMPS is built with the appropriate -package"_Section_start.html#start_3. - -"cossq (o)"_improper_cossq.html, -"distance"_improper_distance.html, -"fourier (o)"_improper_fourier.html, -"ring (o)"_improper_ring.html :tb(c=4,ea=c) - -:line - -Kspace solvers :h3 - -See the "kspace_style"_kspace_style.html command for an overview of -Kspace solvers. Click on the style itself for a full description. -Some of the styles have accelerated versions, which can be used if -LAMMPS is built with the "appropriate accelerated -package"_Section_accelerate.html. This is indicated by additional -letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = -USER-OMP, t = OPT. - -"ewald (o)"_kspace_style.html, -"ewald/disp"_kspace_style.html, -"msm (o)"_kspace_style.html, -"msm/cg (o)"_kspace_style.html, -"pppm (gok)"_kspace_style.html, -"pppm/cg (o)"_kspace_style.html, -"pppm/disp (i)"_kspace_style.html, -"pppm/disp/tip4p"_kspace_style.html, -"pppm/stagger"_kspace_style.html, -"pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Section_history.txt b/doc/src/Section_history.txt deleted file mode 100644 index 7b9041062855136866e909b7c37a451c41460256..0000000000000000000000000000000000000000 --- a/doc/src/Section_history.txt +++ /dev/null @@ -1,135 +0,0 @@ -"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Manual.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -13. Future and history :h2 - -This section lists features we plan to add to LAMMPS, features of -previous versions of LAMMPS, and features of other parallel molecular -dynamics codes our group has distributed. - -13.1 "Coming attractions"_#hist_1 -13.2 "Past versions"_#hist_2 :all(b) - -:line -:line - -13.1 Coming attractions :h3,link(hist_1) - -As of summer 2016 we are using the "LAMMPS project issue tracker -on GitHub"_https://github.com/lammps/lammps/issues for keeping -track of suggested, planned or pending new features. This includes -discussions of how to best implement them, or why they would be -useful. Especially if a planned or proposed feature is non-trivial -to add, e.g. because it requires changes to some of the core -classes of LAMMPS, people planning to contribute a new feature to -LAMMS are encouraged to submit an issue about their planned -implementation this way in order to receive feedback from the -LAMMPS core developers. They will provide suggestions about -the validity of the proposed approach and possible improvements, -pitfalls or alternatives. - -Please see some of the closed issues for examples of how to -suggest code enhancements, submit proposed changes, or report -possible bugs and how they are resolved. - -As an alternative to using GitHub, you may e-mail the -"core developers"_http://lammps.sandia.gov/authors.html or send -an e-mail to the "LAMMPS Mail list"_http://lammps.sandia.gov/mail.html -if you want to have your suggestion added to the list. - -:line - -13.2 Past versions :h3,link(hist_2) - -LAMMPS development began in the mid 1990s under a cooperative research -& development agreement (CRADA) between two DOE labs (Sandia and LLNL) -and 3 companies (Cray, Bristol Myers Squibb, and Dupont). The goal was -to develop a large-scale parallel classical MD code; the coding effort -was led by Steve Plimpton at Sandia. - -After the CRADA ended, a final F77 version, LAMMPS 99, was -released. As development of LAMMPS continued at Sandia, its memory -management was converted to F90; a final F90 version was released as -LAMMPS 2001. - -The current LAMMPS is a rewrite in C++ and was first publicly released -as an open source code in 2004. It includes many new features beyond -those in LAMMPS 99 or 2001. It also includes features from older -parallel MD codes written at Sandia, namely ParaDyn, Warp, and -GranFlow (see below). - -In late 2006 we began merging new capabilities into LAMMPS that were -developed by Aidan Thompson at Sandia for his MD code GRASP, which has -a parallel framework similar to LAMMPS. Most notably, these have -included many-body potentials - Stillinger-Weber, Tersoff, ReaxFF - -and the associated charge-equilibration routines needed for ReaxFF. - -The "History link"_http://lammps.sandia.gov/history.html on the -LAMMPS WWW page gives a timeline of features added to the -C++ open-source version of LAMMPS over the last several years. - -These older codes are available for download from the "LAMMPS WWW -site"_lws, except for Warp & GranFlow which were primarily used -internally. A brief listing of their features is given here. - -LAMMPS 2001 - - F90 + MPI - dynamic memory - spatial-decomposition parallelism - NVE, NVT, NPT, NPH, rRESPA integrators - LJ and Coulombic pairwise force fields - all-atom, united-atom, bead-spring polymer force fields - CHARMM-compatible force fields - class 2 force fields - 3d/2d Ewald & PPPM - various force and temperature constraints - SHAKE - Hessian-free truncated-Newton minimizer - user-defined diagnostics :ul - -LAMMPS 99 - - F77 + MPI - static memory allocation - spatial-decomposition parallelism - most of the LAMMPS 2001 features with a few exceptions - no 2d Ewald & PPPM - molecular force fields are missing a few CHARMM terms - no SHAKE :ul - -Warp - - F90 + MPI - spatial-decomposition parallelism - embedded atom method (EAM) metal potentials + LJ - lattice and grain-boundary atom creation - NVE, NVT integrators - boundary conditions for applying shear stresses - temperature controls for actively sheared systems - per-atom energy and centro-symmetry computation and output :ul - -ParaDyn - - F77 + MPI - atom- and force-decomposition parallelism - embedded atom method (EAM) metal potentials - lattice atom creation - NVE, NVT, NPT integrators - all serial DYNAMO features for controls and constraints :ul - -GranFlow - - F90 + MPI - spatial-decomposition parallelism - frictional granular potentials - NVE integrator - boundary conditions for granular flow and packing and walls - particle insertion :ul diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt deleted file mode 100644 index e852e0abd452b707fc0eb25f0783cfb14bf85507..0000000000000000000000000000000000000000 --- a/doc/src/Section_howto.txt +++ /dev/null @@ -1,2959 +0,0 @@ -"Previous Section"_Section_accelerate.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_example.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -6. How-to discussions :h2 - -This section describes how to perform common tasks using LAMMPS. - -6.1 "Restarting a simulation"_#howto_1 -6.2 "2d simulations"_#howto_2 -6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3 -6.4 "Running multiple simulations from one input script"_#howto_4 -6.5 "Multi-replica simulations"_#howto_5 -6.6 "Granular models"_#howto_6 -6.7 "TIP3P water model"_#howto_7 -6.8 "TIP4P water model"_#howto_8 -6.9 "SPC water model"_#howto_9 -6.10 "Coupling LAMMPS to other codes"_#howto_10 -6.11 "Visualizing LAMMPS snapshots"_#howto_11 -6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12 -6.13 "NEMD simulations"_#howto_13 -6.14 "Finite-size spherical and aspherical particles"_#howto_14 -6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15 -6.16 "Thermostatting, barostatting and computing temperature"_#howto_16 -6.17 "Walls"_#howto_17 -6.18 "Elastic constants"_#howto_18 -6.19 "Library interface to LAMMPS"_#howto_19 -6.20 "Calculating thermal conductivity"_#howto_20 -6.21 "Calculating viscosity"_#howto_21 -6.22 "Calculating a diffusion coefficient"_#howto_22 -6.23 "Using chunks to calculate system properties"_#howto_23 -6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24 -6.25 "Polarizable models"_#howto_25 -6.26 "Adiabatic core/shell model"_#howto_26 -6.27 "Drude induced dipoles"_#howto_27 :all(b) - -The example input scripts included in the LAMMPS distribution and -highlighted in "Section 7"_Section_example.html also show how to -setup and run various kinds of simulations. - -:line -:line - -6.1 Restarting a simulation :link(howto_1),h4 - -There are 3 ways to continue a long LAMMPS simulation. Multiple -"run"_run.html commands can be used in the same input script. Each -run will continue from where the previous run left off. Or binary -restart files can be saved to disk using the "restart"_restart.html -command. At a later time, these binary files can be read via a -"read_restart"_read_restart.html command in a new script. Or they can -be converted to text data files using the "-r command-line -switch"_Section_start.html#start_6 and read by a -"read_data"_read_data.html command in a new script. - -Here we give examples of 2 scripts that read either a binary restart -file or a converted data file and then issue a new run command to -continue where the previous run left off. They illustrate what -settings must be made in the new script. Details are discussed in the -documentation for the "read_restart"_read_restart.html and -"read_data"_read_data.html commands. - -Look at the {in.chain} input script provided in the {bench} directory -of the LAMMPS distribution to see the original script that these 2 -scripts are based on. If that script had the line - -restart 50 tmp.restart :pre - -added to it, it would produce 2 binary restart files (tmp.restart.50 -and tmp.restart.100) as it ran. - -This script could be used to read the 1st restart file and re-run the -last 50 timesteps: - -read_restart tmp.restart.50 :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -run 50 :pre - -Note that the following commands do not need to be repeated because -their settings are included in the restart file: {units, atom_style, -special_bonds, pair_style, bond_style}. However these commands do -need to be used, since their settings are not in the restart file: -{neighbor, fix, timestep}. - -If you actually use this script to perform a restarted run, you will -notice that the thermodynamic data match at step 50 (if you also put a -"thermo 50" command in the original script), but do not match at step -100. This is because the "fix langevin"_fix_langevin.html command -uses random numbers in a way that does not allow for perfect restarts. - -As an alternate approach, the restart file could be converted to a data -file as follows: - -lmp_g++ -r tmp.restart.50 tmp.restart.data :pre - -Then, this script could be used to re-run the last 50 steps: - -units lj -atom_style bond -pair_style lj/cut 1.12 -pair_modify shift yes -bond_style fene -special_bonds 0.0 1.0 1.0 :pre - -read_data tmp.restart.data :pre - -neighbor 0.4 bin -neigh_modify every 1 delay 1 :pre - -fix 1 all nve -fix 2 all langevin 1.0 1.0 10.0 904297 :pre - -timestep 0.012 :pre - -reset_timestep 50 -run 50 :pre - -Note that nearly all the settings specified in the original {in.chain} -script must be repeated, except the {pair_coeff} and {bond_coeff} -commands since the new data file lists the force field coefficients. -Also, the "reset_timestep"_reset_timestep.html command is used to tell -LAMMPS the current timestep. This value is stored in restart files, -but not in data files. - -:line - -6.2 2d simulations :link(howto_2),h4 - -Use the "dimension"_dimension.html command to specify a 2d simulation. - -Make the simulation box periodic in z via the "boundary"_boundary.html -command. This is the default. - -If using the "create box"_create_box.html command to define a -simulation box, set the z dimensions narrow, but finite, so that the -create_atoms command will tile the 3d simulation box with a single z -plane of atoms - e.g. - -"create box"_create_box.html 1 -10 10 -10 10 -0.25 0.25 :pre - -If using the "read data"_read_data.html command to read in a file of -atom coordinates, set the "zlo zhi" values to be finite but narrow, -similar to the create_box command settings just described. For each -atom in the file, assign a z coordinate so it falls inside the -z-boundaries of the box - e.g. 0.0. - -Use the "fix enforce2d"_fix_enforce2d.html command as the last -defined fix to insure that the z-components of velocities and forces -are zeroed out every timestep. The reason to make it the last fix is -so that any forces induced by other fixes will be zeroed out. - -Many of the example input scripts included in the LAMMPS distribution -are for 2d models. - -NOTE: Some models in LAMMPS treat particles as finite-size spheres, as -opposed to point particles. See the "atom_style -sphere"_atom_style.html and "fix nve/sphere"_fix_nve_sphere.html -commands for details. By default, for 2d simulations, such particles -will still be modeled as 3d spheres, not 2d discs (circles), meaning -their moment of inertia will be that of a sphere. If you wish to -model them as 2d discs, see the "set density/disc"_set.html command -and the {disc} option for the "fix nve/sphere"_fix_nve_sphere.html, -"fix nvt/sphere"_fix_nvt_sphere.html, "fix -nph/sphere"_fix_nph_sphere.html, "fix npt/sphere"_fix_npt_sphere.html -commands. - -:line - -6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4 - -A force field has 2 parts: the formulas that define it and the -coefficients used for a particular system. Here we only discuss -formulas implemented in LAMMPS that correspond to formulas commonly -used in the CHARMM, AMBER, and DREIDING force fields. Setting -coefficients is done in the input data file via the -"read_data"_read_data.html command or in the input script with -commands like "pair_coeff"_pair_coeff.html or -"bond_coeff"_bond_coeff.html. See "Section 9"_Section_tools.html -for additional tools that can use CHARMM or AMBER to assign force -field coefficients and convert their output into LAMMPS input. - -See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force -field. See "(Cornell)"_#howto-Cornell for a description of the AMBER force -field. - -:link(charmm,http://www.scripps.edu/brooks) -:link(amber,http://amber.scripps.edu) - -These style choices compute force field formulas that are consistent -with common options in CHARMM or AMBER. See each command's -documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"angle_style"_angle_charmm.html charmm -"dihedral_style"_dihedral_charmm.html charmmfsh -"dihedral_style"_dihedral_charmm.html charmm -"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh -"pair_style"_pair_charmm.html lj/charmmfsw/coul/long -"pair_style"_pair_charmm.html lj/charmm/coul/charmm -"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit -"pair_style"_pair_charmm.html lj/charmm/coul/long :ul - -"special_bonds"_special_bonds.html charmm -"special_bonds"_special_bonds.html amber :ul - -NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were -released in March 2017. We recommend they be used instead of the -older {charmm} styles. See discussion of the differences on the "pair -charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html -doc pages. - -DREIDING is a generic force field developed by the "Goddard -group"_http://www.wag.caltech.edu at Caltech and is useful for -predicting structures and dynamics of organic, biological and -main-group inorganic molecules. The philosophy in DREIDING is to use -general force constants and geometry parameters based on simple -hybridization considerations, rather than individual force constants -and geometric parameters that depend on the particular combinations of -atoms involved in the bond, angle, or torsion terms. DREIDING has an -"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe -interactions involving a hydrogen atom on very electronegative atoms -(N, O, F). - -See "(Mayo)"_#howto-Mayo for a description of the DREIDING force field - -These style choices compute force field formulas that are consistent -with the DREIDING force field. See each command's -documentation for the formula it computes. - -"bond_style"_bond_harmonic.html harmonic -"bond_style"_bond_morse.html morse :ul - -"angle_style"_angle_harmonic.html harmonic -"angle_style"_angle_cosine.html cosine -"angle_style"_angle_cosine_periodic.html cosine/periodic :ul - -"dihedral_style"_dihedral_charmm.html charmm -"improper_style"_improper_umbrella.html umbrella :ul - -"pair_style"_pair_buck.html buck -"pair_style"_pair_buck.html buck/coul/cut -"pair_style"_pair_buck.html buck/coul/long -"pair_style"_pair_lj.html lj/cut -"pair_style"_pair_lj.html lj/cut/coul/cut -"pair_style"_pair_lj.html lj/cut/coul/long :ul - -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj -"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul - -"special_bonds"_special_bonds.html dreiding :ul - -:line - -6.4 Running multiple simulations from one input script :link(howto_4),h4 - -This can be done in several ways. See the documentation for -individual commands for more details on how these examples work. - -If "multiple simulations" means continue a previous simulation for -more timesteps, then you simply use the "run"_run.html command -multiple times. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -run 10000 -run 10000 -run 10000 -run 10000 :pre - -would run 5 successive simulations of the same system for a total of -50,000 timesteps. - -If you wish to run totally different simulations, one after the other, -the "clear"_clear.html command can be used in between them to -re-initialize LAMMPS. For example, this script - -units lj -atom_style atomic -read_data data.lj -run 10000 -clear -units lj -atom_style atomic -read_data data.lj.new -run 10000 :pre - -would run 2 independent simulations, one after the other. - -For large numbers of independent simulations, you can use -"variables"_variable.html and the "next"_next.html and -"jump"_jump.html commands to loop over the same input script -multiple times with different settings. For example, this -script, named in.polymer - -variable d index run1 run2 run3 run4 run5 run6 run7 run8 -shell cd $d -read_data data.polymer -run 10000 -shell cd .. -clear -next d -jump in.polymer :pre - -would run 8 simulations in different directories, using a data.polymer -file in each directory. The same concept could be used to run the -same system at 8 different temperatures, using a temperature variable -and storing the output in different log and dump files, for example - -variable a loop 8 -variable t index 0.8 0.85 0.9 0.95 1.0 1.05 1.1 1.15 -log log.$a -read data.polymer -velocity all create $t 352839 -fix 1 all nvt $t $t 100.0 -dump 1 all atom 1000 dump.$a -run 100000 -clear -next t -next a -jump in.polymer :pre - -All of the above examples work whether you are running on 1 or -multiple processors, but assumed you are running LAMMPS on a single -partition of processors. LAMMPS can be run on multiple partitions via -the "-partition" command-line switch as described in "this -section"_Section_start.html#start_6 of the manual. - -In the last 2 examples, if LAMMPS were run on 3 partitions, the same -scripts could be used if the "index" and "loop" variables were -replaced with {universe}-style variables, as described in the -"variable"_variable.html command. Also, the "next t" and "next a" -commands would need to be replaced with a single "next a t" command. -With these modifications, the 8 simulations of each script would run -on the 3 partitions one after the other until all were finished. -Initially, 3 simulations would be started simultaneously, one on each -partition. When one finished, that partition would then start -the 4th simulation, and so forth, until all 8 were completed. - -:line - -6.5 Multi-replica simulations :link(howto_5),h4 - -Several commands in LAMMPS run mutli-replica simulations, meaning -that multiple instances (replicas) of your simulation are run -simultaneously, with small amounts of data exchanged between replicas -periodically. - -These are the relevant commands: - -"neb"_neb.html for nudged elastic band calculations -"prd"_prd.html for parallel replica dynamics -"tad"_tad.html for temperature accelerated dynamics -"temper"_temper.html for parallel tempering -"fix pimd"_fix_pimd.html for path-integral molecular dynamics (PIMD) :ul - -NEB is a method for finding transition states and barrier energies. -PRD and TAD are methods for performing accelerated dynamics to find -and perform infrequent events. Parallel tempering or replica exchange -runs different replicas at a series of temperature to facilitate -rare-event sampling. - -These commands can only be used if LAMMPS was built with the REPLICA -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. - -PIMD runs different replicas whose individual particles are coupled -together by springs to model a system or ring-polymers. - -This commands can only be used if LAMMPS was built with the USER-MISC -package. See the "Making LAMMPS"_Section_start.html#start_3 section -for more info on packages. - -In all these cases, you must run with one or more processors per -replica. The processors assigned to each replica are determined at -run-time by using the "-partition command-line -switch"_Section_start.html#start_6 to launch LAMMPS on multiple -partitions, which in this context are the same as replicas. E.g. -these commands: - -mpirun -np 16 lmp_linux -partition 8x2 -in in.temper -mpirun -np 8 lmp_linux -partition 8x1 -in in.neb :pre - -would each run 8 replicas, on either 16 or 8 processors. Note the use -of the "-in command-line switch"_Section_start.html#start_6 to specify -the input script which is required when running in multi-replica mode. - -Also note that with MPI installed on a machine (e.g. your desktop), -you can run on more (virtual) processors than you have physical -processors. Thus the above commands could be run on a -single-processor (or few-processor) desktop so that you can run -a multi-replica simulation on more replicas than you have -physical processors. - -:line - -6.6 Granular models :link(howto_6),h4 - -Granular system are composed of spherical particles with a diameter, -as opposed to point particles. This means they have an angular -velocity and torque can be imparted to them to cause them to rotate. - -To run a simulation of a granular model, you will want to use -the following commands: - -"atom_style sphere"_atom_style.html -"fix nve/sphere"_fix_nve_sphere.html -"fix gravity"_fix_gravity.html :ul - -This compute - -"compute erotate/sphere"_compute_erotate_sphere.html :ul - -calculates rotational kinetic energy which can be "output with -thermodynamic info"_Section_howto.html#howto_15. - -Use one of these 3 pair potentials, which compute forces and torques -between interacting pairs of particles: - -"pair_style"_pair_style.html gran/history -"pair_style"_pair_style.html gran/no_history -"pair_style"_pair_style.html gran/hertzian :ul - -These commands implement fix options specific to granular systems: - -"fix freeze"_fix_freeze.html -"fix pour"_fix_pour.html -"fix viscous"_fix_viscous.html -"fix wall/gran"_fix_wall_gran.html :ul - -The fix style {freeze} zeroes both the force and torque of frozen -atoms, and should be used for granular system instead of the fix style -{setforce}. - -For computational efficiency, you can eliminate needless pairwise -computations between frozen atoms by using this command: - -"neigh_modify"_neigh_modify.html exclude :ul - -NOTE: By default, for 2d systems, granular particles are still modeled -as 3d spheres, not 2d discs (circles), meaning their moment of inertia -will be the same as in 3d. If you wish to model granular particles in -2d as 2d discs, see the note on this topic in "Section -6.2"_Section_howto.html#howto_2, where 2d simulations are discussed. - -:line - -6.7 TIP3P water model :link(howto_7),h4 - -The TIP3P water model as implemented in CHARMM -"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP3P-CHARMM model with a -cutoff. The K values can be used if a flexible TIP3P model (without -fix shake) is desired. If the LJ epsilon and sigma for HH and OH are -set to 0.0, it corresponds to the original 1983 TIP3P model -"(Jorgensen)"_#Jorgensen1. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.834 -H charge = 0.417 -LJ epsilon of OO = 0.1521 -LJ sigma of OO = 3.1507 -LJ epsilon of HH = 0.0460 -LJ sigma of HH = 0.4000 -LJ epsilon of OH = 0.0836 -LJ sigma of OH = 1.7753 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -These are the parameters to use for TIP3P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS), see "(Price)"_#Price1 for -details: - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.830 -H charge = 0.415 -LJ epsilon of OO = 0.102 -LJ sigma of OO = 3.188 -LJ epsilon, sigma of OH, HH = 0.0 -K of OH bond = 450 -r0 of OH bond = 0.9572 -K of HOH angle = 55 -theta of HOH angle = 104.52 :all(b),p - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.8 TIP4P water model :link(howto_8),h4 - -The four-point TIP4P rigid water model extends the traditional -three-point TIP3P model by adding an additional site, usually -massless, where the charge associated with the oxygen atom is placed. -This site M is located at a fixed distance away from the oxygen along -the bisector of the HOH bond angle. A bond style of {harmonic} and an -angle style of {harmonic} or {charmm} should also be used. - -A TIP4P model is run with LAMMPS using either this command -for a cutoff model: - -"pair_style lj/cut/tip4p/cut"_pair_lj.html - -or these two commands for a long-range model: - -"pair_style lj/cut/tip4p/long"_pair_lj.html -"kspace_style pppm/tip4p"_kspace_style.html :ul - -For both models, the bond lengths and bond angles should be held fixed -using the "fix shake"_fix_shake.html command. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP4P model with a cutoff -"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in -the "pair_style"_pair_style.html command, not as part of the pair -coefficients. - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.040 -H charge = 0.520 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.15 -LJ epsilon of O-O = 0.1550 -LJ sigma of O-O = 3.1536 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -http://dx.doi.org/10.1063/1.1931662) these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1794 -H charge = 0.5897 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1577 -LJ epsilon of O-O = 0.21084 -LJ sigma of O-O = 3.1668 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -http://dx.doi.org/10.1063/1.2121687), these values can be used: - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.1128 -H charge = 0.5564 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1546 -LJ epsilon of O-O = 0.1852 -LJ sigma of O-O = 3.1589 -LJ epsilon, sigma of OH, HH = 0.0 -Coulombic cutoff = 8.5 :all(b),p - -These are the parameters to use for TIP4P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS): - -O mass = 15.9994 -H mass = 1.008 -O charge = -1.0484 -H charge = 0.5242 -r0 of OH bond = 0.9572 -theta of HOH angle = 104.52 -OM distance = 0.1250 -LJ epsilon of O-O = 0.16275 -LJ sigma of O-O = 3.16435 -LJ epsilon, sigma of OH, HH = 0.0 :all(b),p - -Note that the when using the TIP4P pair style, the neighbor list -cutoff for Coulomb interactions is effectively extended by a distance -2 * (OM distance), to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*(OM distance), to shrink the size of the neighbor list. -This leads to slightly larger cost for the long-range calculation, so -you can test the trade-off for your model. The OM distance and the LJ -and Coulombic cutoffs are set in the "pair_style -lj/cut/tip4p/long"_pair_lj.html command. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.9 SPC water model :link(howto_9),h4 - -The SPC water model specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the "fix shake"_fix_shake.html command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -{harmonic} and an angle style of {harmonic} or {charmm} should also be -used. - -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid SPC model. - -O mass = 15.9994 -H mass = 1.008 -O charge = -0.820 -H charge = 0.410 -LJ epsilon of OO = 0.1553 -LJ sigma of OO = 3.166 -LJ epsilon, sigma of OH, HH = 0.0 -r0 of OH bond = 1.0 -theta of HOH angle = 109.47 :all(b),p - -Note that as originally proposed, the SPC model was run with a 9 -Angstrom cutoff for both LJ and Coulommbic terms. It can also be used -with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing -any of the parameters above, though it becomes a different model in -that mode of usage. - -The SPC/E (extended) water model is the same, except -the partial charge assignments change: - -O charge = -0.8476 -H charge = 0.4238 :all(b),p - -See the "(Berendsen)"_#howto-Berendsen reference for more details on both -the SPC and SPC/E models. - -Wikipedia also has a nice article on "water -models"_http://en.wikipedia.org/wiki/Water_model. - -:line - -6.10 Coupling LAMMPS to other codes :link(howto_10),h4 - -LAMMPS is designed to allow it to be coupled to other codes. For -example, a quantum mechanics code might compute forces on a subset of -atoms and pass those forces to LAMMPS. Or a continuum finite element -(FE) simulation might use atom positions as boundary conditions on FE -nodal points, compute a FE solution, and return interpolated forces on -MD atoms. - -LAMMPS can be coupled to other codes in at least 3 ways. Each has -advantages and disadvantages, which you'll have to think about in the -context of your application. - -(1) Define a new "fix"_fix.html command that calls the other code. In -this scenario, LAMMPS is the driver code. During its timestepping, -the fix is invoked, and can make library calls to the other code, -which has been linked to LAMMPS as a library. This is the way the -"POEMS"_poems package that performs constrained rigid-body motion on -groups of atoms is hooked to LAMMPS. See the -"fix poems"_fix_poems.html command for more details. See "this -section"_Section_modify.html of the documentation for info on how to add -a new fix to LAMMPS. - -:link(poems,http://www.rpi.edu/~anderk5/lab) - -(2) Define a new LAMMPS command that calls the other code. This is -conceptually similar to method (1), but in this case LAMMPS and the -other code are on a more equal footing. Note that now the other code -is not called during the timestepping of a LAMMPS run, but between -runs. The LAMMPS input script can be used to alternate LAMMPS runs -with calls to the other code, invoked via the new command. The -"run"_run.html command facilitates this with its {every} option, which -makes it easy to run a few steps, invoke the command, run a few steps, -invoke the command, etc. - -In this scenario, the other code can be called as a library, as in -(1), or it could be a stand-alone code, invoked by a system() call -made by the command (assuming your parallel machine allows one or more -processors to start up another program). In the latter case the -stand-alone code could communicate with LAMMPS thru files that the -command writes and reads. - -See "Section 10"_Section_modify.html of the documentation for how -to add a new command to LAMMPS. - -(3) Use LAMMPS as a library called by another code. In this case the -other code is the driver and calls LAMMPS as needed. Or a wrapper -code could link and call both LAMMPS and another code as libraries. -Again, the "run"_run.html command has options that allow it to be -invoked with minimal overhead (no setup or clean-up) if you wish to do -multiple short runs, driven by another program. - -Examples of driver codes that call LAMMPS as a library are included in -the examples/COUPLE directory of the LAMMPS distribution; see -examples/COUPLE/README for more details: - -simple: simple driver programs in C++ and C which invoke LAMMPS as a -library :ulb,l - -lammps_quest: coupling of LAMMPS and "Quest"_quest, to run classical -MD with quantum forces calculated by a density functional code :l - -lammps_spparks: coupling of LAMMPS and "SPPARKS"_spparks, to couple -a kinetic Monte Carlo model for grain growth using MD to calculate -strain induced across grain boundaries :l -:ule - -:link(quest,http://dft.sandia.gov/Quest) -:link(spparks,http://www.sandia.gov/~sjplimp/spparks.html) - -"This section"_Section_start.html#start_5 of the documentation -describes how to build LAMMPS as a library. Once this is done, you -can interface with LAMMPS either via C++, C, Fortran, or Python (or -any other language that supports a vanilla C-like interface). For -example, from C++ you could create one (or more) "instances" of -LAMMPS, pass it an input script to process, or execute individual -commands, all by invoking the correct class methods in LAMMPS. From C -or Fortran you can make function calls to do the same things. See -"Section 11"_Section_python.html of the manual for a description -of the Python wrapper provided with LAMMPS that operates through the -LAMMPS library interface. - -The files src/library.cpp and library.h contain the C-style interface -to LAMMPS. See "Section 6.19"_Section_howto.html#howto_19 of the -manual for a description of the interface and how to extend it for -your needs. - -Note that the lammps_open() function that creates an instance of -LAMMPS takes an MPI communicator as an argument. This means that -instance of LAMMPS will run on the set of processors in the -communicator. Thus the calling code can run LAMMPS on all or a subset -of processors. For example, a wrapper script might decide to -alternate between LAMMPS and another code, allowing them both to run -on all the processors. Or it might allocate half the processors to -LAMMPS and half to the other code and run both codes simultaneously -before syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -:line - -6.11 Visualizing LAMMPS snapshots :link(howto_11),h4 - -LAMMPS itself does not do visualization, but snapshots from LAMMPS -simulations can be visualized (and analyzed) in a variety of ways. - -LAMMPS snapshots are created by the "dump"_dump.html command which can -create files in several formats. The native LAMMPS dump format is a -text file (see "dump atom" or "dump custom") which can be visualized -by several popular visualization tools. The "dump image"_dump_image.html -and "dump movie"_dump_image.html styles can output internally rendered -images and convert a sequence of them to a movie during the MD run. -Several programs included with LAMMPS as auxiliary tools can convert -between LAMMPS format files and other formats. -See the "Section 9"_Section_tools.html doc page for details. - -A Python-based toolkit distributed by our group can read native LAMMPS -dump files, including custom dump files with additional columns of -user-specified atom information, and convert them to various formats -or pipe them into visualization software directly. See the "Pizza.py -WWW site"_pizza for details. Specifically, Pizza.py can convert -LAMMPS dump files into PDB, XYZ, "Ensight"_ensight, and VTK formats. -Pizza.py can pipe LAMMPS dump files directly into the Raster3d and -RasMol visualization programs. Pizza.py has tools that do interactive -3d OpenGL visualization and one that creates SVG images of dump file -snapshots. - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(ensight,http://www.ensight.com) -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) - -:line - -6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4 - -By default, LAMMPS uses an orthogonal simulation box to encompass the -particles. The "boundary"_boundary.html command sets the boundary -conditions of the box (periodic, non-periodic, etc). The orthogonal -box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors -starting from the origin given by [a] = (xhi-xlo,0,0); [b] = -(0,yhi-ylo,0); [c] = (0,0,zhi-zlo). The 6 parameters -(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simulation box -is created, e.g. by the "create_box"_create_box.html or -"read_data"_read_data.html or "read_restart"_read_restart.html -commands. Additionally, LAMMPS defines box size parameters lx,ly,lz -where lx = xhi-xlo, and similarly in the y and z dimensions. The 6 -parameters, as well as lx,ly,lz, can be output via the "thermo_style -custom"_thermo_style.html command. - -LAMMPS also allows simulations to be performed in triclinic -(non-orthogonal) simulation boxes shaped as a parallelepiped with -triclinic symmetry. The parallelepiped has its "origin" at -(xlo,ylo,zlo) and is defined by 3 edge vectors starting from the -origin given by [a] = (xhi-xlo,0,0); [b] = (xy,yhi-ylo,0); [c] = -(xz,yz,zhi-zlo). {xy,xz,yz} can be 0.0 or positive or negative values -and are called "tilt factors" because they are the amount of -displacement applied to faces of an originally orthogonal box to -transform it into the parallelepiped. In LAMMPS the triclinic -simulation box edge vectors [a], [b], and [c] cannot be arbitrary -vectors. As indicated, [a] must lie on the positive x axis. [b] must -lie in the xy plane, with strictly positive y component. [c] may have -any orientation with strictly positive z component. The requirement -that [a], [b], and [c] have strictly positive x, y, and z components, -respectively, ensures that [a], [b], and [c] form a complete -right-handed basis. These restrictions impose no loss of generality, -since it is possible to rotate/invert any set of 3 crystal basis -vectors so that they conform to the restrictions. - -For example, assume that the 3 vectors [A],[B],[C] are the edge -vectors of a general parallelepiped, where there is no restriction on -[A],[B],[C] other than they form a complete right-handed basis i.e. -[A] x [B] . [C] > 0. The equivalent LAMMPS [a],[b],[c] are a linear -rotation of [A], [B], and [C] and can be computed as follows: - -:c,image(Eqs/transform.jpg) - -where A = | [A] | indicates the scalar length of [A]. The hat symbol (^) -indicates the corresponding unit vector. {beta} and {gamma} are angles -between the vectors described below. Note that by construction, -[a], [b], and [c] have strictly positive x, y, and z components, respectively. -If it should happen that -[A], [B], and [C] form a left-handed basis, then the above equations -are not valid for [c]. In this case, it is necessary -to first apply an inversion. This can be achieved -by interchanging two basis vectors or by changing the sign of one of them. - -For consistency, the same rotation/inversion applied to the basis vectors -must also be applied to atom positions, velocities, -and any other vector quantities. -This can be conveniently achieved by first converting to -fractional coordinates in the -old basis and then converting to distance coordinates in the new basis. -The transformation is given by the following equation: - -:c,image(Eqs/rotate.jpg) - -where {V} is the volume of the box, [X] is the original vector quantity and -[x] is the vector in the LAMMPS basis. - -There is no requirement that a triclinic box be periodic in any -dimension, though it typically should be in at least the 2nd dimension -of the tilt (y in xy) if you want to enforce a shift in periodic -boundary conditions across that boundary. Some commands that work -with triclinic boxes, e.g. the "fix deform"_fix_deform.html and "fix -npt"_fix_nh.html commands, require periodicity or non-shrink-wrap -boundary conditions in specific dimensions. See the command doc pages -for details. - -The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the -time the simulation box is created. This happens in one of 3 ways. -If the "create_box"_create_box.html command is used with a region of -style {prism}, then a triclinic box is setup. See the -"region"_region.html command for details. If the -"read_data"_read_data.html command is used to define the simulation -box, and the header of the data file contains a line with the "xy xz -yz" keyword, then a triclinic box is setup. See the -"read_data"_read_data.html command for details. Finally, if the -"read_restart"_read_restart.html command reads a restart file which -was written from a simulation using a triclinic box, then a triclinic -box will be setup for the restarted simulation. - -Note that you can define a triclinic box with all 3 tilt factors = -0.0, so that it is initially orthogonal. This is necessary if the box -will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or -"fix deform"_fix_deform.html commands. Alternatively, you can use the -"change_box"_change_box.html command to convert a simulation box from -orthogonal to triclinic and vice versa. - -As with orthogonal boxes, LAMMPS defines triclinic box size parameters -lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions. -The 9 parameters, as well as lx,ly,lz, can be output via the -"thermo_style custom"_thermo_style.html command. - -To avoid extremely tilted boxes (which would be computationally -inefficient), LAMMPS normally requires that no tilt factor can skew -the box more than half the distance of the parallel box length, which -is the 1st dimension in the tilt factor (x for xz). This is required -both when the simulation box is created, e.g. via the -"create_box"_create_box.html or "read_data"_read_data.html commands, -as well as when the box shape changes dynamically during a simulation, -e.g. via the "fix deform"_fix_deform.html or "fix npt"_fix_nh.html -commands. - -For example, if xlo = 2 and xhi = 12, then the x box length is 10 and -the xy tilt factor must be between -5 and 5. Similarly, both xz and -yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is -not a limitation, since if the maximum tilt factor is 5 (as in this -example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are geometrically all equivalent. If the box tilt exceeds this -limit during a dynamics run (e.g. via the "fix deform"_fix_deform.html -command), then the box is "flipped" to an equivalent shape with a tilt -factor within the bounds, so the run can continue. See the "fix -deform"_fix_deform.html doc page for further details. - -One exception to this rule is if the 1st dimension in the tilt -factor (x for xy) is non-periodic. In that case, the limits on the -tilt factor are not enforced, since flipping the box in that dimension -does not change the atom positions due to non-periodicity. In this -mode, if you tilt the system to extreme angles, the simulation will -simply become inefficient, due to the highly skewed simulation box. - -The limitation on not creating a simulation box with a tilt factor -skewing the box more than half the distance of the parallel box length -can be overridden via the "box"_box.html command. Setting the {tilt} -keyword to {large} allows any tilt factors to be specified. - -Box flips that may occur using the "fix deform"_fix_deform.html or -"fix npt"_fix_nh.html commands can be turned off using the {flip no} -option with either of the commands. - -Note that if a simulation box has a large tilt factor, LAMMPS will run -less efficiently, due to the large volume of communication needed to -acquire ghost atoms around a processor's irregular-shaped sub-domain. -For extreme values of tilt, LAMMPS may also lose atoms and generate an -error. - -Triclinic crystal structures are often defined using three lattice -constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and -{gamma}. Note that in this nomenclature, the a, b, and c lattice -constants are the scalar lengths of the edge vectors [a], [b], and [c] -defined above. The relationship between these 6 quantities -(a,b,c,alpha,beta,gamma) and the LAMMPS box sizes (lx,ly,lz) = -(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows: - -:c,image(Eqs/box.jpg) - -The inverse relationship can be written as follows: - -:c,image(Eqs/box_inverse.jpg) - -The values of {a}, {b}, {c} , {alpha}, {beta} , and {gamma} can be printed -out or accessed by computes using the -"thermo_style custom"_thermo_style.html keywords -{cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, -respectively. - -As discussed on the "dump"_dump.html command doc page, when the BOX -BOUNDS for a snapshot is written to a dump file for a triclinic box, -an orthogonal bounding box which encloses the triclinic simulation box -is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic -box, formatted as follows: - -ITEM: BOX BOUNDS xy xz yz -xlo_bound xhi_bound xy -ylo_bound yhi_bound xz -zlo_bound zhi_bound yz :pre - -This bounding box is convenient for many visualization programs and is -calculated from the 9 triclinic box parameters -(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows: - -xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz) -xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz) -ylo_bound = ylo + MIN(0.0,yz) -yhi_bound = yhi + MAX(0.0,yz) -zlo_bound = zlo -zhi_bound = zhi :pre - -These formulas can be inverted if you need to convert the bounding box -back into the triclinic box parameters, e.g. xlo = xlo_bound - -MIN(0.0,xy,xz,xy+xz). - -One use of triclinic simulation boxes is to model solid-state crystals -with triclinic symmetry. The "lattice"_lattice.html command can be -used with non-orthogonal basis vectors to define a lattice that will -tile a triclinic simulation box via the -"create_atoms"_create_atoms.html command. - -A second use is to run Parinello-Rahman dynamics via the "fix -npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt -factors to compensate for off-diagonal components of the pressure -tensor. The analog for an "energy minimization"_minimize.html is -the "fix box/relax"_fix_box_relax.html command. - -A third use is to shear a bulk solid to study the response of the -material. The "fix deform"_fix_deform.html command can be used for -this purpose. It allows dynamic control of the xy, xz, yz tilt -factors as a simulation runs. This is discussed in the next section -on non-equilibrium MD (NEMD) simulations. - -:line - -6.13 NEMD simulations :link(howto_13),h4 - -Non-equilibrium molecular dynamics or NEMD simulations are typically -used to measure a fluid's rheological properties such as viscosity. -In LAMMPS, such simulations can be performed by first setting up a -non-orthogonal simulation box (see the preceding Howto section). - -A shear strain can be applied to the simulation box at a desired -strain rate by using the "fix deform"_fix_deform.html command. The -"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat -the sheared fluid and integrate the SLLOD equations of motion for the -system. Fix nvt/sllod uses "compute -temp/deform"_compute_temp_deform.html to compute a thermal temperature -by subtracting out the streaming velocity of the shearing atoms. The -velocity profile or other properties of the fluid can be monitored via -the "fix ave/chunk"_fix_ave_chunk.html command. - -As discussed in the previous section on non-orthogonal simulation -boxes, the amount of tilt or skew that can be applied is limited by -LAMMPS for computational efficiency to be 1/2 of the parallel box -length. However, "fix deform"_fix_deform.html can continuously strain -a box by an arbitrary amount. As discussed in the "fix -deform"_fix_deform.html command, when the tilt value reaches a limit, -the box is flipped to the opposite limit which is an equivalent tiling -of periodic space. The strain rate can then continue to change as -before. In a long NEMD simulation these box re-shaping events may -occur many times. - -In a NEMD simulation, the "remap" option of "fix -deform"_fix_deform.html should be set to "remap v", since that is what -"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity -profile consistent with the applied shear strain rate. - -An alternative method for calculating viscosities is provided via the -"fix viscosity"_fix_viscosity.html command. - -NEMD simulations can also be used to measure transport properties of a fluid -through a pore or channel. Simulations of steady-state flow can be performed -using the "fix flow/gauss"_fix_flow_gauss.html command. - -:line - -6.14 Finite-size spherical and aspherical particles :link(howto_14),h4 - -Typical MD models treat atoms or particles as point masses. Sometimes -it is desirable to have a model with finite-size particles such as -spheroids or ellipsoids or generalized aspherical bodies. The -difference is that such particles have a moment of inertia, rotational -energy, and angular momentum. Rotation is induced by torque coming -from interactions with other particles. - -LAMMPS has several options for running simulations with these kinds of -particles. The following aspects are discussed in turn: - -atom styles -pair potentials -time integration -computes, thermodynamics, and dump output -rigid bodies composed of finite-size particles :ul - -Example input scripts for these kinds of models are in the body, -colloid, dipole, ellipse, line, peri, pour, and tri directories of the -"examples directory"_Section_example.html in the LAMMPS distribution. - -Atom styles :h4 - -There are several "atom styles"_atom_style.html that allow for -definition of finite-size particles: sphere, dipole, ellipsoid, line, -tri, peri, and body. - -The sphere style defines particles that are spheriods and each -particle can have a unique diameter and mass (or density). These -particles store an angular velocity (omega) and can be acted upon by -torque. The "set" command can be used to modify the diameter and mass -of individual particles, after then are created. - -The dipole style does not actually define finite-size particles, but -is often used in conjunction with spherical particles, via a command -like - -atom_style hybrid sphere dipole :pre - -This is because when dipoles interact with each other, they induce -torques, and a particle must be finite-size (i.e. have a moment of -inertia) in order to respond and rotate. See the "atom_style -dipole"_atom_style.html command for details. The "set" command can be -used to modify the orientation and length of the dipole moment of -individual particles, after then are created. - -The ellipsoid style defines particles that are ellipsoids and thus can -be aspherical. Each particle has a shape, specified by 3 diameters, -and mass (or density). These particles store an angular momentum and -their orientation (quaternion), and can be acted upon by torque. They -do not store an angular velocity (omega), which can be in a different -direction than angular momentum, rather they compute it as needed. -The "set" command can be used to modify the diameter, orientation, and -mass of individual particles, after then are created. It also has a -brief explanation of what quaternions are. - -The line style defines line segment particles with two end points and -a mass (or density). They can be used in 2d simulations, and they can -be joined together to form rigid bodies which represent arbitrary -polygons. - -The tri style defines triangular particles with three corner points -and a mass (or density). They can be used in 3d simulations, and they -can be joined together to form rigid bodies which represent arbitrary -particles with a triangulated surface. - -The peri style is used with "Peridynamic models"_pair_peri.html and -defines particles as having a volume, that is used internally in the -"pair_style peri"_pair_peri.html potentials. - -The body style allows for definition of particles which can represent -complex entities, such as surface meshes of discrete points, -collections of sub-particles, deformable objects, etc. The body style -is discussed in more detail on the "body"_body.html doc page. - -Note that if one of these atom styles is used (or multiple styles via -the "atom_style hybrid"_atom_style.html command), not all particles in -the system are required to be finite-size or aspherical. - -For example, in the ellipsoid style, if the 3 shape parameters are set -to the same value, the particle will be a sphere rather than an -ellipsoid. If the 3 shape parameters are all set to 0.0 or if the -diameter is set to 0.0, it will be a point particle. In the line or -tri style, if the lineflag or triflag is specified as 0, then it -will be a point particle. - -Some of the pair styles used to compute pairwise interactions between -finite-size particles also compute the correct interaction with point -particles as well, e.g. the interaction between a point particle and a -finite-size particle or between two point particles. If necessary, -"pair_style hybrid"_pair_hybrid.html can be used to insure the correct -interactions are computed for the appropriate style of interactions. -Likewise, using groups to partition particles (ellipsoids versus -spheres versus point particles) will allow you to use the appropriate -time integrators and temperature computations for each class of -particles. See the doc pages for various commands for details. - -Also note that for "2d simulations"_dimension.html, atom styles sphere -and ellipsoid still use 3d particles, rather than as circular disks or -ellipses. This means they have the same moment of inertia as the 3d -object. When temperature is computed, the correct degrees of freedom -are used for rotation in a 2d versus 3d system. - -Pair potentials :h4 - -When a system with finite-size particles is defined, the particles -will only rotate and experience torque if the force field computes -such interactions. These are the various "pair -styles"_pair_style.html that generate torque: - -"pair_style gran/history"_pair_gran.html -"pair_style gran/hertzian"_pair_gran.html -"pair_style gran/no_history"_pair_gran.html -"pair_style dipole/cut"_pair_dipole.html -"pair_style gayberne"_pair_gayberne.html -"pair_style resquared"_pair_resquared.html -"pair_style brownian"_pair_brownian.html -"pair_style lubricate"_pair_lubricate.html -"pair_style line/lj"_pair_line_lj.html -"pair_style tri/lj"_pair_tri_lj.html -"pair_style body"_pair_body.html :ul - -The granular pair styles are used with spherical particles. The -dipole pair style is used with the dipole atom style, which could be -applied to spherical or ellipsoidal particles. The GayBerne and -REsquared potentials require ellipsoidal particles, though they will -also work if the 3 shape parameters are the same (a sphere). The -Brownian and lubrication potentials are used with spherical particles. -The line, tri, and body potentials are used with line segment, -triangular, and body particles respectively. - -Time integration :h4 - -There are several fixes that perform time integration on finite-size -spherical particles, meaning the integrators update the rotational -orientation and angular velocity or angular momentum of the particles: - -"fix nve/sphere"_fix_nve_sphere.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix npt/sphere"_fix_npt_sphere.html :ul - -Likewise, there are 3 fixes that perform time integration on -ellipsoidal particles: - -"fix nve/asphere"_fix_nve_asphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix npt/asphere"_fix_npt_asphere.html :ul - -The advantage of these fixes is that those which thermostat the -particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. The "fix langevin"_fix_langevin -command can also be used with its {omgea} or {angmom} options to -thermostat the rotational degrees of freedom for spherical or -ellipsoidal particles. Other thermostatting fixes only operate on the -translational kinetic energy of finite-size particles. - -These fixes perform constant NVE time integration on line segment, -triangular, and body particles: - -"fix nve/line"_fix_nve_line.html -"fix nve/tri"_fix_nve_tri.html -"fix nve/body"_fix_nve_body.html :ul - -Note that for mixtures of point and finite-size particles, these -integration fixes can only be used with "groups"_group.html which -contain finite-size particles. - -Computes, thermodynamics, and dump output :h4 - -There are several computes that calculate the temperature or -rotational energy of spherical or ellipsoidal particles: - -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute erotate/sphere"_compute_erotate_sphere.html -"compute erotate/asphere"_compute_erotate_asphere.html :ul - -These include rotational degrees of freedom in their computation. If -you wish the thermodynamic output of temperature or pressure to use -one of these computes (e.g. for a system entirely composed of -finite-size particles), then the compute can be defined and the -"thermo_modify"_thermo_modify.html command used. Note that by default -thermodynamic quantities will be calculated with a temperature that -only includes translational degrees of freedom. See the -"thermo_style"_thermo_style.html command for details. - -These commands can be used to output various attributes of finite-size -particles: - -"dump custom"_dump.html -"compute property/atom"_compute_property_atom.html -"dump local"_dump.html -"compute body/local"_compute_body_local.html :ul - -Attributes include the dipole moment, the angular velocity, the -angular momentum, the quaternion, the torque, the end-point and -corner-point coordinates (for line and tri particles), and -sub-particle attributes of body particles. - -Rigid bodies composed of finite-size particles :h4 - -The "fix rigid"_fix_rigid.html command treats a collection of -particles as a rigid body, computes its inertia tensor, sums the total -force and torque on the rigid body each timestep due to forces on its -constituent particles, and integrates the motion of the rigid body. - -If any of the constituent particles of a rigid body are finite-size -particles (spheres or ellipsoids or line segments or triangles), then -their contribution to the inertia tensor of the body is different than -if they were point particles. This means the rotational dynamics of -the rigid body will be different. Thus a model of a dimer is -different if the dimer consists of two point masses versus two -spheroids, even if the two particles have the same mass. Finite-size -particles that experience torque due to their interaction with other -particles will also impart that torque to a rigid body they are part -of. - -See the "fix rigid" command for example of complex rigid-body models -it is possible to define in LAMMPS. - -Note that the "fix shake"_fix_shake.html command can also be used to -treat 2, 3, or 4 particles as a rigid body, but it always assumes the -particles are point masses. - -Also note that body particles cannot be modeled with the "fix -rigid"_fix_rigid.html command. Body particles are treated by LAMMPS -as single particles, though they can store internal state, such as a -list of sub-particles. Individual body partices are typically treated -as rigid bodies, and their motion integrated with a command like "fix -nve/body"_fix_nve_body.html. Interactions between pairs of body -particles are computed via a command like "pair_style -body"_pair_body.html. - -:line - -6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4 - -There are four basic kinds of LAMMPS output: - -"Thermodynamic output"_thermo_style.html, which is a list -of quantities printed every few timesteps to the screen and logfile. :ulb,l - -"Dump files"_dump.html, which contain snapshots of atoms and various -per-atom values and are written at a specified frequency. :l - -Certain fixes can output user-specified quantities to files: "fix -ave/time"_fix_ave_time.html for time averaging, "fix -ave/chunk"_fix_ave_chunk.html for spatial or other averaging, and "fix -print"_fix_print.html for single-line output of -"variables"_variable.html. Fix print can also output to the -screen. :l - -"Restart files"_restart.html. :l -:ule - -A simulation prints one set of thermodynamic output and (optionally) -restart files. It can generate any number of dump files and fix -output files, depending on what "dump"_dump.html and "fix"_fix.html -commands you specify. - -As discussed below, LAMMPS gives you a variety of ways to determine -what quantities are computed and printed when the thermodynamics, -dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also "add their own computes and fixes -to LAMMPS"_Section_modify.html which can then generate values that can -then be output with these commands. - -The following sub-sections discuss different LAMMPS command related -to output and the kind of data they operate on and produce: - -"Global/per-atom/local data"_#global -"Scalar/vector/array data"_#scalar -"Thermodynamic output"_#thermo -"Dump file output"_#dump -"Fixes that write output files"_#fixoutput -"Computes that process output quantities"_#computeoutput -"Fixes that process output quantities"_#fixprocoutput -"Computes that generate values to output"_#compute -"Fixes that generate values to output"_#fix -"Variables that generate values to output"_#variable -"Summary table of output options and data flow between commands"_#table :ul - -Global/per-atom/local data :h4,link(global) - -Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. - -Scalar/vector/array data :h4,link(scalar) - -Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. - -When a quantity is accessed, as in many of the output commands -discussed below, it can be referenced via the following bracket -notation, where ID in this case is the ID of a compute. The leading -"c_" would be replaced by "f_" for a fix, or "v_" for a variable: - -c_ID | entire scalar, vector, or array -c_ID\[I\] | one element of vector, one column of array -c_ID\[I\]\[J\] | one element of array :tb(s=|) - -In other words, using one bracket reduces the dimension of the data -once (vector -> scalar, array -> vector). Using two brackets reduces -the dimension twice (array -> scalar). Thus a command that uses -scalar values as input can typically also process elements of a vector -or array. - -Thermodynamic output :h4,link(thermo) - -The frequency and format of thermodynamic output is set by the -"thermo"_thermo.html, "thermo_style"_thermo_style.html, and -"thermo_modify"_thermo_modify.html commands. The -"thermo_style"_thermo_style.html command also specifies what values -are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc). Three additional kinds of keywords can -also be specified (c_ID, f_ID, v_name), where a "compute"_compute.html -or "fix"_fix.html or "variable"_variable.html provides the value to be -output. In each case, the compute, fix, or variable must generate -global values for input to the "thermo_style custom"_dump.html -command. - -Note that thermodynamic output values can be "extensive" or -"intensive". The former scale with the number of atoms in the system -(e.g. total energy), the latter do not (e.g. temperature). The -setting for "thermo_modify norm"_thermo_modify.html determines whether -extensive quantities are normalized or not. Computes and fixes -produce either extensive or intensive values; see their individual doc -pages for details. "Equal-style variables"_variable.html produce only -intensive values; you can include a division by "natoms" in the -formula if desired, to make an extensive calculation produce an -intensive result. - -Dump file output :h4,link(dump) - -Dump file output is specified by the "dump"_dump.html and -"dump_modify"_dump_modify.html commands. There are several -pre-defined formats (dump atom, dump xtc, etc). - -There is also a "dump custom"_dump.html format where the user -specifies what values are output with each atom. Pre-defined atom -attributes can be specified (id, x, fx, etc). Three additional kinds -of keywords can also be specified (c_ID, f_ID, v_name), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the "dump -custom"_dump.html command. - -There is also a "dump local"_dump.html format where the user specifies -what local values to output. A pre-defined index keyword can be -specified to enumerate the local values. Two additional kinds of -keywords can also be specified (c_ID, f_ID), where a -"compute"_compute.html or "fix"_fix.html or "variable"_variable.html -provides the values to be output. In each case, the compute or fix -must generate local values for input to the "dump local"_dump.html -command. - -Fixes that write output files :h4,link(fixoutput) - -Several fixes take various quantities as input and can write output -files: "fix ave/time"_fix_ave_time.html, "fix -ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/correlate"_fix_ave_correlate.html, and "fix -print"_fix_print.html. - -The "fix ave/time"_fix_ave_time.html command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global -"compute"_compute.html values, global "fix"_fix.html values, or -"variables"_variable.html of any style except the atom style which -produces per-atom values. Since a variable can refer to keywords used -by the "thermo_style custom"_thermo_style.html command (like temp or -press) and individual per-atom values, a wide variety of quantities -can be time averaged and/or output in this way. If the inputs are one -or more scalar values, then the fix generate a global scalar or vector -of output. If the inputs are one or more vector values, then the fix -generates a global vector or array of output. The time-averaged -output of this fix can also be used as input to other output commands. - -The "fix ave/chunk"_fix_ave_chunk.html command enables direct output -to a file of chunk-averaged per-atom quantities like those output in -dump files. Chunks can represent spatial bins or other collections of -atoms, e.g. individual molecules. The per-atom quantities can be atom -density (mass or number) or atom attributes such as position, -velocity, force. They can also be per-atom quantities calculated by a -"compute"_compute.html, by a "fix"_fix.html, or by an atom-style -"variable"_variable.html. The chunk-averaged output of this fix can -also be used as input to other output commands. - -The "fix ave/histo"_fix_ave_histo.html command enables direct output -to a file of histogrammed quantities, which can be global or per-atom -or local quantities. The histogram output of this fix can also be -used as input to other output commands. - -The "fix ave/correlate"_fix_ave_correlate.html command enables direct -output to a file of time-correlated quantities, which can be global -values. The correlation matrix output of this fix can also be used as -input to other output commands. - -The "fix print"_fix_print.html command can generate a line of output -written to the screen and log file or to a separate file, periodically -during a running simulation. The line can contain one or more -"variable"_variable.html values for any style variable except the -vector or atom styles). As explained above, variables themselves can -contain references to global values generated by "thermodynamic -keywords"_thermo_style.html, "computes"_compute.html, -"fixes"_fix.html, or other "variables"_variable.html, or to per-atom -values for a specific atom. Thus the "fix print"_fix_print.html -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. - -Computes that process output quantities :h4,link(computeoutput) - -The "compute reduce"_compute_reduce.html and "compute -reduce/region"_compute_reduce.html commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, -ave) to scalar quantities. These are produced as output values which -can be used as input to other output commands. - -The "compute slice"_compute_slice.html command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. - -The "compute property/atom"_compute_property_atom.html command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and -stores the values in a per-atom vector or array. These are produced -as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the "dump -custom"_dump.html command. - -The "compute property/local"_compute_property_local.html command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. - -Fixes that process output quantities :h4,link(fixprocoutput) - -The "fix vector"_fix_vector.html command can create global vectors as -output from global scalars as input, accumulating them one element at -a time. - -The "fix ave/atom"_fix_ave_atom.html command performs time-averaging -of per-atom vectors. The per-atom quantities can be atom attributes -such as position, velocity, force. They can also be per-atom -quantities calculated by a "compute"_compute.html, by a -"fix"_fix.html, or by an atom-style "variable"_variable.html. The -time-averaged per-atom output of this fix can be used as input to -other output commands. - -The "fix store/state"_fix_store_state.html command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the "dump custom"_dump.html command, -including per-atom quantities calculated by a "compute"_compute.html, -by a "fix"_fix.html, or by an atom-style "variable"_variable.html. -The output of this fix can be used as input to other output commands. - -Computes that generate values to output :h4,link(compute) - -Every "compute"_compute.html in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The doc page for each compute command -describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. - -Fixes that generate values to output :h4,link(fix) - -Some "fixes"_fix.html in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The doc page for -each fix command tells whether it produces any output quantities and -describes them. - -Variables that generate values to output :h4,link(variable) - -"Variables"_variable.html defined in an input script can store one or -more strings. But equal-style, vector-style, and atom-style or -atomfile-style variables generate a global scalar value, global vector -or values, or a per-atom vector, respectively, when accessed. The -formulas used to define these variables can contain references to the -thermodynamic keywords and to global and per-atom data generated by -computes, fixes, and other variables. The values generated by -variables can be used as input to and thus output by the other -commands described in this section. - -Summary table of output options and data flow between commands :h4,link(table) - -This table summarizes the various commands that can be used for -generating output from LAMMPS. Each command produces output data of -some kind and/or writes data to a file. Most of the commands can take -data from other commands as input. Thus you can link many of these -commands together in pipeline form, where data produced by one command -is used as input to another command and eventually written to the -screen or to a file. Note that to hook two commands together the -output and input data types must match, e.g. global/per-atom/local -data and scalar/vector/array data. - -Also note that, as described above, when a command takes a scalar as -input, that could be an element of a vector or array. Likewise a -vector input could be a column of an array. - -Command: Input: Output: -"thermo_style custom"_thermo_style.html: global scalars: screen, log file: -"dump custom"_dump.html: per-atom vectors: dump file: -"dump local"_dump.html: local vectors: dump file: -"fix print"_fix_print.html: global scalar from variable: screen, file: -"print"_print.html: global scalar from variable: screen: -"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array: -"fixes"_fix.html: N/A: global/per-atom/local scalar/vector/array: -"variables"_variable.html: global scalars and vectors, per-atom vectors: global scalar and vector, per-atom vector: -"compute reduce"_compute_reduce.html: per-atom/local vectors: global scalar/vector: -"compute slice"_compute_slice.html: global vectors/arrays: global vector/array: -"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array: -"compute property/local"_compute_property_local.html: local vectors: local vector/array: -"fix vector"_fix_vector.html: global scalars: global vector: -"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array: -"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file: -"fix ave/chunk"_fix_ave_chunk.html: per-atom vectors: global array, file: -"fix ave/histo"_fix_ave_histo.html: global/per-atom/local scalars and vectors: global array, file: -"fix ave/correlate"_fix_ave_correlate.html: global scalars: global array, file: -"fix store/state"_fix_store_state.html: per-atom vectors: per-atom vector/array :tb(c=3,s=:) - -:line - -6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4 - -Thermostatting means controlling the temperature of particles in an MD -simulation. Barostatting means controlling the pressure. Since the -pressure includes a kinetic component due to particle velocities, both -these operations require calculation of the temperature. Typically a -target temperature (T) and/or pressure (P) is specified by the user, -and the thermostat or barostat attempts to equilibrate the system to -the requested T and/or P. - -Temperature is computed as kinetic energy divided by some number of -degrees of freedom (and the Boltzmann constant). Since kinetic energy -is a function of particle velocity, there is often a need to -distinguish between a particle's advection velocity (due to some -aggregate motion of particles) and its thermal velocity. The sum of -the two is the particle's total velocity, but the latter is often what -is wanted to compute a temperature. - -LAMMPS has several options for computing temperatures, any of which -can be used in thermostatting and barostatting. These "compute -commands"_compute.html calculate temperature, and the "compute -pressure"_compute_pressure.html command calculates pressure. - -"compute temp"_compute_temp.html -"compute temp/sphere"_compute_temp_sphere.html -"compute temp/asphere"_compute_temp_asphere.html -"compute temp/com"_compute_temp_com.html -"compute temp/deform"_compute_temp_deform.html -"compute temp/partial"_compute_temp_partial.html -"compute temp/profile"_compute_temp_profile.html -"compute temp/ramp"_compute_temp_ramp.html -"compute temp/region"_compute_temp_region.html :ul - -All but the first 3 calculate velocity biases directly (e.g. advection -velocities) that are removed when computing the thermal temperature. -"Compute temp/sphere"_compute_temp_sphere.html and "compute -temp/asphere"_compute_temp_asphere.html compute kinetic energy for -finite-size particles that includes rotational degrees of freedom. -They both allow for velocity biases indirectly, via an optional extra -argument, another temperature compute that subtracts a velocity bias. -This allows the translational velocity of spherical or aspherical -particles to be adjusted in prescribed ways. - -Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one -case by a pair style. Several thermostatting fixes are available: -Nose-Hoover (nvt), Berendsen, CSVR, Langevin, and direct rescaling -(temp/rescale). Dissipative particle dynamics (DPD) thermostatting -can be invoked via the {dpd/tstat} pair style: - -"fix nvt"_fix_nh.html -"fix nvt/sphere"_fix_nvt_sphere.html -"fix nvt/asphere"_fix_nvt_asphere.html -"fix nvt/sllod"_fix_nvt_sllod.html -"fix temp/berendsen"_fix_temp_berendsen.html -"fix temp/csvr"_fix_temp_csvr.html -"fix langevin"_fix_langevin.html -"fix temp/rescale"_fix_temp_rescale.html -"pair_style dpd/tstat"_pair_dpd.html :ul - -"Fix nvt"_fix_nh.html only thermostats the translational velocity of -particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except -that it subtracts out a velocity bias due to a deforming box and -integrates the SLLOD equations of motion. See the "NEMD -simulations"_#howto_13 section of this page for further details. "Fix -nvt/sphere"_fix_nvt_sphere.html and "fix -nvt/asphere"_fix_nvt_asphere.html thermostat not only translation -velocities but also rotational velocities for spherical and aspherical -particles. - -DPD thermostatting alters pairwise interactions in a manner analogous -to the per-particle thermostatting of "fix -langevin"_fix_langevin.html. - -Any of the thermostatting fixes can use temperature computes that -remove bias which has two effects. First, the current calculated -temperature, which is compared to the requested target temperature, is -calculated with the velocity bias removed. Second, the thermostat -adjusts only the thermal temperature component of the particle's -velocities, which are the velocities with the bias removed. The -removed bias is then added back to the adjusted velocities. See the -doc pages for the individual fixes and for the -"fix_modify"_fix_modify.html command for instructions on how to assign -a temperature compute to a thermostatting fix. For example, you can -apply a thermostat to only the x and z components of velocity by using -it in conjunction with "compute -temp/partial"_compute_temp_partial.html. Of you could thermostat only -the thermal temperature of a streaming flow of particles without -affecting the streaming velocity, by using "compute -temp/profile"_compute_temp_profile.html. - -NOTE: Only the nvt fixes perform time integration, meaning they update -the velocities and positions of particles due to forces and velocities -respectively. The other thermostat fixes only adjust velocities; they -do NOT perform time integration updates. Thus they should be used in -conjunction with a constant NVE integration fix such as these: - -"fix nve"_fix_nve.html -"fix nve/sphere"_fix_nve_sphere.html -"fix nve/asphere"_fix_nve_asphere.html :ul - -Barostatting in LAMMPS is also performed by "fixes"_fix.html. Two -barosttating methods are currently available: Nose-Hoover (npt and -nph) and Berendsen: - -"fix npt"_fix_nh.html -"fix npt/sphere"_fix_npt_sphere.html -"fix npt/asphere"_fix_npt_asphere.html -"fix nph"_fix_nh.html -"fix press/berendsen"_fix_press_berendsen.html :ul - -The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat -and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat; -it does no thermostatting. Both "fix nph"_fix_nh.html and "fix -press/berendsen"_fix_press_berendsen.html can be used in conjunction -with any of the thermostatting fixes. - -As with the thermostats, "fix npt"_fix_nh.html and "fix -nph"_fix_nh.html only use translational motion of the particles in -computing T and P and performing thermo/barostatting. "Fix -npt/sphere"_fix_npt_sphere.html and "fix -npt/asphere"_fix_npt_asphere.html thermo/barostat using not only -translation velocities but also rotational velocities for spherical -and aspherical particles. - -All of the barostatting fixes use the "compute -pressure"_compute_pressure.html compute to calculate a current -pressure. By default, this compute is created with a simple "compute -temp"_compute_temp.html (see the last argument of the "compute -pressure"_compute_pressure.html command), which is used to calculated -the kinetic component of the pressure. The barostatting fixes can -also use temperature computes that remove bias for the purpose of -computing the kinetic component which contributes to the current -pressure. See the doc pages for the individual fixes and for the -"fix_modify"_fix_modify.html command for instructions on how to assign -a temperature or pressure compute to a barostatting fix. - -NOTE: As with the thermostats, the Nose/Hoover methods ("fix -npt"_fix_nh.html and "fix nph"_fix_nh.html) perform time integration. -"Fix press/berendsen"_fix_press_berendsen.html does NOT, so it should -be used with one of the constant NVE fixes or with one of the NVT -fixes. - -Finally, thermodynamic output, which can be setup via the -"thermo_style"_thermo_style.html command, often includes temperature -and pressure values. As explained on the doc page for the -"thermo_style"_thermo_style.html command, the default T and P are -setup by the thermo command itself. They are NOT the ones associated -with any thermostatting or barostatting fix you have defined or with -any compute that calculates a temperature or pressure. Thus if you -want to view these values of T and P, you need to specify them -explicitly via a "thermo_style custom"_thermo_style.html command. Or -you can use the "thermo_modify"_thermo_modify.html command to -re-define what temperature or pressure compute is used for default -thermodynamic output. - -:line - -6.17 Walls :link(howto_17),h4 - -Walls in an MD simulation are typically used to bound particle motion, -i.e. to serve as a boundary condition. - -Walls in LAMMPS can be of rough (made of particles) or idealized -surfaces. Ideal walls can be smooth, generating forces only in the -normal direction, or frictional, generating forces also in the -tangential direction. - -Rough walls, built of particles, can be created in various ways. The -particles themselves can be generated like any other particle, via the -"lattice"_lattice.html and "create_atoms"_create_atoms.html commands, -or read in via the "read_data"_read_data.html command. - -Their motion can be constrained by many different commands, so that -they do not move at all, move together as a group at constant velocity -or in response to a net force acting on them, move in a prescribed -fashion (e.g. rotate around a point), etc. Note that if a time -integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html -is not used with the group that contains wall particles, their -positions and velocities will not be updated. - -"fix aveforce"_fix_aveforce.html - set force on particles to average value, so they move together -"fix setforce"_fix_setforce.html - set force on particles to a value, e.g. 0.0 -"fix freeze"_fix_freeze.html - freeze particles for use as granular walls -"fix nve/noforce"_fix_nve_noforce.html - advect particles by their velocity, but without force -"fix move"_fix_move.html - prescribe motion of particles by a linear velocity, oscillation, rotation, variable :ul - -The "fix move"_fix_move.html command offers the most generality, since -the motion of individual particles can be specified with -"variable"_variable.html formula which depends on time and/or the -particle position. - -For rough walls, it may be useful to turn off pairwise interactions -between wall particles via the "neigh_modify -exclude"_neigh_modify.html command. - -Rough walls can also be created by specifying frozen particles that do -not move and do not interact with mobile particles, and then tethering -other particles to the fixed particles, via a "bond"_bond_style.html. -The bonded particles do interact with other mobile particles. - -Idealized walls can be specified via several fix commands. "Fix -wall/gran"_fix_wall_gran.html creates frictional walls for use with -granular particles; all the other commands create smooth walls. - -"fix wall/reflect"_fix_wall_reflect.html - reflective flat walls -"fix wall/lj93"_fix_wall.html - flat walls, with Lennard-Jones 9/3 potential -"fix wall/lj126"_fix_wall.html - flat walls, with Lennard-Jones 12/6 potential -"fix wall/colloid"_fix_wall.html - flat walls, with "pair_style colloid"_pair_colloid.html potential -"fix wall/harmonic"_fix_wall.html - flat walls, with repulsive harmonic spring potential -"fix wall/region"_fix_wall_region.html - use region surface as wall -"fix wall/gran"_fix_wall_gran.html - flat or curved walls with "pair_style granular"_pair_gran.html potential :ul - -The {lj93}, {lj126}, {colloid}, and {harmonic} styles all allow the -flat walls to move with a constant velocity, or oscillate in time. -The "fix wall/region"_fix_wall_region.html command offers the most -generality, since the region surface is treated as a wall, and the -geometry of the region can be a simple primitive volume (e.g. a -sphere, or cube, or plane), or a complex volume made from the union -and intersection of primitive volumes. "Regions"_region.html can also -specify a volume "interior" or "exterior" to the specified primitive -shape or {union} or {intersection}. "Regions"_region.html can also be -"dynamic" meaning they move with constant velocity, oscillate, or -rotate. - -The only frictional idealized walls currently in LAMMPS are flat or -curved surfaces specified by the "fix wall/gran"_fix_wall_gran.html -command. At some point we plan to allow regoin surfaces to be used as -frictional walls, as well as triangulated surfaces. - -:line - -6.18 Elastic constants :link(howto_18),h4 - -Elastic constants characterize the stiffness of a material. The formal -definition is provided by the linear relation that holds between the -stress and strain tensors in the limit of infinitesimal deformation. -In tensor notation, this is expressed as s_ij = C_ijkl * e_kl, where -the repeated indices imply summation. s_ij are the elements of the -symmetric stress tensor. e_kl are the elements of the symmetric strain -tensor. C_ijkl are the elements of the fourth rank tensor of elastic -constants. In three dimensions, this tensor has 3^4=81 elements. Using -Voigt notation, the tensor can be written as a 6x6 matrix, where C_ij -is now the derivative of s_i w.r.t. e_j. Because s_i is itself a -derivative w.r.t. e_i, it follows that C_ij is also symmetric, with at -most 7*6/2 = 21 distinct elements. - -At zero temperature, it is easy to estimate these derivatives by -deforming the simulation box in one of the six directions using the -"change_box"_change_box.html command and measuring the change in the -stress tensor. A general-purpose script that does this is given in the -examples/elastic directory described in "this -section"_Section_example.html. - -Calculating elastic constants at finite temperature is more -challenging, because it is necessary to run a simulation that perfoms -time averages of differential properties. One way to do this is to -measure the change in average stress tensor in an NVT simulations when -the cell volume undergoes a finite deformation. In order to balance -the systematic and statistical errors in this method, the magnitude of -the deformation must be chosen judiciously, and care must be taken to -fully equilibrate the deformed cell before sampling the stress -tensor. Another approach is to sample the triclinic cell fluctuations -that occur in an NPT simulation. This method can also be slow to -converge and requires careful post-processing "(Shinoda)"_#Shinoda1 - -:line - -6.19 Library interface to LAMMPS :link(howto_19),h4 - -As described in "Section 2.5"_Section_start.html#start_5, LAMMPS -can be built as a library, so that it can be called by another code, -used in a "coupled manner"_Section_howto.html#howto_10 with other -codes, or driven through a "Python interface"_Section_python.html. - -All of these methodologies use a C-style interface to LAMMPS that is -provided in the files src/library.cpp and src/library.h. The -functions therein have a C-style argument list, but contain C++ code -you could write yourself in a C++ application that was invoking LAMMPS -directly. The C++ code in the functions illustrates how to invoke -internal LAMMPS operations. Note that LAMMPS classes are defined -within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ -application. - -The examples/COUPLE and python/examples directories have example C++ -and C and Python codes which show how a driver code can link to LAMMPS -as a library, run LAMMPS on a subset of processors, grab data from -LAMMPS, change it, and put it back into LAMMPS. - -The file src/library.cpp contains the following functions for creating -and destroying an instance of LAMMPS and sending it commands to -execute. See the documentation in the src/library.cpp file for -details. - -NOTE: You can write code for additional functions as needed to define -how your code talks to LAMMPS and add them to src/library.cpp and -src/library.h, as well as to the "Python -interface"_Section_python.html. The added functions can access or -change any internal LAMMPS data you wish. - -void lammps_open(int, char **, MPI_Comm, void **) -void lammps_open_no_mpi(int, char **, void **) -void lammps_close(void *) -int lammps_version(void *) -void lammps_file(void *, char *) -char *lammps_command(void *, char *) -void lammps_commands_list(void *, int, char **) -void lammps_commands_string(void *, char *) -void lammps_free(void *) :pre - -The lammps_open() function is used to initialize LAMMPS, passing in a -list of strings as if they were "command-line -arguments"_Section_start.html#start_6 when LAMMPS is run in -stand-alone mode from the command line, and a MPI communicator for -LAMMPS to run under. It returns a ptr to the LAMMPS object that is -created, and which is used in subsequent library calls. The -lammps_open() function can be called multiple times, to create -multiple instances of LAMMPS. - -LAMMPS will run on the set of processors in the communicator. This -means the calling code can run LAMMPS on all or a subset of -processors. For example, a wrapper script might decide to alternate -between LAMMPS and another code, allowing them both to run on all the -processors. Or it might allocate half the processors to LAMMPS and -half to the other code and run both codes simultaneously before -syncing them up periodically. Or it might instantiate multiple -instances of LAMMPS to perform different calculations. - -The lammps_open_no_mpi() function is similar except that no MPI -communicator is passed from the caller. Instead, MPI_COMM_WORLD is -used to instantiate LAMMPS, and MPI is initialized if necessary. - -The lammps_close() function is used to shut down an instance of LAMMPS -and free all its memory. - -The lammps_version() function can be used to determined the specific -version of the underlying LAMMPS code. This is particularly useful -when loading LAMMPS as a shared library via dlopen(). The code using -the library interface can than use this information to adapt to -changes to the LAMMPS command syntax between versions. The returned -LAMMPS version code is an integer (e.g. 2 Sep 2015 results in -20150902) that grows with every new LAMMPS version. - -The lammps_file(), lammps_command(), lammps_commands_list(), and -lammps_commands_string() functions are used to pass one or more -commands to LAMMPS to execute, the same as if they were coming from an -input script. - -Via these functions, the calling code can read or generate a series of -LAMMPS commands one or multiple at a time and pass it thru the library -interface to setup a problem and then run it in stages. The caller -can interleave the command function calls with operations it performs, -calls to extract information from or set information within LAMMPS, or -calls to another code's library. - -The lammps_file() function passes the filename of an input script. -The lammps_command() function passes a single command as a string. -The lammps_commands_list() function passes multiple commands in a -char** list. In both lammps_command() and lammps_commands_list(), -individual commands may or may not have a trailing newline. The -lammps_commands_string() function passes multiple commands -concatenated into one long string, separated by newline characters. -In both lammps_commands_list() and lammps_commands_string(), a single -command can be spread across multiple lines, if the last printable -character of all but the last line is "&", the same as if the lines -appeared in an input script. - -The lammps_free() function is a clean-up function to free memory that -the library allocated previously via other function calls. See -comments in src/library.cpp file for which other functions need this -clean-up. - -The file src/library.cpp also contains these functions for extracting -information from LAMMPS and setting value within LAMMPS. Again, see -the documentation in the src/library.cpp file for details, including -which quantities can be queried by name: - -int lammps_extract_setting(void *, char *) -void *lammps_extract_global(void *, char *) -void lammps_extract_box(void *, double *, double *, - double *, double *, double *, int *, int *) -void *lammps_extract_atom(void *, char *) -void *lammps_extract_compute(void *, char *, int, int) -void *lammps_extract_fix(void *, char *, int, int, int, int) -void *lammps_extract_variable(void *, char *, char *) :pre - -The extract_setting() function returns info on the size -of data types (e.g. 32-bit or 64-bit atom IDs) used -by the LAMMPS executable (a compile-time choice). - -The other extract functions return a pointer to various global or -per-atom quantities stored in LAMMPS or to values calculated by a -compute, fix, or variable. The pointer returned by the -extract_global() function can be used as a permanent reference to a -value which may change. For the extract_atom() method, see the -extract() method in the src/atom.cpp file for a list of valid per-atom -properties. New names could easily be added if the property you want -is not listed. For the other extract functions, the underlying -storage may be reallocated as LAMMPS runs, so you need to re-call the -function to assure a current pointer or returned value(s). - -double lammps_get_thermo(void *, char *) -int lammps_get_natoms(void *) :pre - -int lammps_set_variable(void *, char *, char *) -void lammps_reset_box(void *, double *, double *, double, double, double) :pre - -The lammps_get_thermo() function returns the current value of a thermo -keyword as a double precision value. - -The lammps_get_natoms() function returns the total number of atoms in -the system and can be used by the caller to allocate memory for the -lammps_gather_atoms() and lammps_scatter_atoms() functions. - -The lammps_set_variable() function can set an existing string-style -variable to a new string value, so that subsequent LAMMPS commands can -access the variable. - -The lammps_reset_box() function resets the size and shape of the -simulation box, e.g. as part of restoring a previously extracted and -saved state of a simulation. - -void lammps_gather_atoms(void *, char *, int, int, void *) -void lammps_gather_atoms_concat(void *, char *, int, int, void *) -void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *) -void lammps_scatter_atoms(void *, char *, int, int, void *) -void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre - -void lammps_create_atoms(void *, int, tagint *, int *, double *, double *, - imageint *, int) :pre - -The gather functions collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. - -The lammps_gather_atoms() function does this for all N atoms in the -system, ordered by atom ID, from 1 to N. The -lammps_gather_atoms_concat() function does it for all N atoms, but -simply concatenates the subset of atoms owned by each processor. The -resulting vector is not ordered by atom ID. Atom IDs can be requetsed -by the same function if the caller needs to know the ordering. The -lammps_gather_subset() function allows the caller to request values -for only a subset of atoms (identified by ID). -For all 3 gather function, per-atom image flags can be retrieved in 2 ways. -If the count is specified as 1, they are returned -in a packed format with all three image flags stored in a single integer. -If the count is specified as 3, the values are unpacked into xyz flags -by the library before returning them. - -The lammps_scatter_atoms() function takes a list of values for all N -atoms in the system, ordered by atom ID, from 1 to N, and assigns -those values to each atom in the system. The -lammps_scatter_atoms_subset() function takes a subset of IDs as an -argument and only scatters those values to the owning atoms. - -The lammps_create_atoms() function takes a list of N atoms as input -with atom types and coords (required), an optionally atom IDs and -velocities and image flags. It uses the coords of each atom to assign -it as a new atom to the processor that owns it. This function is -useful to add atoms to a simulation or (in tandem with -lammps_reset_box()) to restore a previously extracted and saved state -of a simulation. Additional properties for the new atoms can then be -assigned via the lammps_scatter_atoms() or lammps_extract_atom() -functions. - -:line - -6.20 Calculating thermal conductivity :link(howto_20),h4 - -The thermal conductivity kappa of a material can be measured in at -least 4 ways using various options in LAMMPS. See the examples/KAPPA -directory for scripts that implement the 4 methods discussed here for -a simple Lennard-Jones fluid model. Also, see "this -section"_Section_howto.html#howto_21 of the manual for an analogous -discussion for viscosity. - -The thermal conductivity tensor kappa is a measure of the propensity -of a material to transmit heat energy in a diffusive manner as given -by Fourier's law - -J = -kappa grad(T) - -where J is the heat flux in units of energy per area per time and -grad(T) is the spatial gradient of temperature. The thermal -conductivity thus has units of energy per distance per time per degree -K and is often approximated as an isotropic quantity, i.e. as a -scalar. - -The first method is to setup two thermostatted regions at opposite -ends of a simulation box, or one in the middle and one at the end of a -periodic box. By holding the two regions at different temperatures -with a "thermostatting fix"_Section_howto.html#howto_13, the energy -added to the hot region should equal the energy subtracted from the -cold region and be proportional to the heat flux moving between the -regions. See the papers by "Ikeshoji and Hafskjold"_#howto-Ikeshoji -and "Wirnsberger et al"_#howto-Wirnsberger for details of this idea. -Note that thermostatting fixes such as "fix nvt"_fix_nh.html, "fix -langevin"_fix_langevin.html, and "fix -temp/rescale"_fix_temp_rescale.html store the cumulative energy they -add/subtract. - -Alternatively, as a second method, the "fix heat"_fix_heat.html or -"fix ehex"_fix_ehex.html commands can be used in place of thermostats -on each of two regions to add/subtract specified amounts of energy to -both regions. In both cases, the resulting temperatures of the two -regions can be monitored with the "compute temp/region" command and -the temperature profile of the intermediate region can be monitored -with the "fix ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix thermal/conductivity"_fix_thermal_conductivity.html -command which implements the rNEMD algorithm of Muller-Plathe. -Kinetic energy is swapped between atoms in two different layers of the -simulation box. This induces a temperature gradient between the two -layers which can be monitored with the "fix -ave/chunk"_fix_ave_chunk.html and "compute -ke/atom"_compute_ke_atom.html commands. The fix tallies the -cumulative energy transfer that it performs. See the "fix -thermal/conductivity"_fix_thermal_conductivity.html command for -details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the heat flux -to kappa. The heat flux can be calculated from the fluctuations of -per-atom potential and kinetic energies and per-atom stress tensor in -a steady-state equilibrated simulation. This is in contrast to the -two preceding non-equilibrium methods, where energy flows continuously -between hot and cold regions of the simulation box. - -The "compute heat/flux"_compute_heat_flux.html command can calculate -the needed heat flux and describes how to implement the Green_Kubo -formalism using additional LAMMPS commands, such as the "fix -ave/correlate"_fix_ave_correlate.html command to calculate the needed -auto-correlation. See the doc page for the "compute -heat/flux"_compute_heat_flux.html command for an example input script -that calculates the thermal conductivity of solid Ar via the GK -formalism. - -:line - -6.21 Calculating viscosity :link(howto_21),h4 - -The shear viscosity eta of a fluid can be measured in at least 5 ways -using various options in LAMMPS. See the examples/VISCOSITY directory -for scripts that implement the 5 methods discussed here for a simple -Lennard-Jones fluid model. Also, see "this -section"_Section_howto.html#howto_20 of the manual for an analogous -discussion for thermal conductivity. - -Eta is a measure of the propensity of a fluid to transmit momentum in -a direction perpendicular to the direction of velocity or momentum -flow. Alternatively it is the resistance the fluid has to being -sheared. It is given by - -J = -eta grad(Vstream) - -where J is the momentum flux in units of momentum per area per time. -and grad(Vstream) is the spatial gradient of the velocity of the fluid -moving in another direction, normal to the area through which the -momentum flows. Viscosity thus has units of pressure-time. - -The first method is to perform a non-equilibrium MD (NEMD) simulation -by shearing the simulation box via the "fix deform"_fix_deform.html -command, and using the "fix nvt/sllod"_fix_nvt_sllod.html command to -thermostat the fluid via the SLLOD equations of motion. -Alternatively, as a second method, one or more moving walls can be -used to shear the fluid in between them, again with some kind of -thermostat that modifies only the thermal (non-shearing) components of -velocity to prevent the fluid from heating up. - -In both cases, the velocity profile setup in the fluid by this -procedure can be monitored by the "fix -ave/chunk"_fix_ave_chunk.html command, which determines -grad(Vstream) in the equation above. E.g. the derivative in the -y-direction of the Vx component of fluid motion or grad(Vstream) = -dVx/dy. The Pxy off-diagonal component of the pressure or stress -tensor, as calculated by the "compute pressure"_compute_pressure.html -command, can also be monitored, which is the J term in the equation -above. See "this section"_Section_howto.html#howto_13 of the manual -for details on NEMD simulations. - -The third method is to perform a reverse non-equilibrium MD simulation -using the "fix viscosity"_fix_viscosity.html command which implements -the rNEMD algorithm of Muller-Plathe. Momentum in one dimension is -swapped between atoms in two different layers of the simulation box in -a different dimension. This induces a velocity gradient which can be -monitored with the "fix ave/chunk"_fix_ave_chunk.html command. -The fix tallies the cumulative momentum transfer that it performs. -See the "fix viscosity"_fix_viscosity.html command for details. - -The fourth method is based on the Green-Kubo (GK) formula which -relates the ensemble average of the auto-correlation of the -stress/pressure tensor to eta. This can be done in a fully -equilibrated simulation which is in contrast to the two preceding -non-equilibrium methods, where momentum flows continuously through the -simulation box. - -Here is an example input script that calculates the viscosity of -liquid Ar via the GK formalism: - -# Sample LAMMPS input script for viscosity of liquid Ar :pre - -units real -variable T equal 86.4956 -variable V equal vol -variable dt equal 4.0 -variable p equal 400 # correlation length -variable s equal 5 # sample interval -variable d equal $p*$s # dump interval :pre - -# convert from LAMMPS real units to SI :pre - -variable kB equal 1.3806504e-23 # \[J/K/] Boltzmann -variable atm2Pa equal 101325.0 -variable A2m equal 1.0e-10 -variable fs2s equal 1.0e-15 -variable convert equal $\{atm2Pa\}*$\{atm2Pa\}*$\{fs2s\}*$\{A2m\}*$\{A2m\}*$\{A2m\} :pre - -# setup problem :pre - -dimension 3 -boundary p p p -lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 -region box block 0 4 0 4 0 4 -create_box 1 box -create_atoms 1 box -mass 1 39.948 -pair_style lj/cut 13.0 -pair_coeff * * 0.2381 3.405 -timestep $\{dt\} -thermo $d :pre - -# equilibration and thermalization :pre - -velocity all create $T 102486 mom yes rot yes dist gaussian -fix NVT all nvt temp $T $T 10 drag 0.2 -run 8000 :pre - -# viscosity calculation, switch to NVE if desired :pre - -#unfix NVT -#fix NVE all nve :pre - -reset_timestep 0 -variable pxy equal pxy -variable pxz equal pxz -variable pyz equal pyz -fix SS all ave/correlate $s $p $d & - v_pxy v_pxz v_pyz type auto file S0St.dat ave running -variable scale equal $\{convert\}/($\{kB\}*$T)*$V*$s*$\{dt\} -variable v11 equal trap(f_SS\[3\])*$\{scale\} -variable v22 equal trap(f_SS\[4\])*$\{scale\} -variable v33 equal trap(f_SS\[5\])*$\{scale\} -thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 -run 100000 -variable v equal (v_v11+v_v22+v_v33)/3.0 -variable ndens equal count(all)/vol -print "average viscosity: $v \[Pa.s\] @ $T K, $\{ndens\} /A^3" :pre - -The fifth method is related to the above Green-Kubo method, -but uses the Einstein formulation, analogous to the Einstein -mean-square-displacement formulation for self-diffusivity. The -time-integrated momentum fluxes play the role of Cartesian -coordinates, whose mean-square displacement increases linearly -with time at sufficiently long times. - -:line - -6.22 Calculating a diffusion coefficient :link(howto_22),h4 - -The diffusion coefficient D of a material can be measured in at least -2 ways using various options in LAMMPS. See the examples/DIFFUSE -directory for scripts that implement the 2 methods discussed here for -a simple Lennard-Jones fluid model. - -The first method is to measure the mean-squared displacement (MSD) of -the system, via the "compute msd"_compute_msd.html command. The slope -of the MSD versus time is proportional to the diffusion coefficient. -The instantaneous MSD values can be accumulated in a vector via the -"fix vector"_fix_vector.html command, and a line fit to the vector to -compute its slope via the "variable slope"_variable.html function, and -thus extract D. - -The second method is to measure the velocity auto-correlation function -(VACF) of the system, via the "compute vacf"_compute_vacf.html -command. The time-integral of the VACF is proportional to the -diffusion coefficient. The instantaneous VACF values can be -accumulated in a vector via the "fix vector"_fix_vector.html command, -and time integrated via the "variable trap"_variable.html function, -and thus extract D. - -:line - -6.23 Using chunks to calculate system properties :link(howto_23),h4 - -In LAMMS, "chunks" are collections of atoms, as defined by the -"compute chunk/atom"_compute_chunk_atom.html command, which assigns -each atom to a chunk ID (or to no chunk at all). The number of chunks -and the assignment of chunk IDs to atoms can be static or change over -time. Examples of "chunks" are molecules or spatial bins or atoms -with similar values (e.g. coordination number or potential energy). - -The per-atom chunk IDs can be used as input to two other kinds of -commands, to calculate various properties of a system: - -"fix ave/chunk"_fix_ave_chunk.html -any of the "compute */chunk"_compute.html commands :ul - -Here, each of the 3 kinds of chunk-related commands is briefly -overviewed. Then some examples are given of how to compute different -properties with chunk commands. - -Compute chunk/atom command: :h4 - -This compute can assign atoms to chunks of various styles. Only atoms -in the specified group and optional specified region are assigned to a -chunk. Here are some possible chunk definitions: - -atoms in same molecule | chunk ID = molecule ID | -atoms of same atom type | chunk ID = atom type | -all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | -atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | -atoms in same spatial bin | chunk ID = bin ID | -atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | -atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | -atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) - -Note that chunk IDs are integer values, so for atom properties or -computes that produce a floating point value, they will be truncated -to an integer. You could also use the compute in a variable that -scales the floating point value to spread it across multiple integers. - -Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = -pencils, 3d bins = boxes, spherical bins, cylindrical bins. - -This compute also calculates the number of chunks {Nchunk}, which is -used by other commands to tally per-chunk data. {Nchunk} can be a -static value or change over time (e.g. the number of clusters). The -chunk ID for an individual atom can also be static (e.g. a molecule -ID), or dynamic (e.g. what spatial bin an atom is in as it moves). - -Note that this compute allows the per-atom output of other -"computes"_compute.html, "fixes"_fix.html, and -"variables"_variable.html to be used to define chunk IDs for each -atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID. See -"Section 10"_Section_modify.html of the documentation for how to -do this. You can also define a "per-atom variable"_variable.html in -the input script that uses a formula to generate a chunk ID for each -atom. - -Fix ave/chunk command: :h4 - -This fix takes the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. For each chunk, -it then sums one or more specified per-atom values over the atoms in -each chunk. The per-atom values can be any atom property, such as -velocity, force, charge, potential energy, kinetic energy, stress, -etc. Additional keywords are defined for per-chunk properties like -density and temperature. More generally any per-atom value generated -by other "computes"_compute.html, "fixes"_fix.html, and "per-atom -variables"_variable.html, can be summed over atoms in each chunk. - -Similar to other averaging fixes, this fix allows the summed per-chunk -values to be time-averaged in various ways, and output to a file. The -fix produces a global array as output with one row of values per -chunk. - -Compute */chunk commands: :h4 - -Currently the following computes operate on chunks of atoms to produce -per-chunk values. - -"compute com/chunk"_compute_com_chunk.html -"compute gyration/chunk"_compute_gyration_chunk.html -"compute inertia/chunk"_compute_inertia_chunk.html -"compute msd/chunk"_compute_msd_chunk.html -"compute property/chunk"_compute_property_chunk.html -"compute temp/chunk"_compute_temp_chunk.html -"compute torque/chunk"_compute_vcm_chunk.html -"compute vcm/chunk"_compute_vcm_chunk.html :ul - -They each take the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. As their names -indicate, they calculate the center-of-mass, radius of gyration, -moments of inertia, mean-squared displacement, temperature, torque, -and velocity of center-of-mass for each chunk of atoms. The "compute -property/chunk"_compute_property_chunk.html command can tally the -count of atoms in each chunk and extract other per-chunk properties. - -The reason these various calculations are not part of the "fix -ave/chunk command"_fix_ave_chunk.html, is that each requires a more -complicated operation than simply summing and averaging over per-atom -values in each chunk. For example, many of them require calculation -of a center of mass, which requires summing mass*position over the -atoms and then dividing by summed mass. - -All of these computes produce a global vector or global array as -output, wih one or more values per chunk. They can be used -in various ways: - -As input to the "fix ave/time"_fix_ave_time.html command, which can -write the values to a file and optionally time average them. :ulb,l - -As input to the "fix ave/histo"_fix_ave_histo.html command to -histogram values across chunks. E.g. a histogram of cluster sizes or -molecule diffusion rates. :l - -As input to special functions of "equal-style -variables"_variable.html, like sum() and max(). E.g. to find the -largest cluster or fastest diffusing molecule. :l -:ule - -Example calculations with chunks :h4 - -Here are examples using chunk commands to calculate various -properties: - -(1) Average velocity in each of 1000 2d spatial bins: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced -fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out :pre - -(2) Temperature in each spatial bin, after subtracting a flow -velocity: - -compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced -compute vbias all temp/profile 1 0 0 y 10 -fix 1 all ave/chunk 100 10 1000 cc1 temp bias vbias file tmp.out :pre - -(3) Center of mass of each molecule: - -compute cc1 all chunk/atom molecule -compute myChunk all com/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre - -(4) Total force on each molecule and ave/max across all molecules: - -compute cc1 all chunk/atom molecule -fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out -variable xave equal ave(f_1\[2\]) -variable xmax equal max(f_1\[2\]) -thermo 1000 -thermo_style custom step temp v_xave v_xmax :pre - -(5) Histogram of cluster sizes: - -compute cluster all cluster/atom 1.0 -compute cc1 all chunk/atom c_cluster compress yes -compute size all property/chunk cc1 count -fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo :pre - -:line - -6.24 Setting parameters for the "kspace_style pppm/disp"_kspace_style.html command :link(howto_24),h4 - -The PPPM method computes interactions by splitting the pair potential -into two parts, one of which is computed in a normal pairwise fashion, -the so-called real-space part, and one of which is computed using the -Fourier transform, the so called reciprocal-space or kspace part. For -both parts, the potential is not computed exactly but is approximated. -Thus, there is an error in both parts of the computation, the -real-space and the kspace error. The just mentioned facts are true -both for the PPPM for Coulomb as well as dispersion interactions. The -deciding difference - and also the reason why the parameters for -pppm/disp have to be selected with more care - is the impact of the -errors on the results: The kspace error of the PPPM for Coulomb and -dispersion interaction and the real-space error of the PPPM for -Coulomb interaction have the character of noise. In contrast, the -real-space error of the PPPM for dispersion has a clear physical -interpretation: the underprediction of cohesion. As a consequence, the -real-space error has a much stronger effect than the kspace error on -simulation results for pppm/disp. Parameters must thus be chosen in a -way that this error is much smaller than the kspace error. - -When using pppm/disp and not making any specifications on the PPPM -parameters via the kspace modify command, parameters will be tuned -such that the real-space error and the kspace error are equal. This -will result in simulations that are either inaccurate or slow, both of -which is not desirable. For selecting parameters for the pppm/disp -that provide fast and accurate simulations, there are two approaches, -which both have their up- and downsides. - -The first approach is to set desired real-space an kspace accuracies -via the {kspace_modify force/disp/real} and {kspace_modify -force/disp/kspace} commands. Note that the accuracies have to be -specified in force units and are thus dependent on the chosen unit -settings. For real units, 0.0001 and 0.002 seem to provide reasonable -accurate and efficient computations for the real-space and kspace -accuracies. 0.002 and 0.05 work well for most systems using lj -units. PPPM parameters will be generated based on the desired -accuracies. The upside of this approach is that it usually provides a -good set of parameters and will work for both the {kspace_modify diff -ad} and {kspace_modify diff ik} options. The downside of the method -is that setting the PPPM parameters will take some time during the -initialization of the simulation. - -The second approach is to set the parameters for the pppm/disp -explicitly using the {kspace_modify mesh/disp}, {kspace_modify -order/disp}, and {kspace_modify gewald/disp} commands. This approach -requires a more experienced user who understands well the impact of -the choice of parameters on the simulation accuracy and -performance. This approach provides a fast initialization of the -simulation. However, it is sensitive to errors: A combination of -parameters that will perform well for one system might result in -far-from-optimal conditions for other simulations. For example, -parameters that provide accurate and fast computations for -all-atomistic force fields can provide insufficient accuracy or -united-atomistic force fields (which is related to that the latter -typically have larger dispersion coefficients). - -To avoid inaccurate or inefficient simulations, the pppm/disp stops -simulations with an error message if no action is taken to control the -PPPM parameters. If the automatic parameter generation is desired and -real-space and kspace accuracies are desired to be equal, this error -message can be suppressed using the {kspace_modify disp/auto yes} -command. - -A reasonable approach that combines the upsides of both methods is to -make the first run using the {kspace_modify force/disp/real} and -{kspace_modify force/disp/kspace} commands, write down the PPPM -parameters from the outut, and specify these parameters using the -second approach in subsequent runs (which have the same composition, -force field, and approximately the same volume). - -Concerning the performance of the pppm/disp there are two more things -to consider. The first is that when using the pppm/disp, the cutoff -parameter does no longer affect the accuracy of the simulation -(subject to that gewald/disp is adjusted when changing the cutoff). -The performance can thus be increased by examining different values -for the cutoff parameter. A lower bound for the cutoff is only set by -the truncation error of the repulsive term of pair potentials. - -The second is that the mixing rule of the pair style has an impact on -the computation time when using the pppm/disp. Fastest computations -are achieved when using the geometric mixing rule. Using the -arithmetic mixing rule substantially increases the computational cost. -The computational overhead can be reduced using the {kspace_modify -mix/disp geom} and {kspace_modify splittol} commands. The first -command simply enforces geometric mixing of the dispersion -coefficients in kspace computations. This introduces some error in -the computations but will also significantly speed-up the -simulations. The second keyword sets the accuracy with which the -dispersion coefficients are approximated using a matrix factorization -approach. This may result in better accuracy then using the first -command, but will usually also not provide an equally good increase of -efficiency. - -Finally, pppm/disp can also be used when no mixing rules apply. -This can be achieved using the {kspace_modify mix/disp none} command. -Note that the code does not check automatically whether any mixing -rule is fulfilled. If mixing rules do not apply, the user will have -to specify this command explicitly. - -:line - -6.25 Polarizable models :link(howto_25),h4 - -In polarizable force fields the charge distributions in molecules and -materials respond to their electrostatic environments. Polarizable -systems can be simulated in LAMMPS using three methods: - -the fluctuating charge method, implemented in the "QEQ"_fix_qeq.html -package, :ulb,l -the adiabatic core-shell method, implemented in the -"CORESHELL"_#howto_26 package, :l -the thermalized Drude dipole method, implemented in the -"USER-DRUDE"_#howto_27 package. :l -:ule - -The fluctuating charge method calculates instantaneous charges on -interacting atoms based on the electronegativity equalization -principle. It is implemented in the "fix qeq"_fix_qeq.html which is -available in several variants. It is a relatively efficient technique -since no additional particles are introduced. This method allows for -charge transfer between molecules or atom groups. However, because the -charges are located at the interaction sites, off-plane components of -polarization cannot be represented in planar molecules or atom groups. - -The two other methods share the same basic idea: polarizable atoms are -split into one core atom and one satellite particle (called shell or -Drude particle) attached to it by a harmonic spring. Both atoms bear -a charge and they represent collectively an induced electric dipole. -These techniques are computationally more expensive than the QEq -method because of additional particles and bonds. These two -charge-on-spring methods differ in certain features, with the -core-shell model being normally used for ionic/crystalline materials, -whereas the so-called Drude model is normally used for molecular -systems and fluid states. - -The core-shell model is applicable to crystalline materials where the -high symmetry around each site leads to stable trajectories of the -core-shell pairs. However, bonded atoms in molecules can be so close -that a core would interact too strongly or even capture the Drude -particle of a neighbor. The Drude dipole model is relatively more -complex in order to remediate this and other issues. Specifically, the -Drude model includes specific thermostating of the core-Drude pairs -and short-range damping of the induced dipoles. - -The three polarization methods can be implemented through a -self-consistent calculation of charges or induced dipoles at each -timestep. In the fluctuating charge scheme this is done by the matrix -inversion method in "fix qeq/point"_fix_qeq.html, but for core-shell -or Drude-dipoles the relaxed-dipoles technique would require an slow -iterative procedure. These self-consistent solutions yield accurate -trajectories since the additional degrees of freedom representing -polarization are massless. An alternative is to attribute a mass to -the additional degrees of freedom and perform time integration using -an extended Lagrangian technique. For the fluctuating charge scheme -this is done by "fix qeq/dynamic"_fix_qeq.html, and for the -charge-on-spring models by the methods outlined in the next two -sections. The assignment of masses to the additional degrees of -freedom can lead to unphysical trajectories if care is not exerted in -choosing the parameters of the polarizable models and the simulation -conditions. - -In the core-shell model the vibration of the shells is kept faster -than the ionic vibrations to mimic the fast response of the -polarizable electrons. But in molecular systems thermalizing the -core-Drude pairs at temperatures comparable to the rest of the -simulation leads to several problems (kinetic energy transfer, too -short a timestep, etc.) In order to avoid these problems the relative -motion of the Drude particles with respect to their cores is kept -"cold" so the vibration of the core-Drude pairs is very slow, -approaching the self-consistent regime. In both models the -temperature is regulated using the velocities of the center of mass of -core+shell (or Drude) pairs, but in the Drude model the actual -relative core-Drude particle motion is thermostated separately as -well. - -:line - -6.26 Adiabatic core/shell model :link(howto_26),h4 - -The adiabatic core-shell model by "Mitchell and -Fincham"_#MitchellFincham is a simple method for adding -polarizability to a system. In order to mimic the electron shell of -an ion, a satellite particle is attached to it. This way the ions are -split into a core and a shell where the latter is meant to react to -the electrostatic environment inducing polarizability. - -Technically, shells are attached to the cores by a spring force f = -k*r where k is a parametrized spring constant and r is the distance -between the core and the shell. The charges of the core and the shell -add up to the ion charge, thus q(ion) = q(core) + q(shell). This -setup introduces the ion polarizability (alpha) given by -alpha = q(shell)^2 / k. In a -similar fashion the mass of the ion is distributed on the core and the -shell with the core having the larger mass. - -To run this model in LAMMPS, "atom_style"_atom_style.html {full} can -be used since atom charge and bonds are needed. Each kind of -core/shell pair requires two atom types and a bond type. The core and -shell of a core/shell pair should be bonded to each other with a -harmonic bond that provides the spring force. For example, a data file -for NaCl, as found in examples/coreshell, has this format: - -432 atoms # core and shell atoms -216 bonds # number of core/shell springs :pre - -4 atom types # 2 cores and 2 shells for Na and Cl -2 bond types :pre - -0.0 24.09597 xlo xhi -0.0 24.09597 ylo yhi -0.0 24.09597 zlo zhi :pre - -Masses # core/shell mass ratio = 0.1 :pre - -1 20.690784 # Na core -2 31.90500 # Cl core -3 2.298976 # Na shell -4 3.54500 # Cl shell :pre - -Atoms :pre - -1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1 -2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1 -3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2 -4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2 -(...) :pre - -Bonds # Bond topology for spring forces :pre - -1 2 1 2 # spring for core/shell pair 1 -2 2 3 4 # spring for core/shell pair 2 -(...) :pre - -Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only -defined between the shells. Coulombic interactions are defined -between all cores and shells. If desired, additional bonds can be -specified between cores. - -The "special_bonds"_special_bonds.html command should be used to -turn-off the Coulombic interaction within core/shell pairs, since that -interaction is set by the bond spring. This is done using the -"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0, -which is the default value. It needs to be considered whether one has -to adjust the "special_bonds"_special_bonds.html weighting according -to the molecular topology since the interactions of the shells are -bypassed over an extra bond. - -Note that this core/shell implementation does not require all ions to -be polarized. One can mix core/shell pairs and ions without a -satellite particle if desired. - -Since the core/shell model permits distances of r = 0.0 between the -core and shell, a pair style with a "cs" suffix needs to be used to -implement a valid long-range Coulombic correction. Several such pair -styles are provided in the CORESHELL package. See "this doc -page"_pair_cs.html for details. All of the core/shell enabled pair -styles require the use of a long-range Coulombic solver, as specified -by the "kspace_style"_kspace_style.html command. Either the PPPM or -Ewald solvers can be used. - -For the NaCL example problem, these pair style and bond style settings -are used: - -pair_style born/coul/long/cs 20.0 20.0 -pair_coeff * * 0.0 1.000 0.00 0.00 0.00 -pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na -pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl -pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre - -bond_style harmonic -bond_coeff 1 63.014 0.0 -bond_coeff 2 25.724 0.0 :pre - -When running dynamics with the adiabatic core/shell model, the -following issues should be considered. The relative motion of -the core and shell particles corresponds to the polarization, -hereby an instantaneous relaxation of the shells is approximated -and a fast core/shell spring frequency ensures a nearly constant -internal kinetic energy during the simulation. -Thermostats can alter this polarization behaviour, by scaling the -internal kinetic energy, meaning the shell will not react freely to -its electrostatic environment. -Therefore it is typically desirable to decouple the relative motion of -the core/shell pair, which is an imaginary degree of freedom, from the -real physical system. To do that, the "compute -temp/cs"_compute_temp_cs.html command can be used, in conjunction with -any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix -langevin"_fix_langevin. This compute uses the center-of-mass velocity -of the core/shell pairs to calculate a temperature, and insures that -velocity is what is rescaled for thermostatting purposes. This -compute also works for a system with both core/shell pairs and -non-polarized ions (ions without an attached satellite particle). The -"compute temp/cs"_compute_temp_cs.html command requires input of two -groups, one for the core atoms, another for the shell atoms. -Non-polarized ions which might also be included in the treated system -should not be included into either of these groups, they are taken -into account by the {group-ID} (2nd argument) of the compute. The -groups can be defined using the "group {type}"_group.html command. -Note that to perform thermostatting using this definition of -temperature, the "fix modify temp"_fix_modify.html command should be -used to assign the compute to the thermostat fix. Likewise the -"thermo_modify temp"_thermo_modify.html command can be used to make -this temperature be output for the overall system. - -For the NaCl example, this can be done as follows: - -group cores type 1 2 -group shells type 3 4 -compute CSequ all temp/cs cores shells -fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system -fix thermostatequ all nve # integrator as needed for the berendsen thermostat -fix_modify thermoberendsen temp CSequ -thermo_modify temp CSequ # output of center-of-mass derived temperature :pre - -The pressure for the core/shell system is computed via the regular -LAMMPS convention by "treating the cores and shells as individual -particles"_#MitchellFincham2. For the thermo output of the pressure -as well as for the application of a barostat, it is necessary to -use an additional "pressure"_compute_pressure compute based on the -default "temperature"_compute_temp and specifying it as a second -argument in "fix modify"_fix_modify.html and -"thermo_modify"_thermo_modify.html resulting in: - -(...) -compute CSequ all temp/cs cores shells -compute thermo_press_lmp all pressure thermo_temp # pressure for individual particles -thermo_modify temp CSequ press thermo_press_lmp # modify thermo to regular pressure -fix press_bar all npt temp 300 300 0.04 iso 0 0 0.4 -fix_modify press_bar temp CSequ press thermo_press_lmp # pressure modification for correct kinetic scalar :pre - -If "compute temp/cs"_compute_temp_cs.html is used, the decoupled -relative motion of the core and the shell should in theory be -stable. However numerical fluctuation can introduce a small -momentum to the system, which is noticable over long trajectories. -Therefore it is recommendable to use the "fix -momentum"_fix_momentum.html command in combination with "compute -temp/cs"_compute_temp_cs.html when equilibrating the system to -prevent any drift. - -When initializing the velocities of a system with core/shell pairs, it -is also desirable to not introduce energy into the relative motion of -the core/shell particles, but only assign a center-of-mass velocity to -the pairs. This can be done by using the {bias} keyword of the -"velocity create"_velocity.html command and assigning the "compute -temp/cs"_compute_temp_cs.html command to the {temp} keyword of the -"velocity"_velocity.html command, e.g. - -velocity all create 1427 134 bias yes temp CSequ -velocity all scale 1427 temp CSequ :pre - -To maintain the correct polarizability of the core/shell pairs, the -kinetic energy of the internal motion shall remain nearly constant. -Therefore the choice of spring force and mass ratio need to ensure -much faster relative motion of the 2 atoms within the core/shell pair -than their center-of-mass velocity. This allows the shells to -effectively react instantaneously to the electrostatic environment and -limits energy transfer to or from the core/shell oscillators. -This fast movement also dictates the timestep that can be used. - -The primary literature of the adiabatic core/shell model suggests that -the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. -The mentioned energy transfer will typically lead to a small drift -in total energy over time. This internal energy can be monitored -using the "compute chunk/atom"_compute_chunk_atom.html and "compute -temp/chunk"_compute_temp_chunk.html commands. The internal kinetic -energies of each core/shell pair can then be summed using the sum() -special function of the "variable"_variable.html command. Or they can -be time/averaged and output using the "fix ave/time"_fix_ave_time.html -command. To use these commands, each core/shell pair must be defined -as a "chunk". If each core/shell pair is defined as its own molecule, -the molecule ID can be used to define the chunks. If cores are bonded -to each other to form larger molecules, the chunks can be identified -by the "fix property/atom"_fix_property_atom.html via assigning a -core/shell ID to each atom using a special field in the data file read -by the "read_data"_read_data.html command. This field can then be -accessed by the "compute property/atom"_compute_property_atom.html -command, to use as input to the "compute -chunk/atom"_compute_chunk_atom.html command to define the core/shell -pairs as chunks. - -For example if core/shell pairs are the only molecules: - -read_data NaCl_CS_x0.1_prop.data -compute prop all property/atom molecule -compute cs_chunk all chunk/atom c_prop -compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs -fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre - -For example if core/shell pairs and other molecules are present: - -fix csinfo all property/atom i_CSID # property/atom command -read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file -compute prop all property/atom i_CSID -(...) :pre - -The additional section in the date file would be formatted like this: - -CS-Info # header of additional section :pre - -1 1 # column 1 = atom ID, column 2 = core/shell ID -2 1 -3 2 -4 2 -5 3 -6 3 -7 4 -8 4 -(...) :pre - -:line - -6.27 Drude induced dipoles :link(howto_27),h4 - -The thermalized Drude model, similarly to the "core-shell"_#howto_26 -model, represents induced dipoles by a pair of charges (the core atom -and the Drude particle) connected by a harmonic spring. The Drude -model has a number of features aimed at its use in molecular systems -("Lamoureux and Roux"_#howto-Lamoureux): - -Thermostating of the additional degrees of freedom associated with the -induced dipoles at very low temperature, in terms of the reduced -coordinates of the Drude particles with respect to their cores. This -makes the trajectory close to that of relaxed induced dipoles. :ulb,l - -Consistent definition of 1-2 to 1-4 neighbors. A core-Drude particle -pair represents a single (polarizable) atom, so the special screening -factors in a covalent structure should be the same for the core and -the Drude particle. Drude particles have to inherit the 1-2, 1-3, 1-4 -special neighbor relations from their respective cores. :l - -Stabilization of the interactions between induced dipoles. Drude -dipoles on covalently bonded atoms interact too strongly due to the -short distances, so an atom may capture the Drude particle of a -neighbor, or the induced dipoles within the same molecule may align -too much. To avoid this, damping at short range can be done by Thole -functions (for which there are physical grounds). This Thole damping -is applied to the point charges composing the induced dipole (the -charge of the Drude particle and the opposite charge on the core, not -to the total charge of the core atom). :l -:ule - -A detailed tutorial covering the usage of Drude induced dipoles in -LAMMPS is "available here"_tutorial_drude.html. - -As with the core-shell model, the cores and Drude particles should -appear in the data file as standard atoms. The same holds for the -springs between them, which are described by standard harmonic bonds. -The nature of the atoms (core, Drude particle or non-polarizable) is -specified via the "fix drude"_fix_drude.html command. The special -list of neighbors is automatically refactored to account for the -equivalence of core and Drude particles as regards special 1-2 to 1-4 -screening. It may be necessary to use the {extra/special/per/atom} -keyword of the "read_data"_read_data.html command. If using "fix -shake"_fix_shake.html, make sure no Drude particle is in this fix -group. - -There are two ways to thermostat the Drude particles at a low -temperature: use either "fix langevin/drude"_fix_langevin_drude.html -for a Langevin thermostat, or "fix -drude/transform/*"_fix_drude_transform.html for a Nose-Hoover -thermostat. The former requires use of the command "comm_modify vel -yes"_comm_modify.html. The latter requires two separate integration -fixes like {nvt} or {npt}. The correct temperatures of the reduced -degrees of freedom can be calculated using the "compute -temp/drude"_compute_temp_drude.html. This requires also to use the -command {comm_modify vel yes}. - -Short-range damping of the induced dipole interactions can be achieved -using Thole functions through the "pair style -thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html -with a Coulomb pair style. It may be useful to use {coul/long/cs} or -similar from the CORESHELL package if the core and Drude particle come -too close, which can cause numerical issues. - -:line -:line - -:link(howto-Berendsen) -[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91, -6269-6271 (1987). - -:link(howto-Cornell) -[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, -Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). - -:link(Horn) -[(Horn)] Horn, Swope, Pitera, Madura, Dick, Hura, and Head-Gordon, -J Chem Phys, 120, 9665 (2004). - -:link(howto-Ikeshoji) -[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 -(1994). - -:link(howto-Wirnsberger) -[(Wirnsberger)] Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 -(2015). - -:link(howto-MacKerell) -[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, -Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). - -:link(howto-Mayo) -[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 -(1990). - -:link(Jorgensen1) -[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem -Phys, 79, 926 (1983). - -:link(Price1) -[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). - -:link(Shinoda1) -[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). - -:link(MitchellFincham) -[(Mitchell and Fincham)] Mitchell, Fincham, J Phys Condensed Matter, -5, 1031-1038 (1993). - -:link(MitchellFincham2) -[(Fincham)] Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, -6, 393-404 (1994). - -:link(howto-Lamoureux) -[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003) diff --git a/doc/src/Section_intro.txt b/doc/src/Section_intro.txt deleted file mode 100644 index 67293b2ee3363b422cdb3f2f58bd0da9a037d9ab..0000000000000000000000000000000000000000 --- a/doc/src/Section_intro.txt +++ /dev/null @@ -1,549 +0,0 @@ -"Previous Section"_Manual.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_start.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -1. Introduction :h2 - -This section provides an overview of what LAMMPS can and can't do, -describes what it means for LAMMPS to be an open-source code, and -acknowledges the funding and people who have contributed to LAMMPS -over the years. - -1.1 "What is LAMMPS"_#intro_1 -1.2 "LAMMPS features"_#intro_2 -1.3 "LAMMPS non-features"_#intro_3 -1.4 "Open source distribution"_#intro_4 -1.5 "Acknowledgments and citations"_#intro_5 :all(b) - -:line -:line - -1.1 What is LAMMPS :link(intro_1),h4 - -LAMMPS is a classical molecular dynamics code that models an ensemble -of particles in a liquid, solid, or gaseous state. It can model -atomic, polymeric, biological, metallic, granular, and coarse-grained -systems using a variety of force fields and boundary conditions. - -For examples of LAMMPS simulations, see the Publications page of the -"LAMMPS WWW Site"_lws. - -LAMMPS runs efficiently on single-processor desktop or laptop -machines, but is designed for parallel computers. It will run on any -parallel machine that compiles C++ and supports the "MPI"_mpi -message-passing library. This includes distributed- or shared-memory -parallel machines and Beowulf-style clusters. - -:link(mpi,http://www-unix.mcs.anl.gov/mpi) - -LAMMPS can model systems with only a few particles up to millions or -billions. See "Section 8"_Section_perf.html for information on -LAMMPS performance and scalability, or the Benchmarks section of the -"LAMMPS WWW Site"_lws. - -LAMMPS is a freely-available open-source code, distributed under the -terms of the "GNU Public License"_gnu, which means you can use or -modify the code however you wish. See "this section"_#intro_4 for a -brief discussion of the open-source philosophy. - -:link(gnu,http://www.gnu.org/copyleft/gpl.html) - -LAMMPS is designed to be easy to modify or extend with new -capabilities, such as new force fields, atom types, boundary -conditions, or diagnostics. See "Section 10"_Section_modify.html -for more details. - -The current version of LAMMPS is written in C++. Earlier versions -were written in F77 and F90. See -"Section 13"_Section_history.html for more information on -different versions. All versions can be downloaded from the "LAMMPS -WWW Site"_lws. - -LAMMPS was originally developed under a US Department of Energy CRADA -(Cooperative Research and Development Agreement) between two DOE labs -and 3 companies. It is distributed by "Sandia National Labs"_snl. -See "this section"_#intro_5 for more information on LAMMPS funding and -individuals who have contributed to LAMMPS. - -:link(snl,http://www.sandia.gov) - -In the most general sense, LAMMPS integrates Newton's equations of -motion for collections of atoms, molecules, or macroscopic particles -that interact via short- or long-range forces with a variety of -initial and/or boundary conditions. For computational efficiency -LAMMPS uses neighbor lists to keep track of nearby particles. The -lists are optimized for systems with particles that are repulsive at -short distances, so that the local density of particles never becomes -too large. On parallel machines, LAMMPS uses spatial-decomposition -techniques to partition the simulation domain into small 3d -sub-domains, one of which is assigned to each processor. Processors -communicate and store "ghost" atom information for atoms that border -their sub-domain. LAMMPS is most efficient (in a parallel sense) for -systems whose particles fill a 3d rectangular box with roughly uniform -density. Papers with technical details of the algorithms used in -LAMMPS are listed in "this section"_#intro_5. - -:line - -1.2 LAMMPS features :link(intro_2),h4 - -This section highlights LAMMPS features, with pointers to specific -commands which give more details. If LAMMPS doesn't have your -favorite interatomic potential, boundary condition, or atom type, see -"Section 10"_Section_modify.html, which describes how you can add -it to LAMMPS. - -General features :h4 - - runs on a single processor or in parallel - distributed-memory message-passing parallelism (MPI) - spatial-decomposition of simulation domain for parallelism - open-source distribution - highly portable C++ - optional libraries used: MPI and single-processor FFT - GPU (CUDA and OpenCL), Intel(R) Xeon Phi(TM) coprocessors, and OpenMP support for many code features - easy to extend with new features and functionality - runs from an input script - syntax for defining and using variables and formulas - syntax for looping over runs and breaking out of loops - run one or multiple simulations simultaneously (in parallel) from one script - build as library, invoke LAMMPS thru library interface or provided Python wrapper - couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul - -Particle and model types :h4 -("atom style"_atom_style.html command) - - atoms - coarse-grained particles (e.g. bead-spring polymers) - united-atom polymers or organic molecules - all-atom polymers, organic molecules, proteins, DNA - metals - granular materials - coarse-grained mesoscale models - finite-size spherical and ellipsoidal particles - finite-size line segment (2d) and triangle (3d) particles - point dipole particles - rigid collections of particles - hybrid combinations of these :ul - -Force fields :h4 -("pair style"_pair_style.html, "bond style"_bond_style.html, -"angle style"_angle_style.html, "dihedral style"_dihedral_style.html, -"improper style"_improper_style.html, "kspace style"_kspace_style.html -commands) - - pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, \ - Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated - charged pairwise potentials: Coulombic, point-dipole - manybody potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), \ - embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, \ - REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic - long-range interactions for charge, point-dipoles, and LJ dispersion: \ - Ewald, Wolf, PPPM (similar to particle-mesh Ewald) - polarization models: "QEq"_fix_qeq.html, \ - "core/shell model"_Section_howto.html#howto_26, \ - "Drude dipole model"_Section_howto.html#howto_27 - charge equilibration (QEq via dynamic, point, shielded, Slater methods) - coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO - mesoscopic potentials: granular, Peridynamics, SPH - electron force field (eFF, AWPMD) - bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ - quartic (breakable) - angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, \ - class 2 (COMPASS) - dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, \ - class 2 (COMPASS), OPLS - improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS) - polymer potentials: all-atom, united-atom, bead-spring, breakable - water potentials: TIP3P, TIP4P, SPC - implicit solvent potentials: hydrodynamic lubrication, Debye - force-field compatibility with common CHARMM, AMBER, DREIDING, \ - OPLS, GROMACS, COMPASS options - access to "KIM archive"_http://openkim.org of potentials via \ - "pair kim"_pair_kim.html - hybrid potentials: multiple pair, bond, angle, dihedral, improper \ - potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials :ul - -Atom creation :h4 -("read_data"_read_data.html, "lattice"_lattice.html, -"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html, -"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands) - - read in atom coords from files - create atoms on one or more lattices (e.g. grain boundaries) - delete geometric or logical groups of atoms (e.g. voids) - replicate existing atoms multiple times - displace atoms :ul - -Ensembles, constraints, and boundary conditions :h4 -("fix"_fix.html command) - - 2d or 3d systems - orthogonal or non-orthogonal (triclinic symmetry) simulation domains - constant NVE, NVT, NPT, NPH, Parinello/Rahman integrators - thermostatting options for groups and geometric regions of atoms - pressure control via Nose/Hoover or Berendsen barostatting in 1 to 3 dimensions - simulation box deformation (tensile and shear) - harmonic (umbrella) constraint forces - rigid body constraints - SHAKE bond and angle constraints - Monte Carlo bond breaking, formation, swapping - atom/molecule insertion and deletion - walls of various kinds - non-equilibrium molecular dynamics (NEMD) - variety of additional boundary conditions and constraints :ul - -Integrators :h4 -("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands) - - velocity-Verlet integrator - Brownian dynamics - rigid body integration - energy minimization via conjugate gradient or steepest descent relaxation - rRESPA hierarchical timestepping - rerun command for post-processing of dump files :ul - -Diagnostics :h4 - - see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul - -Output :h4 -("dump"_dump.html, "restart"_restart.html commands) - - log file of thermodynamic info - text dump files of atom coords, velocities, other per-atom quantities - binary restart files - parallel I/O of dump and restart files - per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc) - user-defined system-wide (log file) or per-atom (dump file) calculations - spatial and time averaging of per-atom quantities - time averaging of system-wide quantities - atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul - -Multi-replica models :h4 - -"nudged elastic band"_neb.html -"parallel replica dynamics"_prd.html -"temperature accelerated dynamics"_tad.html -"parallel tempering"_temper.html - -Pre- and post-processing :h4 - -Various pre- and post-processing serial tools are packaged -with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l - -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. :l -:ule - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) -:link(python,http://www.python.org) - -Specialized features :h4 - -LAMMPS can be built with optional packages which implement a variety -of additional capabilities. An overview of all the packages is "given -here"_Section_packages.html. - -These are some LAMMPS capabilities which you may not think of as -typical classical molecular dynamics options: - -"static"_balance.html and "dynamic load-balancing"_fix_balance.html -"generalized aspherical particles"_body.html -"stochastic rotation dynamics (SRD)"_fix_srd.html -"real-time visualization and interactive MD"_fix_imd.html -calculate "virtual diffraction patterns"_compute_xrd.html -"atom-to-continuum coupling"_fix_atc.html with finite elements -coupled rigid body integration via the "POEMS"_fix_poems.html library -"QM/MM coupling"_fix_qmmm.html -"path-integral molecular dynamics (PIMD)"_fix_ipi.html and "this as well"_fix_pimd.html -Monte Carlo via "GCMC"_fix_gcmc.html and "tfMC"_fix_tfmc.html "atom swapping"_fix_atom_swap.html and "bond swapping"_fix_bond_swap.html -"Direct Simulation Monte Carlo"_pair_dsmc.html for low-density fluids -"Peridynamics mesoscale modeling"_pair_peri.html -"Lattice Boltzmann fluid"_fix_lb_fluid.html -"targeted"_fix_tmd.html and "steered"_fix_smd.html molecular dynamics -"two-temperature electron model"_fix_ttm.html :ul - -:line - -1.3 LAMMPS non-features :link(intro_3),h4 - -LAMMPS is designed to efficiently compute Newton's equations of motion -for a system of interacting particles. Many of the tools needed to -pre- and post-process the data for such simulations are not included -in the LAMMPS kernel for several reasons: - -the desire to keep LAMMPS simple -they are not parallel operations -other codes already do them -limited development resources :ul - -Specifically, LAMMPS itself does not: - -run thru a GUI -build molecular systems -assign force-field coefficients automagically -perform sophisticated analyses of your MD simulation -visualize your MD simulation -plot your output data :ul - -A few tools for pre- and post-processing tasks are provided as part of -the LAMMPS package; they are described in "this -section"_Section_tools.html. However, many people use other codes or -write their own tools for these tasks. - -As noted above, our group has also written and released a separate -toolkit called "Pizza.py"_pizza which addresses some of the listed -bullets. It provides tools for doing setup, analysis, plotting, and -visualization for LAMMPS simulations. Pizza.py is written in -"Python"_python and is available for download from "the Pizza.py WWW -site"_pizza. - -LAMMPS requires as input a list of initial atom coordinates and types, -molecular topology information, and force-field coefficients assigned -to all atoms and bonds. LAMMPS will not build molecular systems and -assign force-field parameters for you. - -For atomic systems LAMMPS provides a "create_atoms"_create_atoms.html -command which places atoms on solid-state lattices (fcc, bcc, -user-defined, etc). Assigning small numbers of force field -coefficients can be done via the "pair coeff"_pair_coeff.html, "bond -coeff"_bond_coeff.html, "angle coeff"_angle_coeff.html, etc commands. -For molecular systems or more complicated simulation geometries, users -typically use another code as a builder and convert its output to -LAMMPS input format, or write their own code to generate atom -coordinate and molecular topology for LAMMPS to read in. - -For complicated molecular systems (e.g. a protein), a multitude of -topology information and hundreds of force-field coefficients must -typically be specified. We suggest you use a program like -"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup -such problems and dump its information to a file. You can then -reformat the file as LAMMPS input. Some of the tools in "this -section"_Section_tools.html can assist in this process. - -Similarly, LAMMPS creates output files in a simple format. Most users -post-process these files with their own analysis tools or re-format -them for input into other programs, including visualization packages. -If you are convinced you need to compute something on-the-fly as -LAMMPS runs, see "Section 10"_Section_modify.html for a discussion -of how you can use the "dump"_dump.html and "compute"_compute.html and -"fix"_fix.html commands to print out data of your choosing. Keep in -mind that complicated computations can slow down the molecular -dynamics timestepping, particularly if the computations are not -parallel, so it is often better to leave such analysis to -post-processing codes. - -For high-quality visualization we recommend the -following packages: - -"VMD"_http://www.ks.uiuc.edu/Research/vmd -"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A -"OVITO"_http://www.ovito.org/ -"ParaView"_http://www.paraview.org/ -"PyMol"_http://www.pymol.org -"Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html -"RasMol"_http://www.openrasmol.org :ul - -Other features that LAMMPS does not yet (and may never) support are -discussed in "Section 13"_Section_history.html. - -Finally, these are freely-available molecular dynamics codes, most of -them parallel, which may be well-suited to the problems you want to -model. They can also be used in conjunction with LAMMPS to perform -complementary modeling tasks. - -"CHARMM"_charmm -"AMBER"_amber -"NAMD"_namd -"NWCHEM"_nwchem -"DL_POLY"_dlpoly -"Tinker"_tinker :ul - -:link(charmm,http://www.charmm.org) -:link(amber,http://ambermd.org) -:link(namd,http://www.ks.uiuc.edu/Research/namd/) -:link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html) -:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC) -:link(tinker,http://dasher.wustl.edu/tinker) - -CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for -modeling biological molecules. CHARMM and AMBER use -atom-decomposition (replicated-data) strategies for parallelism; NAMD -and NWCHEM use spatial-decomposition approaches, similar to LAMMPS. -Tinker is a serial code. DL_POLY includes potentials for a variety of -biological and non-biological materials; both a replicated-data and -spatial-decomposition version exist. - -:line - -1.4 Open source distribution :link(intro_4),h4 - -LAMMPS comes with no warranty of any kind. As each source file states -in its header, it is a copyrighted code that is distributed free-of- -charge, under the terms of the "GNU Public License"_gnu (GPL). This -is often referred to as open-source distribution - see -"www.gnu.org"_gnuorg or "www.opensource.org"_opensource for more -details. The legal text of the GPL is in the LICENSE file that is -included in the LAMMPS distribution. - -:link(gnuorg,http://www.gnu.org) -:link(opensource,http://www.opensource.org) - -Here is a summary of what the GPL means for LAMMPS users: - -(1) Anyone is free to use, modify, or extend LAMMPS in any way they -choose, including for commercial purposes. - -(2) If you distribute a modified version of LAMMPS, it must remain -open-source, meaning you distribute it under the terms of the GPL. -You should clearly annotate such a code as a derivative version of -LAMMPS. - -(3) If you release any code that includes LAMMPS source code, then it -must also be open-sourced, meaning you distribute it under the terms -of the GPL. - -(4) If you give LAMMPS files to someone else, the GPL LICENSE file and -source file headers (including the copyright and GPL notices) should -remain part of the code. - -In the spirit of an open-source code, these are various ways you can -contribute to making LAMMPS better. You can send email to the -"developers"_http://lammps.sandia.gov/authors.html on any of these -items. - -Point prospective users to the "LAMMPS WWW Site"_lws. Mention it in -talks or link to it from your WWW site. :ulb,l - -If you find an error or omission in this manual or on the "LAMMPS WWW -Site"_lws, or have a suggestion for something to clarify or include, -send an email to the -"developers"_http://lammps.sandia.gov/authors.html. :l - -If you find a bug, "Section 12.2"_Section_errors.html#err_2 -describes how to report it. :l - -If you publish a paper using LAMMPS results, send the citation (and -any cool pictures or movies if you like) to add to the Publications, -Pictures, and Movies pages of the "LAMMPS WWW Site"_lws, with links -and attributions back to you. :l - -Create a new Makefile.machine that can be added to the src/MAKE -directory. :l - -The tools sub-directory of the LAMMPS distribution has various -stand-alone codes for pre- and post-processing of LAMMPS data. More -details are given in "Section 9"_Section_tools.html. If you write -a new tool that users will find useful, it can be added to the LAMMPS -distribution. :l - -LAMMPS is designed to be easy to extend with new code for features -like potentials, boundary conditions, diagnostic computations, etc. -"This section"_Section_modify.html gives details. If you add a -feature of general interest, it can be added to the LAMMPS -distribution. :l - -The Benchmark page of the "LAMMPS WWW Site"_lws lists LAMMPS -performance on various platforms. The files needed to run the -benchmarks are part of the LAMMPS distribution. If your machine is -sufficiently different from those listed, your timing data can be -added to the page. :l - -You can send feedback for the User Comments page of the "LAMMPS WWW -Site"_lws. It might be added to the page. No promises. :l - -Cash. Small denominations, unmarked bills preferred. Paper sack OK. -Leave on desk. VISA also accepted. Chocolate chip cookies -encouraged. :l -:ule - -:line - -1.5 Acknowledgments and citations :h3,link(intro_5) - -LAMMPS development has been funded by the "US Department of -Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life -programs and its "OASCR"_oascr and "OBER"_ober offices. - -Specifically, work on the latest version was funded in part by the US -Department of Energy's Genomics:GTL program -("www.doegenomestolife.org"_gtl) under the "project"_ourgtl, "Carbon -Sequestration in Synechococcus Sp.: From Molecular Machines to -Hierarchical Modeling". - -:link(doe,http://www.doe.gov) -:link(gtl,http://www.doegenomestolife.org) -:link(ourgtl,http://www.genomes2life.org) -:link(oascr,http://www.sc.doe.gov/ascr/home.html) -:link(ober,http://www.er.doe.gov/production/ober/ober_top.html) - -The following paper describe the basic parallel algorithms used in -LAMMPS. If you use LAMMPS results in your published work, please cite -this paper and include a pointer to the "LAMMPS WWW Site"_lws -(http://lammps.sandia.gov): - -S. Plimpton, [Fast Parallel Algorithms for Short-Range Molecular -Dynamics], J Comp Phys, 117, 1-19 (1995). - -Other papers describing specific algorithms used in LAMMPS are listed -under the "Citing LAMMPS link"_http://lammps.sandia.gov/cite.html of -the LAMMPS WWW page. - -The "Publications link"_http://lammps.sandia.gov/papers.html on the -LAMMPS WWW page lists papers that have cited LAMMPS. If your paper is -not listed there for some reason, feel free to send us the info. If -the simulations in your paper produced cool pictures or animations, -we'll be pleased to add them to the -"Pictures"_http://lammps.sandia.gov/pictures.html or -"Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW -site. - -The primary LAMMPS developers are at Sandia National Labs and Temple University: - -Steve Plimpton, sjplimp at sandia.gov -Aidan Thompson, athomps at sandia.gov -Stan Moore, stamoor at sandia.gov -Axel Kohlmeyer, akohlmey at gmail.com :ul - -Past primary developers include Paul Crozier and Mark Stevens, -both at Sandia, and Ray Shan, now at Materials Design. - -The following folks are responsible for significant contributions to -the code, or other aspects of the LAMMPS development effort. Many of -the packages they have written are somewhat unique to LAMMPS and the -code would not be as general-purpose as it is without their expertise -and efforts. - -Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages -Roy Pollock (LLNL), Ewald and PPPM solvers -Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package -Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC) -Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics -Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion -Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling -Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD -Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA (obsoleted by KOKKOS) and KOKKOS packages -Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field -Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork for granular models and granular/fluid coupling -Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF -Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages -Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul - -As discussed in "Section 13"_Section_history.html, LAMMPS -originated as a cooperative project between DOE labs and industrial -partners. Folks involved in the design and testing of the original -version of LAMMPS were the following: - -John Carpenter (Mayo Clinic, formerly at Cray Research) -Terry Stouch (Lexicon Pharmaceuticals, formerly at Bristol Myers Squibb) -Steve Lustig (Dupont) -Jim Belak (LLNL) :ul diff --git a/doc/src/Section_modify.txt b/doc/src/Section_modify.txt deleted file mode 100644 index f1d55758c8b0b498710d2f9c2e83eb9834817481..0000000000000000000000000000000000000000 --- a/doc/src/Section_modify.txt +++ /dev/null @@ -1,827 +0,0 @@ - "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_python.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -10. Modifying & extending LAMMPS :h2 - -This section describes how to customize LAMMPS by modifying -and extending its source code. - -10.1 "Atom styles"_#mod_1 -10.2 "Bond, angle, dihedral, improper potentials"_#mod_2 -10.3 "Compute styles"_#mod_3 -10.4 "Dump styles"_#mod_4 -10.5 "Dump custom output options"_#mod_5 -10.6 "Fix styles"_#mod_6 which include integrators, \ - temperature and pressure control, force constraints, \ - boundary conditions, diagnostic output, etc -10.7 "Input script commands"_#mod_7 -10.8 "Kspace computations"_#mod_8 -10.9 "Minimization styles"_#mod_9 -10.10 "Pairwise potentials"_#mod_10 -10.11 "Region styles"_#mod_11 -10.12 "Body styles"_#mod_12 -10.13 "Thermodynamic output options"_#mod_13 -10.14 "Variable options"_#mod_14 -10.15 "Submitting new features for inclusion in LAMMPS"_#mod_15 :all(b) - -LAMMPS is designed in a modular fashion so as to be easy to modify and -extend with new functionality. In fact, about 75% of its source code -is files added in this fashion. - -In this section, changes and additions users can make are listed along -with minimal instructions. If you add a new feature to LAMMPS and -think it will be of interest to general users, we encourage you to -submit it to the developers for inclusion in the released version of -LAMMPS. Information about how to do this is provided -"below"_#mod_14. - -The best way to add a new feature is to find a similar feature in -LAMMPS and look at the corresponding source and header files to figure -out what it does. You will need some knowledge of C++ to be able to -understand the hi-level structure of LAMMPS and its class -organization, but functions (class methods) that do actual -computations are written in vanilla C-style code and operate on simple -C-style data structures (vectors and arrays). - -Most of the new features described in this section require you to -write a new C++ derived class (except for exceptions described below, -where you can make small edits to existing files). Creating a new -class requires 2 files, a source code file (*.cpp) and a header file -(*.h). The derived class must provide certain methods to work as a -new option. Depending on how different your new feature is compared -to existing features, you can either derive from the base class -itself, or from a derived class that already exists. Enabling LAMMPS -to invoke the new class is as simple as putting the two source -files in the src dir and re-building LAMMPS. - -The advantage of C++ and its object-orientation is that all the code -and variables needed to define the new feature are in the 2 files you -write, and thus shouldn't make the rest of LAMMPS more complex or -cause side-effect bugs. - -Here is a concrete example. Suppose you write 2 files pair_foo.cpp -and pair_foo.h that define a new class PairFoo that computes pairwise -potentials described in the classic 1997 "paper"_#Foo by Foo, et al. -If you wish to invoke those potentials in a LAMMPS input script with a -command like - -pair_style foo 0.1 3.5 :pre - -then your pair_foo.h file should be structured as follows: - -#ifdef PAIR_CLASS -PairStyle(foo,PairFoo) -#else -... -(class definition for PairFoo) -... -#endif :pre - -where "foo" is the style keyword in the pair_style command, and -PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h -files. - -When you re-build LAMMPS, your new pairwise potential becomes part of -the executable and can be invoked with a pair_style command like the -example above. Arguments like 0.1 and 3.5 can be defined and -processed by your new class. - -As illustrated by this pairwise example, many kinds of options are -referred to in the LAMMPS documentation as the "style" of a particular -command. - -The instructions below give the header file for the base class that -these styles are derived from. Public variables in that file are ones -used and set by the derived classes which are also used by the base -class. Sometimes they are also used by the rest of LAMMPS. Virtual -functions in the base class header file which are set = 0 are ones you -must define in your new derived class to give it the functionality -LAMMPS expects. Virtual functions that are not set to 0 are functions -you can optionally define. - -Additionally, new output options can be added directly to the -thermo.cpp, dump_custom.cpp, and variable.cpp files as explained -below. - -Here are additional guidelines for modifying LAMMPS and adding new -functionality: - -Think about whether what you want to do would be better as a pre- or -post-processing step. Many computations are more easily and more -quickly done that way. :ulb,l - -Don't do anything within the timestepping of a run that isn't -parallel. E.g. don't accumulate a bunch of data on a single processor -and analyze it. You run the risk of seriously degrading the parallel -efficiency. :l - -If your new feature reads arguments or writes output, make sure you -follow the unit conventions discussed by the "units"_units.html -command. :l - -If you add something you think is truly useful and doesn't impact -LAMMPS performance when it isn't used, send an email to the -"developers"_http://lammps.sandia.gov/authors.html. We might be -interested in adding it to the LAMMPS distribution. See further -details on this at the bottom of this page. :l -:ule - -:line -:line - -10.1 Atom styles :link(mod_1),h4 - -Classes that define an "atom style"_atom_style.html are derived from -the AtomVec class and managed by the Atom class. The atom style -determines what attributes are associated with an atom. A new atom -style can be created if one of the existing atom styles does not -define all the attributes you need to store and communicate with -atoms. - -Atom_vec_atomic.cpp is a simple example of an atom style. - -Here is a brief description of methods you define in your new derived -class. See atom_vec.h for details. - -init: one time setup (optional) -grow: re-allocate atom arrays to longer lengths (required) -grow_reset: make array pointers in Atom and AtomVec classes consistent (required) -copy: copy info for one atom to another atom's array locations (required) -pack_comm: store an atom's info in a buffer communicated every timestep (required) -pack_comm_vel: add velocity info to communication buffer (required) -pack_comm_hybrid: store extra info unique to this atom style (optional) -unpack_comm: retrieve an atom's info from the buffer (required) -unpack_comm_vel: also retrieve velocity info (required) -unpack_comm_hybrid: retrieve extra info unique to this atom style (optional) -pack_reverse: store an atom's info in a buffer communicating partial forces (required) -pack_reverse_hybrid: store extra info unique to this atom style (optional) -unpack_reverse: retrieve an atom's info from the buffer (required) -unpack_reverse_hybrid: retrieve extra info unique to this atom style (optional) -pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required) -pack_border_vel: add velocity info to buffer (required) -pack_border_hybrid: store extra info unique to this atom style (optional) -unpack_border: retrieve an atom's info from the buffer (required) -unpack_border_vel: also retrieve velocity info (required) -unpack_border_hybrid: retrieve extra info unique to this atom style (optional) -pack_exchange: store all an atom's info to migrate to another processor (required) -unpack_exchange: retrieve an atom's info from the buffer (required) -size_restart: number of restart quantities associated with proc's atoms (required) -pack_restart: pack atom quantities into a buffer (required) -unpack_restart: unpack atom quantities from a buffer (required) -create_atom: create an individual atom of this style (required) -data_atom: parse an atom line from the data file (required) -data_atom_hybrid: parse additional atom info unique to this atom style (optional) -data_vel: parse one line of velocity information from data file (optional) -data_vel_hybrid: parse additional velocity data unique to this atom style (optional) -memory_usage: tally memory allocated by atom arrays (required) :tb(s=:) - -The constructor of the derived class sets values for several variables -that you must set when defining a new atom style, which are documented -in atom_vec.h. New atom arrays are defined in atom.cpp. Search for -the word "customize" and you will find locations you will need to -modify. - -NOTE: It is possible to add some attributes, such as a molecule ID, to -atom styles that do not have them via the "fix -property/atom"_fix_property_atom.html command. This command also -allows new custom attributes consisting of extra integer or -floating-point values to be added to atoms. See the "fix -property/atom"_fix_property_atom.html doc page for examples of cases -where this is useful and details on how to initialize, access, and -output the custom values. - -New "pair styles"_pair_style.html, "fixes"_fix.html, or -"computes"_compute.html can be added to LAMMPS, as discussed below. -The code for these classes can use the per-atom properties defined by -fix property/atom. The Atom class has a find_custom() method that is -useful in this context: - -int index = atom->find_custom(char *name, int &flag); :pre - -The "name" of a custom attribute, as specified in the "fix -property/atom"_fix_property_atom.html command, is checked to verify -that it exists and its index is returned. The method also sets flag = -0/1 depending on whether it is an integer or floating-point attribute. -The vector of values associated with the attribute can then be -accessed using the returned index as - -int *ivector = atom->ivector\[index\]; -double *dvector = atom->dvector\[index\]; :pre - -Ivector or dvector are vectors of length Nlocal = # of owned atoms, -which store the attributes of individual atoms. - -:line - -10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4 - -Classes that compute molecular interactions are derived from the Bond, -Angle, Dihedral, and Improper classes. New styles can be created to -add new potentials to LAMMPS. - -Bond_harmonic.cpp is the simplest example of a bond style. Ditto for -the harmonic forms of the angle, dihedral, and improper style -commands. - -Here is a brief description of common methods you define in your -new derived class. See bond.h, angle.h, dihedral.h, and improper.h -for details and specific additional methods. - -init: check if all coefficients are set, calls {init_style} (optional) -init_style: check if style specific conditions are met (optional) -compute: compute the molecular interactions (required) -settings: apply global settings for all types (optional) -coeff: set coefficients for one type (required) -equilibrium_distance: length of bond, used by SHAKE (required, bond only) -equilibrium_angle: opening of angle, used by SHAKE (required, angle only) -write & read_restart: writes/reads coeffs to restart files (required) -single: force and energy of a single bond or angle (required, bond or angle only) -memory_usage: tally memory allocated by the style (optional) :tb(s=:) - -:line - -10.3 Compute styles :link(mod_3),h4 - -Classes that compute scalar and vector quantities like temperature -and the pressure tensor, as well as classes that compute per-atom -quantities like kinetic energy and the centro-symmetry parameter -are derived from the Compute class. New styles can be created -to add new calculations to LAMMPS. - -Compute_temp.cpp is a simple example of computing a scalar -temperature. Compute_ke_atom.cpp is a simple example of computing -per-atom kinetic energy. - -Here is a brief description of methods you define in your new derived -class. See compute.h for details. - -init: perform one time setup (required) -init_list: neighbor list setup, if needed (optional) -compute_scalar: compute a scalar quantity (optional) -compute_vector: compute a vector of quantities (optional) -compute_peratom: compute one or more quantities per atom (optional) -compute_local: compute one or more quantities per processor (optional) -pack_comm: pack a buffer with items to communicate (optional) -unpack_comm: unpack the buffer (optional) -pack_reverse: pack a buffer with items to reverse communicate (optional) -unpack_reverse: unpack the buffer (optional) -remove_bias: remove velocity bias from one atom (optional) -remove_bias_all: remove velocity bias from all atoms in group (optional) -restore_bias: restore velocity bias for one atom after remove_bias (optional) -restore_bias_all: same as before, but for all atoms in group (optional) -pair_tally_callback: callback function for {tally}-style computes (optional). -memory_usage: tally memory usage (optional) :tb(s=:) - -Tally-style computes are a special case, as their computation is done -in two stages: the callback function is registered with the pair style -and then called from the Pair::ev_tally() function, which is called for -each pair after force and energy has been computed for this pair. Then -the tallied values are retrieved with the standard compute_scalar or -compute_vector or compute_peratom methods. The USER-TALLY package -provides {examples}_compute_tally.html for utilizing this mechanism. - -:line - -10.4 Dump styles :link(mod_4),h4 -10.5 Dump custom output options :link(mod_5),h4 - -Classes that dump per-atom info to files are derived from the Dump -class. To dump new quantities or in a new format, a new derived dump -class can be added, but it is typically simpler to modify the -DumpCustom class contained in the dump_custom.cpp file. - -Dump_atom.cpp is a simple example of a derived dump class. - -Here is a brief description of methods you define in your new derived -class. See dump.h for details. - -write_header: write the header section of a snapshot of atoms -count: count the number of lines a processor will output -pack: pack a proc's output data into a buffer -write_data: write a proc's data to a file :tb(s=:) - -See the "dump"_dump.html command and its {custom} style for a list of -keywords for atom information that can already be dumped by -DumpCustom. It includes options to dump per-atom info from Compute -classes, so adding a new derived Compute class is one way to calculate -new quantities to dump. - -Alternatively, you can add new keywords to the dump custom command. -Search for the word "customize" in dump_custom.cpp to see the -half-dozen or so locations where code will need to be added. - -:line - -10.6 Fix styles :link(mod_6),h4 - -In LAMMPS, a "fix" is any operation that is computed during -timestepping that alters some property of the system. Essentially -everything that happens during a simulation besides force computation, -neighbor list construction, and output, is a "fix". This includes -time integration (update of coordinates and velocities), force -constraints or boundary conditions (SHAKE or walls), and diagnostics -(compute a diffusion coefficient). New styles can be created to add -new options to LAMMPS. - -Fix_setforce.cpp is a simple example of setting forces on atoms to -prescribed values. There are dozens of fix options already in LAMMPS; -choose one as a template that is similar to what you want to -implement. - -Here is a brief description of methods you can define in your new -derived class. See fix.h for details. - -setmask: determines when the fix is called during the timestep (required) -init: initialization before a run (optional) -setup_pre_exchange: called before atom exchange in setup (optional) -setup_pre_force: called before force computation in setup (optional) -setup: called immediately before the 1st timestep and after forces are computed (optional) -min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional) -min_setup: like setup, but for minimizations instead of MD runs (optional) -initial_integrate: called at very beginning of each timestep (optional) -pre_exchange: called before atom exchange on re-neighboring steps (optional) -pre_neighbor: called before neighbor list build (optional) -pre_force: called before pair & molecular forces are computed (optional) -post_force: called after pair & molecular forces are computed and communicated (optional) -final_integrate: called at end of each timestep (optional) -end_of_step: called at very end of timestep (optional) -write_restart: dumps fix info to restart file (optional) -restart: uses info from restart file to re-initialize the fix (optional) -grow_arrays: allocate memory for atom-based arrays used by fix (optional) -copy_arrays: copy atom info when an atom migrates to a new processor (optional) -pack_exchange: store atom's data in a buffer (optional) -unpack_exchange: retrieve atom's data from a buffer (optional) -pack_restart: store atom's data for writing to restart file (optional) -unpack_restart: retrieve atom's data from a restart file buffer (optional) -size_restart: size of atom's data (optional) -maxsize_restart: max size of atom's data (optional) -setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional) -initial_integrate_respa: same as initial_integrate, but for rRESPA (optional) -post_integrate_respa: called after the first half integration step is done in rRESPA (optional) -pre_force_respa: same as pre_force, but for rRESPA (optional) -post_force_respa: same as post_force, but for rRESPA (optional) -final_integrate_respa: same as final_integrate, but for rRESPA (optional) -min_pre_force: called after pair & molecular forces are computed in minimizer (optional) -min_post_force: called after pair & molecular forces are computed and communicated in minimizer (optional) -min_store: store extra data for linesearch based minimization on a LIFO stack (optional) -min_pushstore: push the minimization LIFO stack one element down (optional) -min_popstore: pop the minimization LIFO stack one element up (optional) -min_clearstore: clear minimization LIFO stack (optional) -min_step: reset or move forward on line search minimization (optional) -min_dof: report number of degrees of freedom {added} by this fix in minimization (optional) -max_alpha: report maximum allowed step size during linesearch minimization (optional) -pack_comm: pack a buffer to communicate a per-atom quantity (optional) -unpack_comm: unpack a buffer to communicate a per-atom quantity (optional) -pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional) -unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional) -dof: report number of degrees of freedom {removed} by this fix during MD (optional) -compute_scalar: return a global scalar property that the fix computes (optional) -compute_vector: return a component of a vector property that the fix computes (optional) -compute_array: return a component of an array property that the fix computes (optional) -deform: called when the box size is changed (optional) -reset_target: called when a change of the target temperature is requested during a run (optional) -reset_dt: is called when a change of the time step is requested during a run (optional) -modify_param: called when a fix_modify request is executed (optional) -memory_usage: report memory used by fix (optional) -thermo: compute quantities for thermodynamic output (optional) :tb(s=:) - -Typically, only a small fraction of these methods are defined for a -particular fix. Setmask is mandatory, as it determines when the fix -will be invoked during the timestep. Fixes that perform time -integration ({nve}, {nvt}, {npt}) implement initial_integrate() and -final_integrate() to perform velocity Verlet updates. Fixes that -constrain forces implement post_force(). - -Fixes that perform diagnostics typically implement end_of_step(). For -an end_of_step fix, one of your fix arguments must be the variable -"nevery" which is used to determine when to call the fix and you must -set this variable in the constructor of your fix. By convention, this -is the first argument the fix defines (after the ID, group-ID, style). - -If the fix needs to store information for each atom that persists from -timestep to timestep, it can manage that memory and migrate the info -with the atoms as they move from processors to processor by -implementing the grow_arrays, copy_arrays, pack_exchange, and -unpack_exchange methods. Similarly, the pack_restart and -unpack_restart methods can be implemented to store information about -the fix in restart files. If you wish an integrator or force -constraint fix to work with rRESPA (see the "run_style"_run_style.html -command), the initial_integrate, post_force_integrate, and -final_integrate_respa methods can be implemented. The thermo method -enables a fix to contribute values to thermodynamic output, as printed -quantities and/or to be summed to the potential energy of the system. - -:line - -10.7 Input script commands :link(mod_7),h4 - -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. - -The single method your new class must define is as follows: - -command: operations performed by the new command :tb(s=:) - -Of course, the new class can define other methods and variables as -needed. - -:line - -10.8 Kspace computations :link(mod_8),h4 - -Classes that compute long-range Coulombic interactions via K-space -representations (Ewald, PPPM) are derived from the KSpace class. New -styles can be created to add new K-space options to LAMMPS. - -Ewald.cpp is an example of computing K-space interactions. - -Here is a brief description of methods you define in your new derived -class. See kspace.h for details. - -init: initialize the calculation before a run -setup: computation before the 1st timestep of a run -compute: every-timestep computation -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.9 Minimization styles :link(mod_9),h4 - -Classes that perform energy minimization derived from the Min class. -New styles can be created to add new minimization algorithms to -LAMMPS. - -Min_cg.cpp is an example of conjugate gradient minimization. - -Here is a brief description of methods you define in your new derived -class. See min.h for details. - -init: initialize the minimization before a run -run: perform the minimization -memory_usage: tally of memory usage :tb(s=:) - -:line - -10.10 Pairwise potentials :link(mod_10),h4 - -Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials -such as EAM or Tersoff where particles interact without a static bond -topology. New styles can be created to add new pair potentials to -LAMMPS. - -Pair_lj_cut.cpp is a simple example of a Pair class, though it -includes some optional methods to enable its use with rRESPA. - -Here is a brief description of the class methods in pair.h: - -compute: workhorse routine that computes pairwise interactions -settings: reads the input script line with arguments you define -coeff: set coefficients for one i,j type pair -init_one: perform initialization for one i,j type pair -init_style: initialization specific to this pair style -write & read_restart: write/read i,j pair coeffs to restart files -write & read_restart_settings: write/read global settings to restart files -single: force and energy of a single pairwise interaction between 2 atoms -compute_inner/middle/outer: versions of compute used by rRESPA :tb(s=:) - -The inner/middle/outer routines are optional. - -:line - -10.11 Region styles :link(mod_11),h4 - -Classes that define geometric regions are derived from the Region -class. Regions are used elsewhere in LAMMPS to group atoms, delete -atoms to create a void, insert atoms in a specified region, etc. New -styles can be created to add new region shapes to LAMMPS. - -Region_sphere.cpp is an example of a spherical region. - -Here is a brief description of methods you define in your new derived -class. See region.h for details. - -inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surc -surface_exterior: determine if a point is within a cutoff distance outside of surf -shape_update : change region shape if set by time-dependent variable :tb(s=:) - -:line - -10.12 Body styles :link(mod_12),h4 - -Classes that define body particles are derived from the Body class. -Body particles can represent complex entities, such as surface meshes -of discrete points, collections of sub-particles, deformable objects, -etc. - -See "Section 6.14"_Section_howto.html#howto_14 of the manual for -an overview of using body particles and the "body"_body.html doc page -for details on the various body styles LAMMPS supports. New styles -can be created to add new kinds of body particles to LAMMPS. - -Body_nparticle.cpp is an example of a body particle that is treated as -a rigid body containing N sub-particles. - -Here is a brief description of methods you define in your new derived -class. See body.h for details. - -data_body: process a line from the Bodies section of a data file -noutrow: number of sub-particles output is generated for -noutcol: number of values per-sub-particle output is generated for -output: output values for the Mth sub-particle -pack_comm_body: body attributes to communicate every timestep -unpack_comm_body: unpacking of those attributes -pack_border_body: body attributes to communicate when reneighboring is done -unpack_border_body: unpacking of those attributes :tb(s=:) - -:line - -10.13 Thermodynamic output options :link(mod_13),h4 - -There is one class that computes and prints thermodynamic information -to the screen and log file; see the file thermo.cpp. - -There are two styles defined in thermo.cpp: "one" and "multi". There -is also a flexible "custom" style which allows the user to explicitly -list keywords for quantities to print when thermodynamic info is -output. See the "thermo_style"_thermo_style.html command for a list -of defined quantities. - -The thermo styles (one, multi, etc) are simply lists of keywords. -Adding a new style thus only requires defining a new list of keywords. -Search for the word "customize" with references to "thermo style" in -thermo.cpp to see the two locations where code will need to be added. - -New keywords can also be added to thermo.cpp to compute new quantities -for output. Search for the word "customize" with references to -"keyword" in thermo.cpp to see the several locations where code will -need to be added. - -Note that the "thermo_style custom"_thermo.html command already allows -for thermo output of quantities calculated by "fixes"_fix.html, -"computes"_compute.html, and "variables"_variable.html. Thus, it may -be simpler to compute what you wish via one of those constructs, than -by adding a new keyword to the thermo command. - -:line - -10.14 Variable options :link(mod_14),h4 - -There is one class that computes and stores "variable"_variable.html -information in LAMMPS; see the file variable.cpp. The value -associated with a variable can be periodically printed to the screen -via the "print"_print.html, "fix print"_fix_print.html, or -"thermo_style custom"_thermo_style.html commands. Variables of style -"equal" can compute complex equations that involve the following types -of arguments: - -thermo keywords = ke, vol, atoms, ... -other variables = v_a, v_myvar, ... -math functions = div(x,y), mult(x,y), add(x,y), ... -group functions = mass(group), xcm(group,x), ... -atom values = x\[123\], y\[3\], vx\[34\], ... -compute values = c_mytemp\[0\], c_thermo_press\[3\], ... :pre - -Adding keywords for the "thermo_style custom"_thermo_style.html command -(which can then be accessed by variables) was discussed -"here"_Section_modify.html#mod_13 on this page. - -Adding a new math function of one or two arguments can be done by -editing one section of the Variable::evaluate() method. Search for -the word "customize" to find the appropriate location. - -Adding a new group function can be done by editing one section of the -Variable::evaluate() method. Search for the word "customize" to find -the appropriate location. You may need to add a new method to the -Group class as well (see the group.cpp file). - -Accessing a new atom-based vector can be done by editing one section -of the Variable::evaluate() method. Search for the word "customize" -to find the appropriate location. - -Adding new "compute styles"_compute.html (whose calculated values can -then be accessed by variables) was discussed -"here"_Section_modify.html#mod_3 on this page. - -:line -:line - -10.15 Submitting new features for inclusion in LAMMPS :link(mod_15),h4 - -We encourage users to submit new features or modifications for -LAMMPS to "the core developers"_http://lammps.sandia.gov/authors.html -so they can be added to the LAMMPS distribution. The preferred way to -manage and coordinate this is as of Fall 2016 via the LAMMPS project on -"GitHub"_https://github.com/lammps/lammps. An alternative is to contact -the LAMMPS developers or the indicated developer of a package or feature -directly and send in your contribution via e-mail. - -For any larger modifications or programming project, you are encouraged -to contact the LAMMPS developers ahead of time, in order to discuss -implementation strategies and coding guidelines, that will make it -easier to integrate your contribution and result in less work for -everybody involved. You are also encouraged to search through the list -of "open issues on GitHub"_https://github.com/lammps/lammps/issues and -submit a new issue for a planned feature, so you would not duplicate -the work of others (and possibly get scooped by them) or have your work -duplicated by others. - -How quickly your contribution will be integrated -depends largely on how much effort it will cause to integrate and test -it, how much it requires changes to the core codebase, and of how much -interest it is to the larger LAMMPS community. Please see below for a -checklist of typical requirements. Once you have prepared everything, -see "this tutorial"_tutorial_github.html for instructions on how to -submit your changes or new files through a GitHub pull request. If you -prefer to submit patches or full files, you should first make certain, -that your code works correctly with the latest patch-level version of -LAMMPS and contains all bugfixes from it. Then create a gzipped tar -file of all changed or added files or a corresponding patch file using -'diff -u' or 'diff -c' and compress it with gzip. Please only use -gzip compression, as this works well on all platforms. - -If the new features/files are broadly useful we may add them as core -files to LAMMPS or as part of a "standard -package"_Section_start.html#start_3. Else we will add them as a -user-contributed file or package. Examples of user packages are in -src sub-directories that start with USER. The USER-MISC package is -simply a collection of (mostly) unrelated single files, which is the -simplest way to have your contribution quickly added to the LAMMPS -distribution. You can see a list of the both standard and user -packages by typing "make package" in the LAMMPS src directory. - -Note that by providing us files to release, you are agreeing to make -them open-source, i.e. we can release them under the terms of the GPL, -used as a license for the rest of LAMMPS. See "Section -1.4"_Section_intro.html#intro_4 for details. - -With user packages and files, all we are really providing (aside from -the fame and fortune that accompanies having your name in the source -code and on the "Authors page"_http://lammps.sandia.gov/authors.html -of the "LAMMPS WWW site"_lws), is a means for you to distribute your -work to the LAMMPS user community, and a mechanism for others to -easily try out your new feature. This may help you find bugs or make -contact with new collaborators. Note that you're also implicitly -agreeing to support your code which means answer questions, fix bugs, -and maintain it if LAMMPS changes in some way that breaks it (an -unusual event). - -NOTE: If you prefer to actively develop and support your add-on -feature yourself, then you may wish to make it available for download -from your own website, as a user package that LAMMPS users can add to -their copy of LAMMPS. See the "Offsite LAMMPS packages and -tools"_http://lammps.sandia.gov/offsite.html page of the LAMMPS web -site for examples of groups that do this. We are happy to advertise -your package and web site from that page. Simply email the -"developers"_http://lammps.sandia.gov/authors.html with info about -your package and we will post it there. - -The previous sections of this doc page describe how to add new "style" -files of various kinds to LAMMPS. Packages are simply collections of -one or more new class files which are invoked as a new style within a -LAMMPS input script. If designed correctly, these additions typically -do not require changes to the main core of LAMMPS; they are simply -add-on files. If you think your new feature requires non-trivial -changes in core LAMMPS files, you'll need to "communicate with the -developers"_http://lammps.sandia.gov/authors.html, since we may or may -not want to make those changes. An example of a trivial change is -making a parent-class method "virtual" when you derive a new child -class from it. - -Here is a checklist of steps you need to follow to submit a single file -or user package for our consideration. Following these steps will save -both you and us time. See existing files in packages in the src dir for -examples. If you are uncertain, please ask. - -All source files you provide must compile with the most current -version of LAMMPS with multiple configurations. In particular you -need to test compiling LAMMPS from scratch with -DLAMMPS_BIGBIG -set in addition to the default -DLAMMPS_SMALLBIG setting. Your code -will need to work correctly in serial and in parallel using MPI. :ulb,l - -For consistency with the rest of LAMMPS and especially, if you want -your contribution(s) to be added to main LAMMPS code or one of its -standard packages, it needs to be written in a style compatible with -other LAMMPS source files. This means: 2-character indentation per -level, [no tabs], no lines over 80 characters. I/O is done via -the C-style stdio library, class header files should not import any -system headers outside , STL containers should be avoided -in headers, and forward declarations used where possible or needed. -All added code should be placed into the LAMMPS_NS namespace or a -sub-namespace; global or static variables should be avoided, as they -conflict with the modular nature of LAMMPS and the C++ class structure. -Header files must [not] import namespaces with {using}. -This all is so the developers can more easily understand, integrate, -and maintain your contribution and reduce conflicts with other parts -of LAMMPS. This basically means that the code accesses data -structures, performs its operations, and is formatted similar to other -LAMMPS source files, including the use of the error class for error -and warning messages. :l - -If you want your contribution to be added as a user-contributed -feature, and it's a single file (actually a *.cpp and *.h file) it can -rapidly be added to the USER-MISC directory. Send us the one-line -entry to add to the USER-MISC/README file in that dir, along with the -2 source files. You can do this multiple times if you wish to -contribute several individual features. :l - -If you want your contribution to be added as a user-contribution and -it is several related features, it is probably best to make it a user -package directory with a name like USER-FOO. In addition to your new -files, the directory should contain a README text file. The README -should contain your name and contact information and a brief -description of what your new package does. If your files depend on -other LAMMPS style files also being installed (e.g. because your file -is a derived class from the other LAMMPS class), then an Install.sh -file is also needed to check for those dependencies. See other README -and Install.sh files in other USER directories as examples. Send us a -tarball of this USER-FOO directory. :l - -Your new source files need to have the LAMMPS copyright, GPL notice, -and your name and email address at the top, like other -user-contributed LAMMPS source files. They need to create a class -that is inside the LAMMPS namespace. If the file is for one of the -USER packages, including USER-MISC, then we are not as picky about the -coding style (see above). I.e. the files do not need to be in the -same stylistic format and syntax as other LAMMPS files, though that -would be nice for developers as well as users who try to read your -code. :l - -You [must] also create a [documentation] file for each new command or -style you are adding to LAMMPS. For simplicity and convenience, the -documentation of groups of closely related commands or styles may be -combined into a single file. This will be one file for a single-file -feature. For a package, it might be several files. These are simple -text files with a specific markup language, that are then auto-converted -to HTML and PDF. The tools for this conversion are included in the -source distribution, and the translation can be as simple as doing -"make html pdf" in the doc folder. -Thus the documentation source files must be in the same format and -style as other *.txt files in the lammps/doc/src directory for similar -commands and styles; use one or more of them as a starting point. -A description of the markup can also be found in -lammps/doc/utils/txt2html/README.html -As appropriate, the text files can include links to equations -(see doc/Eqs/*.tex for examples, we auto-create the associated JPG -files), or figures (see doc/JPG for examples), or even additional PDF -files with further details (see doc/PDF for examples). The doc page -should also include literature citations as appropriate; see the -bottom of doc/fix_nh.txt for examples and the earlier part of the same -file for how to format the cite itself. The "Restrictions" section of -the doc page should indicate that your command is only available if -LAMMPS is built with the appropriate USER-MISC or USER-FOO package. -See other user package doc files for examples of how to do this. The -prerequisite for building the HTML format files are Python 3.x and -virtualenv, the requirement for generating the PDF format manual -is the "htmldoc"_http://www.htmldoc.org/ software. Please run at least -"make html" and carefully inspect and proofread the resulting HTML format -doc page before submitting your code. :l - -For a new package (or even a single command) you should include one or -more example scripts demonstrating its use. These should run in no -more than a couple minutes, even on a single processor, and not require -large data files as input. See directories under examples/USER for -examples of input scripts other users provided for their packages. -These example inputs are also required for validating memory accesses -and testing for memory leaks with valgrind :l - -If there is a paper of yours describing your feature (either the -algorithm/science behind the feature itself, or its initial usage, or -its implementation in LAMMPS), you can add the citation to the *.cpp -source file. See src/USER-EFF/atom_vec_electron.cpp for an example. -A LaTeX citation is stored in a variable at the top of the file and a -single line of code that references the variable is added to the -constructor of the class. Whenever a user invokes your feature from -their input script, this will cause LAMMPS to output the citation to a -log.cite file and prompt the user to examine the file. Note that you -should only use this for a paper you or your group authored. -E.g. adding a cite in the code for a paper by Nose and Hoover if you -write a fix that implements their integrator is not the intended -usage. That kind of citation should just be in the doc page you -provide. :l -:ule - -Finally, as a general rule-of-thumb, the more clear and -self-explanatory you make your documentation and README files, and the -easier you make it for people to get started, e.g. by providing example -scripts, the more likely it is that users will try out your new feature. - -:line -:line - -:link(Foo) -[(Foo)] Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997). diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt deleted file mode 100644 index 5427cd67f28d36bb0344012e6f7cfe593f7aca88..0000000000000000000000000000000000000000 --- a/doc/src/Section_python.txt +++ /dev/null @@ -1,867 +0,0 @@ -"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -11. Python interface to LAMMPS :h2 - -LAMMPS can work together with Python in three ways. First, Python can -wrap LAMMPS through the "LAMMPS library -interface"_Section_howto.html#howto_19, so that a Python script can -create one or more instances of LAMMPS and launch one or more -simulations. In Python lingo, this is "extending" Python with LAMMPS. - -Second, the low-level Python interface can be used indirectly through the -PyLammps and IPyLammps wrapper classes in Python. These wrappers try to -simplify the usage of LAMMPS in Python by providing an object-based interface -to common LAMMPS functionality. It also reduces the amount of code necessary to -parameterize LAMMPS scripts through Python and makes variables and computes -directly accessible. See "PyLammps interface"_#py_9 for more details. - -Third, LAMMPS can use the Python interpreter, so that a LAMMPS input -script can invoke Python code, and pass information back-and-forth -between the input script and Python functions you write. The Python -code can also callback to LAMMPS to query or change its attributes. -In Python lingo, this is "embedding" Python in LAMMPS. - -This section describes how to use these three approaches. - -11.1 "Overview of running LAMMPS from Python"_#py_1 -11.2 "Overview of using Python from a LAMMPS script"_#py_2 -11.3 "Building LAMMPS as a shared library"_#py_3 -11.4 "Installing the Python wrapper into Python"_#py_4 -11.5 "Extending Python with MPI to run in parallel"_#py_5 -11.6 "Testing the Python-LAMMPS interface"_#py_6 -11.7 "Using LAMMPS from Python"_#py_7 -11.8 "Example Python scripts that use LAMMPS"_#py_8 -11.9 "PyLammps interface"_#py_9 :ul - -If you are not familiar with it, "Python"_http://www.python.org is a -powerful scripting and programming language which can essentially do -anything that faster, lower-level languages like C or C++ can do, but -typically with much fewer lines of code. When used in embedded mode, -Python can perform operations that the simplistic LAMMPS input script -syntax cannot. Python can be also be used as a "glue" language to -drive a program through its library interface, or to hook multiple -pieces of software together, such as a simulation package plus a -visualization package, or to run a coupled multiscale or multiphysics -model. - -See "Section 6.10"_Section_howto.html#howto_10 of the manual and -the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See "Section -6.19"_Section_howto.html#howto_19 for a description of the LAMMPS -library interface provided in src/library.cpp and src/library.h, and -how to extend it for your needs. As described below, that interface -is what is exposed to Python either when calling LAMMPS from Python or -when calling Python from a LAMMPS input script and then calling back -to LAMMPS from Python code. The library interface is designed to be -easy to add functions to. Thus the Python interface to LAMMPS is also -easy to extend as well. - -If you create interesting Python scripts that run LAMMPS or -interesting Python functions that can be called from a LAMMPS input -script, that you think would be useful to other users, please "email -them to the developers"_http://lammps.sandia.gov/authors.html. We can -include them in the LAMMPS distribution. - -:line -:line - -11.1 Overview of running LAMMPS from Python :link(py_1),h4 - -The LAMMPS distribution includes a python directory with all you need -to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS -library interface, with one wrapper function per LAMMPS library -function. This file makes it is possible to do the following either -from a Python script, or interactively from a Python prompt: create -one or more instances of LAMMPS, invoke LAMMPS commands or give it an -input script, run LAMMPS incrementally, extract LAMMPS results, an -modify internal LAMMPS variables. From a Python script you can do -this in serial or parallel. Running Python interactively in parallel -does not generally work, unless you have a version of Python that -extends standard Python to enable multiple instances of Python to read -what you type. - -To do all of this, you must first build LAMMPS as a shared library, -then insure that your Python can find the python/lammps.py file and -the shared library. These steps are explained in subsequent sections -11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a -parallel Python program and how to test that you are ready to use -LAMMPS from Python. Section 11.7 lists all the functions in the -current LAMMPS library interface and how to call them from Python. - -Section 11.8 gives some examples of coupling LAMMPS to other tools via -Python. For example, LAMMPS can easily be coupled to a GUI or other -visualization tools that display graphs or animations in real time as -LAMMPS runs. Examples of such scripts are included in the python -directory. - -Two advantages of using Python to run LAMMPS are how concise the -language is, and that it can be run interactively, enabling rapid -development and debugging of programs. If you use it to mostly invoke -costly operations within LAMMPS, such as running a simulation for a -reasonable number of timesteps, then the overhead cost of invoking -LAMMPS thru Python will be negligible. - -The Python wrapper for LAMMPS uses the amazing and magical (to me) -"ctypes" package in Python, which auto-generates the interface code -needed between Python and a set of C interface routines for a library. -Ctypes is part of standard Python for versions 2.5 and later. You can -check which version of Python you have installed, by simply typing -"python" at a shell prompt. - -:line - -11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 - -LAMMPS has several commands which can be used to invoke Python -code directly from an input script: - -"python"_python.html -"variable python"_variable.html -"fix python/invoke"_fix_python_invoke.html -"pair_style python"_pair_python.html :ul - -The "python"_python.html command which can be used to define and -execute a Python function that you write the code for. The Python -function can also be assigned to a LAMMPS python-style variable via -the "variable"_variable.html command. Each time the variable is -evaluated, either in the LAMMPS input script itself, or by another -LAMMPS command that uses the variable, this will trigger the Python -function to be invoked. - -The Python code for the function can be included directly in the input -script or in an auxiliary file. The function can have arguments which -are mapped to LAMMPS variables (also defined in the input script) and -it can return a value to a LAMMPS variable. This is thus a mechanism -for your input script to pass information to a piece of Python code, -ask Python to execute the code, and return information to your input -script. - -Note that a Python function can be arbitrarily complex. It can import -other Python modules, instantiate Python classes, call other Python -functions, etc. The Python code that you provide can contain more -code than the single function. It can contain other functions or -Python classes, as well as global variables or other mechanisms for -storing state between calls from LAMMPS to the function. - -The Python function you provide can consist of "pure" Python code that -only performs operations provided by standard Python. However, the -Python function can also "call back" to LAMMPS through its -Python-wrapped library interface, in the manner described in the -previous section 11.1. This means it can issue LAMMPS input script -commands or query and set internal LAMMPS state. As an example, this -can be useful in an input script to create a more complex loop with -branching logic, than can be created using the simple looping and -branching logic enabled by the "next"_next.html and "if"_if.html -commands. - -See the "python"_python.html doc page and the "variable"_variable.html -doc page for its python-style variables for more info, including -examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. - -The "fix python/invoke"_fix_python_invoke.html command can execute -Python code at selected timesteps during a simulation run. - -The "pair_style python"_pair_python command allows you to define -pairwise potentials as python code which encodes a single pairwise -interaction. This is useful for rapid-developement and debugging of a -new potential. - -To use any of these commands, you only need to build LAMMPS with the -PYTHON package installed: - -make yes-python -make machine :pre - -Note that this will link LAMMPS with the Python library on your -system, which typically requires several auxiliary system libraries to -also be linked. The list of these libraries and the paths to find -them are specified in the lib/python/Makefile.lammps file. You need -to insure that file contains the correct information for your version -of Python and your machine to successfully build LAMMPS. See the -lib/python/README file for more info. - -If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the preceding section (11.1) -for running LAMMPS from Python. I.e. you must build LAMMPS as a -shared library and insure that Python can find the python/lammps.py -file and the shared library. - -:line - -11.3 Building LAMMPS as a shared library :link(py_3),h4 - -Instructions on how to build LAMMPS as a shared library are given in -"Section 2.4"_Section_start.html#start_4. A shared library is one -that is dynamically loadable, which is what Python requires to wrap -LAMMPS. On Linux this is a library file that ends in ".so", not ".a". - -From the src directory, type - -make foo mode=shlib :pre - -where foo is the machine target name, such as linux or g++ or serial. -This should create the file liblammps_foo.so in the src directory, as -well as a soft link liblammps.so, which is what the Python wrapper will -load by default. Note that if you are building multiple machine -versions of the shared library, the soft link is always set to the -most recently built version. - -NOTE: If you are building LAMMPS with an MPI or FFT library or other -auxiliary libraries (used by various packages), then all of these -extra libraries must also be shared libraries. If the LAMMPS -shared-library build fails with an error complaining about this, see -"Section 2.4"_Section_start.html#start_4 for more details. - -:line - -11.4 Installing the Python wrapper into Python :link(py_4),h4 - -For Python to invoke LAMMPS, there are 2 files it needs to know about: - -python/lammps.py -src/liblammps.so :ul - -Lammps.py is the Python wrapper on the LAMMPS library interface. -Liblammps.so is the shared LAMMPS library that Python loads, as -described above. - -You can insure Python can find these files in one of two ways: - -set two environment variables -run the python/install.py script :ul - -If you set the paths to these files as environment variables, you only -have to do it once. For the csh or tcsh shells, add something like -this to your ~/.cshrc file, one line for each of the two files: - -setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python -setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre - -If you use the python/install.py script, you need to invoke it every -time you rebuild LAMMPS (as a shared library) or make changes to the -python/lammps.py file. - -You can invoke install.py from the python directory as - -% python install.py \[libdir\] \[pydir\] :pre - -The optional libdir is where to copy the LAMMPS shared library to; the -default is /usr/local/lib. The optional pydir is where to copy the -lammps.py file to; the default is the site-packages directory of the -version of Python that is running the install script. - -Note that libdir must be a location that is in your default -LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a -location that Python looks in by default for imported modules, like -its site-packages dir. If you want to copy these files to -non-standard locations, such as within your own user space, you will -need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables -accordingly, as above. - -If the install.py script does not allow you to copy files into system -directories, prefix the python command with "sudo". If you do this, -make sure that the Python that root runs is the same as the Python you -run. E.g. you may need to do something like - -% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre - -You can also invoke install.py from the make command in the src -directory as - -% make install-python :pre - -In this mode you cannot append optional arguments. Again, you may -need to prefix this with "sudo". In this mode you cannot control -which Python is invoked by root. - -Note that if you want Python to be able to load different versions of -the LAMMPS shared library (see "this section"_#py_5 below), you will -need to manually copy files like liblammps_g++.so into the appropriate -system directory. This is not needed if you set the LD_LIBRARY_PATH -environment variable as described above. - -:line - -11.5 Extending Python with MPI to run in parallel :link(py_5),h4 - -If you wish to run LAMMPS in parallel from Python, you need to extend -your Python with an interface to MPI. This also allows you to -make MPI calls directly from Python in your script, if you desire. - -There are several Python packages available that purport to wrap MPI -as a library and allow MPI functions to be called from Python. However, -development on most of them seems to be halted except on: - -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py -"PyPar"_https://github.com/daleroberts/pypar :ul - -Both packages, PyPar and mpi4py have been successfully tested with -LAMMPS. PyPar is simpler and easy to set up and use, but supports -only a subset of MPI. Mpi4py is more MPI-feature complete, but also a -bit more complex to use. As of version 2.0.0, mpi4py is the only -python MPI wrapper that allows passing a custom MPI communicator to -the LAMMPS constructor, which means one can easily run one or more -LAMMPS instances on subsets of the total MPI ranks. - -:line - -PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org -be installed in your Python. After launching Python, type - -import numpy :pre - -to see if it is installed. If not, here is how to install it (version -1.3.0b1 as of April 2009). Unpack the numpy tarball and from its -top-level directory, type - -python setup.py build -sudo python setup.py install :pre - -The "sudo" is only needed if required to copy Numpy files into your -Python distribution's site-packages directory. - -To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it -and from its "source" directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy PyPar files into -your Python distribution's site-packages directory. - -If you have successfully installed PyPar, you should be able to run -Python and type - -import pypar :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -import pypar -print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use PyPar and LAMMPS in parallel from Python, you must insure -both are using the same version of MPI. If you only have one MPI -installed on your system, this is not an issue, but it can be if you -have multiple MPIs. Your LAMMPS build is explicit about which MPI it -is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. PyPar uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both PyPar and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that PyPar finds -the right one. - -:line - -To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it -and from its main directory, type - -python setup.py build -sudo python setup.py install :pre - -Again, the "sudo" is only needed if required to copy mpi4py files into -your Python distribution's site-packages directory. To install with -user privilege into the user local directory type - -python setup.py install --user :pre - -If you have successfully installed mpi4py, you should be able to run -Python and type - -from mpi4py import MPI :pre - -without error. You should also be able to run python in parallel -on a simple test script - -% mpirun -np 4 python test.py :pre - -where test.py contains the lines - -from mpi4py import MPI -comm = MPI.COMM_WORLD -print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre - -and see one line of output for each processor you run on. - -NOTE: To use mpi4py and LAMMPS in parallel from Python, you must -insure both are using the same version of MPI. If you only have one -MPI installed on your system, this is not an issue, but it can be if -you have multiple MPIs. Your LAMMPS build is explicit about which MPI -it is using, since you specify the details in your lo-level -src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find -information about the MPI it uses to build against. And it tries to -load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find -the MPI library that LAMMPS is using. If you have problems running -both mpi4py and LAMMPS together, this is an issue you may need to -address, e.g. by moving other MPI installations so that mpi4py finds -the right one. - -:line - -11.6 Testing the Python-LAMMPS interface :link(py_6),h4 - -To test if LAMMPS is callable from Python, launch Python interactively -and type: - ->>> from lammps import lammps ->>> lmp = lammps() :pre - -If you get no errors, you're ready to use LAMMPS from Python. If the -2nd command fails, the most common error to see is - -OSError: Could not load LAMMPS dynamic library :pre - -which means Python was unable to load the LAMMPS shared library. This -typically occurs if the system can't find the LAMMPS shared library or -one of the auxiliary shared libraries it depends on, or if something -about the library is incompatible with your Python. The error message -should give you an indication of what went wrong. - -You can also test the load directly in Python as follows, without -first importing from the lammps.py file: - ->>> from ctypes import CDLL ->>> CDLL("liblammps.so") :pre - -If an error occurs, carefully go thru the steps in "Section -2.4"_Section_start.html#start_4 and above about building a shared -library and about insuring Python can find the necessary two files -it needs. - -[Test LAMMPS and Python in serial:] :h4 - -To run a LAMMPS test in serial, type these lines into Python -interactively from the bench directory: - ->>> from lammps import lammps ->>> lmp = lammps() ->>> lmp.file("in.lj") :pre - -Or put the same lines in the file test.py and run it as - -% python test.py :pre - -Either way, you should see the results of running the in.lj benchmark -on a single processor appear on the screen, the same as if you had -typed something like: - -lmp_g++ -in in.lj :pre - -[Test LAMMPS and Python in parallel:] :h4 - -To run LAMMPS in parallel, assuming you have installed the -"PyPar"_https://github.com/daleroberts/pypar package as discussed -above, create a test.py file containing these lines: - -import pypar -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp -pypar.finalize() :pre - -To run LAMMPS in parallel, assuming you have installed the -"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed -above, create a test.py file containing these lines: - -from mpi4py import MPI -from lammps import lammps -lmp = lammps() -lmp.file("in.lj") -me = MPI.COMM_WORLD.Get_rank() -nprocs = MPI.COMM_WORLD.Get_size() -print "Proc %d out of %d procs has" % (me,nprocs),lmp -MPI.Finalize() :pre - -You can either script in parallel as: - -% mpirun -np 4 python test.py :pre - -and you should see the same output as if you had typed - -% mpirun -np 4 lmp_g++ -in in.lj :pre - -Note that if you leave out the 3 lines from test.py that specify PyPar -commands you will instantiate and run LAMMPS independently on each of -the P processors specified in the mpirun command. In this case you -should get 4 sets of output, each showing that a LAMMPS run was made -on a single processor, instead of one set of output showing that -LAMMPS ran on 4 processors. If the 1-processor outputs occur, it -means that PyPar is not working correctly. - -Also note that once you import the PyPar module, PyPar initializes MPI -for you, and you can use MPI calls directly in your Python script, as -described in the PyPar documentation. The last line of your Python -script should be pypar.finalize(), to insure MPI is shut down -correctly. - -[Running Python scripts:] :h4 - -Note that any Python script (not just for LAMMPS) can be invoked in -one of several ways: - -% python foo.script -% python -i foo.script -% foo.script :pre - -The last command requires that the first line of the script be -something like this: - -#!/usr/local/bin/python -#!/usr/local/bin/python -i :pre - -where the path points to where you have Python installed, and that you -have made the script file executable: - -% chmod +x foo.script :pre - -Without the "-i" flag, Python will exit when the script finishes. -With the "-i" flag, you will be left in the Python interpreter when -the script finishes, so you can type subsequent commands. As -mentioned above, you can only run Python interactively when running -Python on a single processor, not in parallel. - -:line -:line - -11.7 Using LAMMPS from Python :link(py_7),h4 - -As described above, the Python interface to LAMMPS consists of a -Python "lammps" module, the source code for which is in -python/lammps.py, which creates a "lammps" object, with a set of -methods that can be invoked on that object. The sample Python code -below assumes you have first imported the "lammps" module in your -Python script, as follows: - -from lammps import lammps :pre - -These are the methods defined by the lammps module. If you look at -the files src/library.cpp and src/library.h you will see they -correspond one-to-one with calls you can make to the LAMMPS library -from a C++ or C or Fortran program, and which are described in -"Section 6.19"_Section_howto.html#howto_19 of the manual. - -The python/examples directory has Python scripts which show how Python -can run LAMMPS, grab data, change it, and put it back into LAMMPS. - -lmp = lammps() # create a LAMMPS object using the default liblammps.so library - # 4 optional args are allowed: name, cmdargs, ptr, comm -lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object -lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later -lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library -lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre - -lmp.close() # destroy a LAMMPS object :pre - -version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre - -lmp.file(file) # run an entire input script, file = "in.lj" -lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" -lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"] -lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre - -size = lmp.extract_setting(name) # return data type info :pre - -xlo = lmp.extract_global(name,type) # extract a global quantity - # name = "boxxlo", "nlocal", etc - # type = 0 = int - # 1 = double :pre - -boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre - -coords = lmp.extract_atom(name,type) # extract a per-atom quantity - # name = "x", "type", etc - # type = 0 = vector of ints - # 1 = array of ints - # 2 = vector of doubles - # 3 = array of doubles :pre - -eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute -v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix - # id = ID of compute or fix - # style = 0 = global data - # 1 = per-atom data - # 2 = local data - # type = 0 = scalar - # 1 = vector - # 2 = array - # i,j = indices of value in global vector or array :pre - -var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable - # name = name of variable - # group = group ID (ignored for equal-style variables) - # flag = 0 = equal-style variable - # 1 = atom-style variable :pre - -value = lmp.get_thermo(name) # return current value of a thermo keyword -natoms = lmp.get_natoms() # total # of atoms as int :pre - -flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful -lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre - -data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID - # name = "x", "charge", "type", etc -data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered) -data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID - # name = "x", "charge", "type", etc - # count = # of per-atom values, 1 or 3, etc :pre -lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre - -lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre - -:line - -The lines - -from lammps import lammps -lmp = lammps() :pre - -create an instance of LAMMPS, wrapped in a Python class by the lammps -Python module, and return an instance of the Python class as lmp. It -is used to make all subsequent calls to the LAMMPS library. - -Additional arguments to lammps() can be used to tell Python the name -of the shared library to load or to pass arguments to the LAMMPS -instance, the same as if LAMMPS were launched from a command-line -prompt. - -If the ptr argument is set like this: - -lmp = lammps(ptr=lmpptr) :pre - -then lmpptr must be an argument passed to Python via the LAMMPS -"python"_python.html command, when it is used to define a Python -function that is invoked by the LAMMPS input script. This mode of -using Python with LAMMPS is described above in 11.2. The variable -lmpptr refers to the instance of LAMMPS that called the embedded -Python interpreter. Using it as an argument to lammps() allows the -returned Python class instance "lmp" to make calls to that instance of -LAMMPS. See the "python"_python.html command doc page for examples -using this syntax. - -Note that you can create multiple LAMMPS objects in your Python -script, and coordinate and run multiple simulations, e.g. - -from lammps import lammps -lmp1 = lammps() -lmp2 = lammps() -lmp1.file("in.file1") -lmp2.file("in.file2") :pre - -The file(), command(), commands_list(), commands_string() methods -allow an input script, a single command, or multiple commands to be -invoked. - -The extract_setting(), extract_global(), extract_box(), -extract_atom(), extract_compute(), extract_fix(), and -extract_variable() methods return values or pointers to data -structures internal to LAMMPS. - -For extract_global() see the src/library.cpp file for the list of -valid names. New names could easily be added. A double or integer is -returned. You need to specify the appropriate data type via the type -argument. - -For extract_atom(), a pointer to internal LAMMPS atom-based data is -returned, which you can use via normal Python subscripting. See the -extract() method in the src/atom.cpp file for a list of valid names. -Again, new names could easily be added if the property you want is not -listed. A pointer to a vector of doubles or integers, or a pointer to -an array of doubles (double **) or integers (int **) is returned. You -need to specify the appropriate data type via the type argument. - -For extract_compute() and extract_fix(), the global, per-atom, or -local data calculated by the compute or fix can be accessed. What is -returned depends on whether the compute or fix calculates a scalar or -vector or array. For a scalar, a single double value is returned. If -the compute or fix calculates a vector or array, a pointer to the -internal LAMMPS data is returned, which you can use via normal Python -subscripting. The one exception is that for a fix that calculates a -global vector or array, a single double value from the vector or array -is returned, indexed by I (vector) or I and J (array). I,J are -zero-based indices. The I,J arguments can be left out if not needed. -See "Section 6.15"_Section_howto.html#howto_15 of the manual for a -discussion of global, per-atom, and local data, and of scalar, vector, -and array data types. See the doc pages for individual -"computes"_compute.html and "fixes"_fix.html for a description of what -they calculate and store. - -For extract_variable(), an "equal-style or atom-style -variable"_variable.html is evaluated and its result returned. - -For equal-style variables a single double value is returned and the -group argument is ignored. For atom-style variables, a vector of -doubles is returned, one value per atom, which you can use via normal -Python subscripting. The values will be zero for atoms not in the -specified group. - -The get_thermo() method returns returns the current value of a thermo -keyword as a float. - -The get_natoms() method returns the total number of atoms in the -simulation, as an int. - -The set_variable() methosd sets an existing string-style variable to a -new string value, so that subsequent LAMMPS commands can access the -variable. - -The reset_box() emthods resets the size and shape of the simulation -box, e.g. as part of restoring a previously extracted and saved state -of a simulation. - -The gather methods collect peratom info of the requested type (atom -coords, atom types, forces, etc) from all processors, and returns the -same vector of values to each callling processor. The scatter -functions do the inverse. They distribute a vector of peratom values, -passed by all calling processors, to invididual atoms, which may be -owned by different processos. - -Note that the data returned by the gather methods, -e.g. gather_atoms("x"), is different from the data structure returned -by extract_atom("x") in four ways. (1) Gather_atoms() returns a -vector which you index as x\[i\]; extract_atom() returns an array -which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms -by atom ID while extract_atom() does not. (3) Gather_atoms() returns -a list of all atoms in the simulation; extract_atoms() returns just -the atoms local to each processor. (4) Finally, the gather_atoms() -data structure is a copy of the atom coords stored internally in -LAMMPS, whereas extract_atom() returns an array that effectively -points directly to the internal data. This means you can change -values inside LAMMPS from Python by assigning a new values to the -extract_atom() array. To do this with the gather_atoms() vector, you -need to change values in the vector, then invoke the scatter_atoms() -method. - -For the scatter methods, the array of coordinates passed to must be a -ctypes vector of ints or doubles, allocated and initialized something -like this: - -from ctypes import * -natoms = lmp.get_natoms() -n3 = 3*natoms -x = (n3*c_double)() -x\[0\] = x coord of atom with ID 1 -x\[1\] = y coord of atom with ID 1 -x\[2\] = z coord of atom with ID 1 -x\[3\] = x coord of atom with ID 2 -... -x\[n3-1\] = z coord of atom with ID natoms -lmp.scatter_atoms("x",1,3,x) :pre - -Alternatively, you can just change values in the vector returned by -the gather methods, since they are also ctypes vectors. - -:line - -As noted above, these Python class methods correspond one-to-one with -the functions in the LAMMPS library interface in src/library.cpp and -library.h. This means you can extend the Python wrapper via the -following steps: - -Add a new interface function to src/library.cpp and -src/library.h. :ulb,l - -Rebuild LAMMPS as a shared library. :l - -Add a wrapper method to python/lammps.py for this interface -function. :l - -You should now be able to invoke the new interface function from a -Python script. Isn't ctypes amazing? :l -:ule - -:line -:line - -11.8 Example Python scripts that use LAMMPS :link(py_8),h4 - -These are the Python scripts included as demos in the python/examples -directory of the LAMMPS distribution, to illustrate the kinds of -things that are possible when Python wraps LAMMPS. If you create your -own scripts, send them to us and we can include them in the LAMMPS -distribution. - -trivial.py, read/run a LAMMPS input script thru Python, -demo.py, invoke various LAMMPS library interface routines, -simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, -split.py, same as simple.py but running in parallel on a subset of procs, -gui.py, GUI go/stop/temperature-slider to control LAMMPS, -plot.py, real-time temperature plot with GnuPlot via Pizza.py, -viz_tool.py, real-time viz via some viz package, -vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2) - -:line - -For the viz_tool.py and vizplotgui_tool.py commands, replace "tool" -with "gl" or "atomeye" or "pymol" or "vmd", depending on what -visualization package you have installed. - -Note that for GL, you need to be able to run the Pizza.py GL tool, -which is included in the pizza sub-directory. See the "Pizza.py doc -pages"_pizza for more info: - -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) - -Note that for AtomEye, you need version 3, and there is a line in the -scripts that specifies the path and name of the executable. See the -AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details: - -http://mt.seas.upenn.edu/Archive/Graphics/A -http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre - -:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) -:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) - -The latter link is to AtomEye 3 which has the scriping -capability needed by these Python scripts. - -Note that for PyMol, you need to have built and installed the -open-source version of PyMol in your Python, so that you can import it -from a Python script. See the PyMol WWW pages "here"_pymolhome or -"here"_pymolopen for more details: - -http://www.pymol.org -http://sourceforge.net/scm/?type=svn&group_id=4546 :pre - -:link(pymolhome,http://www.pymol.org) -:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546) - -The latter link is to the open-source version. - -Note that for VMD, you need a fairly current version (1.8.7 works for -me) and there are some lines in the pizza/vmd.py script for 4 PIZZA -variables that have to match the VMD installation on your system. - -:line - -See the python/README file for instructions on how to run them and the -source code for individual scripts for comments about what they do. - -Here are screenshots of the vizplotgui_tool.py script in action for -different visualization package options. Click to see larger images: - -:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg) -:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg) -:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg) -:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg) - -11.9 PyLammps interface :link(py_9),h4 - -Please see the "PyLammps Tutorial"_tutorial_pylammps.html. diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 7d456171dc5f26a3362b2bbdbb6fe8634a245802..19a798d5dfddbbb14e2d9ccbf9e66b943392d920 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1,8 +1,10 @@ -"Previous Section"_Section_intro.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_commands.html :c +"Previous Section"_Intro.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Commands.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -117,10 +119,11 @@ lower-case name of the package, e.g. replica or user-misc. If you want to do one of the following: -use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html) -build with a package that requires an extra library -build with an accelerator package that requires special compiler/linker settings -run on a machine that has its own compilers, settings, or libraries :ul +use a LAMMPS command that requires an extra library (e.g. "dump +image"_dump_image.html) build with a package that requires an extra +library build with an accelerator package that requires special +compiler/linker settings run on a machine that has its own compilers, +settings, or libraries :ul then building LAMMPS is more complicated. You may need to find where extra libraries exist on your machine or install them if they don't. @@ -695,8 +698,8 @@ are always included, plus optional packages. Packages are groups of files that enable a specific set of features. For example, force fields for molecular systems or granular systems are in packages. -"Section 4"_Section_packages.html in the manual has details about all -the packages, which come in two flavors: [standard] and [user] +The "Packages"_Packages.html doc pages has details about all the +packages, which come in two flavors: [standard] and [user] packages. It also has specific instructions for building LAMMPS with any package which requires an extra library. General instructions are below. @@ -826,45 +829,47 @@ options. Packages that require extra libraries :h4,link(start_3_3) A few of the standard and user packages require extra libraries. See -"Section 4"_Section_packages.html for two tables of packages which -indicate which ones require libraries. For each such package, the -Section 4 doc page gives details on how to build the extra library, -including how to download it if necessary. The basic ideas are -summarized here. +the "Packages"_Packages.html doc pages for two tables of packages +which indicate which ones require libraries. For each such package, +the Section 4 doc page gives details on how to build the extra +library, including how to download it if necessary. The basic ideas +are summarized here. [System libraries:] -Packages in the tables "Section 4"_Section_packages.html with a "sys" -in the last column link to system libraries that typically already -exist on your machine. E.g. the python package links to a system -Python library. If your machine does not have the required library, -you will have to download and install it on your machine, in either -the system or user space. +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with a "sys" in the last column +link to system libraries that typically already exist on your machine. +E.g. the python package links to a system Python library. If your +machine does not have the required library, you will have to download +and install it on your machine, in either the system or user space. [Internal libraries:] -Packages in the tables "Section 4"_Section_packages.html with an "int" -in the last column link to internal libraries whose source code is -included with LAMMPS, in the lib/name directory where name is the -package name. You must first build the library in that directory -before building LAMMPS with that package installed. E.g. the gpu -package links to a library you build in the lib/gpu dir. You can -often do the build in one step by typing "make lib-name args=..." -from the src dir, with appropriate arguments. You can leave off the -args to see a help message. See "Section 4"_Section_packages.html for -details for each package. +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with an "int" in the last column +link to internal libraries whose source code is included with LAMMPS, +in the lib/name directory where name is the package name. You must +first build the library in that directory before building LAMMPS with +that package installed. E.g. the gpu package links to a library you +build in the lib/gpu dir. You can often do the build in one step by +typing "make lib-name args=..." from the src dir, with appropriate +arguments. You can leave off the args to see a help message. See the +"Packages details"_Packages_details.html doc page for details for each +package. [External libraries:] -Packages in the tables "Section 4"_Section_packages.html with an "ext" -in the last column link to external libraries whose source code is not -included with LAMMPS. You must first download and install the library -before building LAMMPS with that package installed. E.g. the voronoi -package links to the freely available "Voro++ library"_voro_home2. You -can often do the download/build in one step by typing "make lib-name +Packages in the standard and user tables of the +"Packages"_Packages.html doc pages with an "ext" in the last column +link to external libraries whose source code is not included with +LAMMPS. You must first download and install the library before +building LAMMPS with that package installed. E.g. the voronoi package +links to the freely available "Voro++ library"_voro_home2. You can +often do the download/build in one step by typing "make lib-name args=..." from the src dir, with appropriate arguments. You can leave -off the args to see a help message. See "Section -4"_Section_packages.html for details for each package. +off the args to see a help message. See the "Packages +details"_Packages_details.html doc page for details for each package. :link(voro_home2,http://math.lbl.gov/voro++) @@ -886,9 +891,9 @@ copied from a lib/name/Makefile.lammps.* file when the library is built. If those settings are not correct for your machine you will need to edit or create an appropriate Makefile.lammps file. -Package-specific details for these steps are given in "Section -4"_Section_packages.html an in README files in the lib/name -directories. +Package-specific details for these steps are given on the "Packages +details"_Packages_details.html doc page and in README files in the +lib/name directories. [Compiler options needed for accelerator packages:] @@ -899,14 +904,14 @@ these accelerator packages for optimal performance requires specific settings in the Makefile.machine file you use. A summary of the Makefile.machine settings needed for each of these -packages is given in "Section 4"_Section_packages.html. More info is -given on the doc pages that describe each package in detail: +packages is given on the "Packages"_Packages.html doc pages. More +info is given on the doc pages that describe each package in detail: -5.3.1 "USER-INTEL package"_accelerate_intel.html -5.3.2 "GPU package"_accelerate_intel.html -5.3.3 "KOKKOS package"_accelerate_kokkos.html -5.3.4 "USER-OMP package"_accelerate_omp.html -5.3.5 "OPT package"_accelerate_opt.html :all(b) +"USER-INTEL package"_Speed_intel.html +"GPU package"_Speed_gpu.html +"KOKKOS package"_Speed_kokkos.html +"USER-OMP package"_Speed_omp.html +"OPT package"_Speed_opt.html :all(b) You can also use or examine the following machine Makefiles in src/MAKE/OPTIONS, which include the settings. Note that the @@ -929,9 +934,9 @@ Makefile.opt :ul LAMMPS can be built as either a static or shared library, which can then be called from another application or a scripting language. See -"this section"_Section_howto.html#howto_10 for more info on coupling -LAMMPS to other codes. See "this section"_Section_python.html for -more info on wrapping and running LAMMPS from Python. +the "Howto couple"_Howto_couple.html doc page for more info on +coupling LAMMPS to other codes. See the "Python"_Python.html doc page +for more info on wrapping and running LAMMPS from Python. Static library :h4 @@ -955,15 +960,15 @@ dynamically loaded, e.g. from Python, type make foo mode=shlib :pre where foo is the machine name. This kind of library is required when -wrapping LAMMPS with Python; see "Section 11"_Section_python.html -for details. This will use the SHFLAGS and SHLIBFLAGS settings in +wrapping LAMMPS with Python; see the "Python"_Python.html doc page for +details. This will use the SHFLAGS and SHLIBFLAGS settings in src/MAKE/Makefile.foo and perform the build in the directory Obj_shared_foo. This is so that each file can be compiled with the -fPIC flag which is required for inclusion in a shared library. The build will create the file liblammps_foo.so which another application -can link to dynamically. It will also create a soft link liblammps.so, -which will point to the most recently built shared library. This is -the file the Python wrapper loads by default. +can link to dynamically. It will also create a soft link +liblammps.so, which will point to the most recently built shared +library. This is the file the Python wrapper loads by default. Note that for a shared library to be usable by a calling program, all the auxiliary libraries it depends on must also exist as shared @@ -1034,16 +1039,16 @@ src/library.cpp and src/library.h. See the sample codes in examples/COUPLE/simple for examples of C++ and C and Fortran codes that invoke LAMMPS thru its library interface. -There are other examples as well in the COUPLE directory which are -discussed in "Section 6.10"_Section_howto.html#howto_10 of the -manual. See "Section 11"_Section_python.html of the manual for a -description of the Python wrapper provided with LAMMPS that operates -through the LAMMPS library interface. +There are other examples as well in the COUPLE directory which use +coupling ideas discussed on the "Howto couple"_Howto_couple.html doc +page. See the "Python"_Python.html doc page for a description of the +Python wrapper provided with LAMMPS that operates through the LAMMPS +library interface. The files src/library.cpp and library.h define the C-style API for -using LAMMPS as a library. See "Section -6.19"_Section_howto.html#howto_19 of the manual for a description of the -interface and how to extend it for your needs. +using LAMMPS as a library. See the "Howto library"_Howto_library.html +doc page for a description of the interface and how to extend it for +your needs. :line @@ -1065,7 +1070,7 @@ the '-in' command-line switch, e.g. lmp_linux -in in.file :pre -"This section"_Section_commands.html describes how input scripts are +The "Commands"_Commands.html doc page describes how input scripts are structured and what commands they contain. You can test LAMMPS on any of the sample inputs provided in the @@ -1177,7 +1182,7 @@ than your working directory, which is probably not what you want. If LAMMPS encounters errors in the input script or while running a simulation it will print an ERROR message and stop or a WARNING -message and continue. See "Section 12"_Section_errors.html for a +message and continue. See the "Errors"_Errors.html doc page for a discussion of the various kinds of errors LAMMPS can or can't detect, a list of all ERROR and WARNING messages, and what to do about them. @@ -1274,8 +1279,8 @@ Either the full word or an abbreviation can be used for the keywords. Note that the keywords do not use a leading minus sign. I.e. the keyword is "t", not "-t". Also note that each of the keywords has a default setting. Example of when to use these options and what -settings to use on different platforms is given in "Section -5.3"_Section_accelerate.html#acc_3. +settings to use on different platforms is given on the "Speed +kokkos"_Speed_kokkos.html doc page. d or device g or gpus @@ -1386,16 +1391,16 @@ processors in all partitions must equal P. Thus the command "-partition 8x2 4 5" has 10 partitions and runs on a total of 25 processors. -Running with multiple partitions can e useful for running -"multi-replica simulations"_Section_howto.html#howto_5, where each -replica runs on on one or a few processors. Note that with MPI -installed on a machine (e.g. your desktop), you can run on more -(virtual) processors than you have physical processors. +Running with multiple partitions can be useful for running +"multi-replica simulations"_Howto_replica.html, where each replica +runs on on one or a few processors. Note that with MPI installed on a +machine (e.g. your desktop), you can run on more (virtual) processors +than you have physical processors. To run multiple independent simulations from one input script, using -multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 -of the manual. World- and universe-style "variables"_variable.html -are useful in this context. +multiple partitions, see the "Howto multiple"_Howto_multiple.html doc +page. World- and universe-style "variables"_variable.html are useful +in this context. -plog file :pre @@ -1459,8 +1464,7 @@ cores within each node are ranked in a desired order. Or when using the "run_style verlet/split"_run_style.html command with 2 partitions to insure that a specific Kspace processor (in the 2nd partition) is matched up with a specific set of processors in the 1st partition. -See the "Section 5"_Section_accelerate.html doc pages for -more details. +See the "Speed tips"_Speed_tips.html doc page for more details. If the keyword {nth} is used with a setting {N}, then it means every Nth processor will be moved to the end of the ranking. This is useful @@ -1611,9 +1615,9 @@ value2 ..." at the beginning of the input script. Defining an index variable as a command-line argument overrides any setting for the same index variable in the input script, since index variables cannot be re-defined. See the "variable"_variable.html command for more info on -defining index and other kinds of variables and "this -section"_Section_commands.html#cmd_2 for more info on using variables -in input scripts. +defining index and other kinds of variables and the "Commands +parse"_Commands_parse.html page for more info on using variables in +input scripts. NOTE: Currently, the command-line parser looks for arguments that start with "-" to indicate new switches. Thus you cannot specify @@ -1783,11 +1787,13 @@ communication, roughly 75% in the example above. The current C++ began with a complete rewrite of LAMMPS 2001, which was written in F90. Features of earlier versions of LAMMPS are listed -in "Section 13"_Section_history.html. The F90 and F77 versions -(2001 and 99) are also freely distributed as open-source codes; check -the "LAMMPS WWW Site"_lws for distribution information if you prefer -those versions. The 99 and 2001 versions are no longer under active -development; they do not have all the features of C++ LAMMPS. +on the "History page"_http://lammps.sandia.gov/history.html of the +LAMMPS website. The F90 and F77 versions (2001 and 99) are also +freely distributed as open-source codes; check the "History +page"_http://lammps.sandia.gov/history.html of the LAMMPS website for +info about those versions. The 99 and 2001 versions are no longer +under active development; they do not have all the features of C++ +LAMMPS. If you are a previous user of LAMMPS 2001, these are the most significant changes you will notice in C++ LAMMPS: diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt new file mode 100644 index 0000000000000000000000000000000000000000..091657082ae75a48d53c433a8fd98428ba6180ff --- /dev/null +++ b/doc/src/Speed.txt @@ -0,0 +1,64 @@ +"Previous Section"_Package.html - "LAMMPS WWW Site"_lws - +"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next +Section"_Howto.html :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Accelerate performance :h2 + +This section describes various methods for improving LAMMPS +performance for different classes of problems running on different +kinds of machines. + +There are two thrusts to the discussion that follows. The first is +using code options that implement alternate algorithms that can +speed-up a simulation. The second is to use one of the several +accelerator packages provided with LAMMPS that contain code optimized +for certain kinds of hardware, including multi-core CPUs, GPUs, and +Intel Xeon Phi coprocessors. + +The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS +web site gives performance results for the various accelerator +packages discussed on the "Speed packages"_Speed_packages.html doc +page, for several of the standard LAMMPS benchmark problems, as a +function of problem size and number of compute nodes, on different +hardware platforms. + + + + + +"Benchmarks"_Speed_bench.html +"Measuring performance"_Speed_measure.html :all(b) + +"General tips"_Speed_tips.html :all(b) + +"Accelerator packages"_Speed_packages.html +"GPU package"_Speed_gpu.html +"USER-INTEL package"_Speed_intel.html +"KOKKOS package"_Speed_kokkos.html +"USER-OMP package"_Speed_omp.html +"OPT package"_Speed_opt.html +"Comparison of accelerator packages"_Speed_compare.html :all(b) + + diff --git a/doc/src/Section_perf.txt b/doc/src/Speed_bench.txt similarity index 85% rename from doc/src/Section_perf.txt rename to doc/src/Speed_bench.txt index 9998cb0d9a1371fdcca7c6e927c49925bb6f81d2..8e407d14ea6bdb7428bff3818a670a9a84244f63 100644 --- a/doc/src/Section_perf.txt +++ b/doc/src/Speed_bench.txt @@ -1,17 +1,18 @@ -"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -8. Performance & scalability :h2 +Benchmarks :h3 -Current LAMMPS performance is discussed on the Benchmarks page of the -"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are -listed. The page has several sections, which are briefly described -below: +Current LAMMPS performance is discussed on the "Benchmarks +page"_http://lammps.sandia.gov/bench.html of the "LAMMPS website"_lws +where timings and parallel efficiencies are listed. The page has +several sections, which are briefly described below: CPU performance on 5 standard problems, strong and weak scaling GPU and Xeon Phi performance on same and related problems @@ -51,8 +52,8 @@ of these 5 problems on 1 or 4 cores of Linux desktop. The bench/FERMI and bench/KEPLER dirs have input files and scripts and instructions for running the same (or similar) problems using OpenMP or GPU or Xeon Phi acceleration options. See the README files in those dirs and the -"Section 5.3"_Section_accelerate.html#acc_3 doc pages for -instructions on how to build LAMMPS and run on that kind of hardware. +"Speed packages"_Speed_packages.html doc pages for instructions on how +to build LAMMPS and run on that kind of hardware. The bench/POTENTIALS directory has input files which correspond to the table of results on the diff --git a/doc/src/Speed_compare.txt b/doc/src/Speed_compare.txt new file mode 100644 index 0000000000000000000000000000000000000000..1a17b39c79b672e43062770253ae5e82fc1f998d --- /dev/null +++ b/doc/src/Speed_compare.txt @@ -0,0 +1,73 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Comparison of various accelerator packages :h3 + +NOTE: this section still needs to be re-worked with additional KOKKOS +and USER-INTEL information. + +The next section compares and contrasts the various accelerator +options, since there are multiple ways to perform OpenMP threading, +run on GPUs, and run on Intel Xeon Phi coprocessors. + +All 3 of these packages accelerate a LAMMPS calculation using NVIDIA +hardware, but they do it in different ways. + +As a consequence, for a particular simulation on specific hardware, +one package may be faster than the other. We give guidelines below, +but the best way to determine which package is faster for your input +script is to try both of them on your machine. See the benchmarking +section below for examples where this has been done. + +[Guidelines for using each package optimally:] + +The GPU package allows you to assign multiple CPUs (cores) to a single +GPU (a common configuration for "hybrid" nodes that contain multicore +CPU(s) and GPU(s)) and works effectively in this mode. :ulb,l + +The GPU package moves per-atom data (coordinates, forces) +back-and-forth between the CPU and GPU every timestep. The +KOKKOS/CUDA package only does this on timesteps when a CPU calculation +is required (e.g. to invoke a fix or compute that is non-GPU-ized). +Hence, if you can formulate your input script to only use GPU-ized +fixes and computes, and avoid doing I/O too often (thermo output, dump +file snapshots, restart files), then the data transfer cost of the +KOKKOS/CUDA package can be very low, causing it to run faster than the +GPU package. :l + +The GPU package is often faster than the KOKKOS/CUDA package, if the +number of atoms per GPU is smaller. The crossover point, in terms of +atoms/GPU at which the KOKKOS/CUDA package becomes faster depends +strongly on the pair style. For example, for a simple Lennard Jones +system the crossover (in single precision) is often about 50K-100K +atoms per GPU. When performing double precision calculations the +crossover point can be significantly smaller. :l + +Both packages compute bonded interactions (bonds, angles, etc) on the +CPU. If the GPU package is running with several MPI processes +assigned to one GPU, the cost of computing the bonded interactions is +spread across more CPUs and hence the GPU package can run faster. :l + +When using the GPU package with multiple CPUs assigned to one GPU, its +performance depends to some extent on high bandwidth between the CPUs +and the GPU. Hence its performance is affected if full 16 PCIe lanes +are not available for each GPU. In HPC environments this can be the +case if S2050/70 servers are used, where two devices generally share +one PCIe 2.0 16x slot. Also many multi-GPU mainboards do not provide +full 16 lanes to each of the PCIe 2.0 16x slots. :l +:ule + +[Differences between the two packages:] + +The GPU package accelerates only pair force, neighbor list, and PPPM +calculations. :ulb,l + +The GPU package requires neighbor lists to be built on the CPU when using +exclusion lists, hybrid pair styles, or a triclinic simulation box. :l +:ule diff --git a/doc/src/accelerate_gpu.txt b/doc/src/Speed_gpu.txt similarity index 96% rename from doc/src/accelerate_gpu.txt rename to doc/src/Speed_gpu.txt index 816a31c788e99592a3f70af5e42c786c2ce75410..ab8ec7e9d164b64c269e729e77936cd92fd6dfc0 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/Speed_gpu.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.1 GPU package :h5 +GPU package :h3 The GPU package was developed by Mike Brown at ORNL and his collaborators, particularly Trung Nguyen (ORNL). It provides GPU @@ -72,10 +70,9 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t [Building LAMMPS with the GPU package:] This requires two steps (a,b): build the GPU library, then build -LAMMPS with the GPU package. - -You can do both these steps in one line as described in -"Section 4"_Section_packages.html of the manual. +LAMMPS with the GPU package. You can do both these steps in one line +as described on the "Packages details"_Packages_details.html#GPU doc +page. Or you can follow these two (a,b) steps: diff --git a/doc/src/accelerate_intel.txt b/doc/src/Speed_intel.txt similarity index 97% rename from doc/src/accelerate_intel.txt rename to doc/src/Speed_intel.txt index 71f5185b154f9f832d0ab5b92bd3d2e49f25df2f..20f49672e02849e2f0b544604bc6a88049eb0f05 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/Speed_intel.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.2 USER-INTEL package :h5 +USER-INTEL package :h3 The USER-INTEL package is maintained by Mike Brown at Intel Corporation. It provides two methods for accelerating simulations, @@ -188,8 +186,8 @@ can start running so that the CPU pipeline is still being used efficiently. Although benefits can be seen by launching a MPI task for every hardware thread, for multinode simulations, we recommend that OpenMP threads are used for SMT instead, either with the -USER-INTEL package, "USER-OMP package"_accelerate_omp.html, or -"KOKKOS package"_accelerate_kokkos.html. In the example above, up +USER-INTEL package, "USER-OMP package"_Speed_omp.html, or +"KOKKOS package"_Speed_kokkos.html. In the example above, up to 36X speedups can be observed by using all 36 physical cores with LAMMPS. By using all 72 hardware threads, an additional 10-30% performance gain can be achieved. @@ -233,9 +231,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Alternatively this can be done as a single command with -suitable make command invocations. This is discussed in "Section -4"_Section_packages.html of the manual. +Alternatively this can be done as a single command with suitable make +command invocations, as described on the "Packages +details"_Packages_details.html#USER-INTEL doc page. Note that if you build with support for a Phi coprocessor, the same binary can be used on nodes with or without coprocessors installed. @@ -391,8 +389,8 @@ performance and/or scalability for simple 2-body potentials such as lj/cut or when using LRT mode on processors supporting AVX-512. Not all styles are supported in the USER-INTEL package. You can mix -the USER-INTEL package with styles from the "OPT"_accelerate_opt.html -package or the "USER-OMP package"_accelerate_omp.html. Of course, +the USER-INTEL package with styles from the "OPT"_Speed_opt.html +package or the "USER-OMP package"_Speed_omp.html. Of course, this requires that these packages were installed at build time. This can performed automatically by using "-sf hybrid intel opt" or "-sf hybrid intel omp" command-line options. Alternatively, the "opt" diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/Speed_kokkos.txt similarity index 59% rename from doc/src/accelerate_kokkos.txt rename to doc/src/Speed_kokkos.txt index 0c9178d6e4f42863003b0a2848f29cd42189620f..14f4103aed8d6df6e782eba0e63c196c2daf380d 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -1,38 +1,41 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.3 KOKKOS package :h5 +KOKKOS package :h3 Kokkos is a templated C++ library that provides abstractions to allow -a single implementation of an application kernel (e.g. a pair style) to run efficiently on -different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core -CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads. -The Kokkos library also provides data abstractions to adjust (at -compile time) the memory layout of data structures like 2d and -3d arrays to optimize performance on different hardware. For more information on Kokkos, see -"Github"_https://github.com/kokkos/kokkos. Kokkos is part of -"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards, -Christian Trott, and Dan Sunderland (all Sandia). - -The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles -that use data structures and macros provided by the Kokkos library, -which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia) -and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar -Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions +a single implementation of an application kernel (e.g. a pair style) +to run efficiently on different kinds of hardware, such as GPUs, Intel +Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto +different backend languages such as CUDA, OpenMP, or Pthreads. The +Kokkos library also provides data abstractions to adjust (at compile +time) the memory layout of data structures like 2d and 3d arrays to +optimize performance on different hardware. For more information on +Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part +of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos +library was written primarily by Carter Edwards, Christian Trott, and +Dan Sunderland (all Sandia). + +The LAMMPS KOKKOS package contains versions of pair, fix, and atom +styles that use data structures and macros provided by the Kokkos +library, which is included with LAMMPS in /lib/kokkos. The KOKKOS +package was developed primarily by Christian Trott (Sandia) and Stan +Moore (Sandia) with contributions of various styles by others, +including Sikandar Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez +(Sandia). For more information on developing using Kokkos abstractions see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf. Kokkos currently provides support for 3 modes of execution (per MPI -task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading -for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to -produce an executable compatible with specific hardware. +task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP +(threading for many-core CPUs and Intel Phi), and CUDA (for NVIDIA +GPUs). You choose the mode at build time to produce an executable +compatible with specific hardware. [Building LAMMPS with the KOKKOS package:] @@ -40,16 +43,18 @@ NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or Clang 3.5.2 or later is required. -The recommended method of building the KOKKOS package is to start with the provided Kokkos -Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile -to match your specific hardware. For example: +The recommended method of building the KOKKOS package is to start with +the provided Kokkos Makefiles in /src/MAKE/OPTIONS/. You may need to +modify the KOKKOS_ARCH variable in the Makefile to match your specific +hardware. For example: for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB for Broadwell CPUs, set KOKKOS_ARCH=BWD for K80 GPUs, set KOKKOS_ARCH=Kepler37 for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul -See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options. +See the [Advanced Kokkos Options] section below for a listing of all +KOKKOS_ARCH options. [Compile for CPU-only (MPI only, no threading):] @@ -63,11 +68,12 @@ make kokkos_mpi_only :pre [Compile for CPU-only (MPI plus OpenMP threading):] -NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the -OpenMP interface. You should have one or more multi-core CPUs so that -multiple threads can be launched by each MPI task running on a CPU. +NOTE: To build with Kokkos support for OpenMP threading, your compiler +must support the OpenMP interface. You should have one or more +multi-core CPUs so that multiple threads can be launched by each MPI +task running on a CPU. -use a C++11 compatible compiler and set KOKKOS_ARCH variable in +Use a C++11 compatible compiler and set KOKKOS_ARCH variable in /src/MAKE/OPTIONS/Makefile.kokkos_omp as described above. Then do the following: @@ -85,14 +91,14 @@ make kokkos_phi :pre [Compile for CPUs and GPUs (with OpenMPI or MPICH):] -NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software -version 7.5 or later must be installed on your system. See the -discussion for the "GPU"_accelerate_gpu.html package for details of -how to check and do this. +NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA +software version 7.5 or later must be installed on your system. See +the discussion for the "GPU package"_Speed_gpu.html for details of how +to check and do this. -use a C++11 compatible compiler and set KOKKOS_ARCH variable in -/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described -above. Then do the following: +Use a C++11 compatible compiler and set KOKKOS_ARCH variable in +/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as +described above. Then do the following: cd lammps/src make yes-kokkos @@ -106,24 +112,24 @@ on the make command line. For example: make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8 # set the KOKKOS_ARCH variable explicitly :pre -Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the -make command line requires a GNU-compatible make command. Try -"gmake" if your system's standard make complains. +Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the make +command line requires a GNU-compatible make command. Try "gmake" if +your system's standard make complains. NOTE: If you build using make line variables and re-build LAMMPS twice -with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all" -or "make clean-machine" before each build. This is to force all the -KOKKOS-dependent files to be re-compiled with the new options. +with different KOKKOS options and the *same* target, then you *must* +perform a "make clean-all" or "make clean-machine" before each +build. This is to force all the KOKKOS-dependent files to be +re-compiled with the new options. [Running LAMMPS with the KOKKOS package:] -All Kokkos operations occur within the -context of an individual MPI task running on a single node of the -machine. The total number of MPI tasks used by LAMMPS (one or -multiple per compute node) is set in the usual manner via the mpirun -or mpiexec commands, and is independent of Kokkos. E.g. the mpirun -command in OpenMPI does this via its --np and -npernode switches. Ditto for MPICH via -np and -ppn. +All Kokkos operations occur within the context of an individual MPI +task running on a single node of the machine. The total number of MPI +tasks used by LAMMPS (one or multiple per compute node) is set in the +usual manner via the mpirun or mpiexec commands, and is independent of +Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and +-npernode switches. Ditto for MPICH via -np and -ppn. [Running on a multi-core CPU:] @@ -135,8 +141,9 @@ mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre -To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command. -You must use the "-k on" "command-line +To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk +kokkos" "command-line switches"_Section_start.html#start_7 in your +mpirun command. You must use the "-k on" "command-line switch"_Section_start.html#start_7 to enable the KOKKOS package. It takes additional arguments for hardware settings appropriate to your system. Those arguments are "documented @@ -144,32 +151,33 @@ here"_Section_start.html#start_7. For OpenMP use: -k on t Nt :pre -The "t Nt" option specifies how many OpenMP threads per MPI -task to use with a node. The default is Nt = 1, which is MPI-only mode. -Note that the product of MPI tasks * OpenMP -threads/task should not exceed the physical number of cores (on a -node), otherwise performance will suffer. If hyperthreading is enabled, then -the product of MPI tasks * OpenMP threads/task should not exceed the -physical number of cores * hardware threads. -The "-k on" switch also issues a "package kokkos" command (with no -additional arguments) which sets various KOKKOS options to default -values, as discussed on the "package"_package.html command doc page. - -The "-sf kk" "command-line switch"_Section_start.html#start_7 -will automatically append the "/kk" suffix to styles that support it. -In this manner no modification to the input script is needed. Alternatively, -one can run with the KOKKOS package by editing the input script as described below. - -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both +The "t Nt" option specifies how many OpenMP threads per MPI task to +use with a node. The default is Nt = 1, which is MPI-only mode. Note +that the product of MPI tasks * OpenMP threads/task should not exceed +the physical number of cores (on a node), otherwise performance will +suffer. If hyperthreading is enabled, then the product of MPI tasks * +OpenMP threads/task should not exceed the physical number of cores * +hardware threads. The "-k on" switch also issues a "package kokkos" +command (with no additional arguments) which sets various KOKKOS +options to default values, as discussed on the "package"_package.html +command doc page. + +The "-sf kk" "command-line switch"_Section_start.html#start_7 will +automatically append the "/kk" suffix to styles that support it. In +this manner no modification to the input script is +needed. Alternatively, one can run with the KOKKOS package by editing +the input script as described below. + +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both pairwise and bonded interactions. However, when running on CPUs, it will typically be faster to use "half" neighbor lists and set the Newton flag to "on", just as is the case for non-accelerated pair -styles. It can also be faster to use non-threaded communication. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: +styles. It can also be faster to use non-threaded communication. Use +the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to +change the default "package kokkos"_package.html options. See its doc +page for details and default settings. Experimenting with its options +can provide a speed-up for specific calculations. For example: mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj # Newton on, Half neighbor list, non-threaded comm :pre @@ -178,9 +186,9 @@ script, it can also override the Newton flag defaults. [Core and Thread Affinity:] -When using multi-threading, it is important for -performance to bind both MPI tasks to physical cores, and threads to -physical cores, so they do not migrate during a simulation. +When using multi-threading, it is important for performance to bind +both MPI tasks to physical cores, and threads to physical cores, so +they do not migrate during a simulation. If you are not certain MPI tasks are being bound (check the defaults for your MPI installation), binding can be forced with these flags: @@ -191,24 +199,24 @@ Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... : For binding threads with KOKKOS OpenMP, use thread affinity environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or later, intel 12 or later) setting the environment variable -OMP_PROC_BIND=true should be sufficient. In general, for best performance -with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads. -For binding threads with the -KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option -as described below. +OMP_PROC_BIND=true should be sufficient. In general, for best +performance with OpenMP 4.0 or better set OMP_PROC_BIND=spread and +OMP_PLACES=threads. For binding threads with the KOKKOS pthreads +option, compile LAMMPS the KOKKOS HWLOC=yes option as described below. [Running on Knight's Landing (KNL) Intel Xeon Phi:] -Here is a quick overview of how to use the KOKKOS package -for the Intel Knight's Landing (KNL) Xeon Phi: +Here is a quick overview of how to use the KOKKOS package for the +Intel Knight's Landing (KNL) Xeon Phi: -KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores -are reserved for the OS, and only 64 or 66 cores are used. Each core -has 4 hyperthreads,so there are effectively N = 256 (4*64) or -N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit, -otherwise performance will suffer. Note that with the KOKKOS package you do not need to -specify how many KNLs there are per node; each -KNL is simply treated as running some number of MPI tasks. +KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores are +reserved for the OS, and only 64 or 66 cores are used. Each core has 4 +hyperthreads,so there are effectively N = 256 (4*64) or N = 264 (4*66) +cores to run on. The product of MPI tasks * OpenMP threads/task should +not exceed this limit, otherwise performance will suffer. Note that +with the KOKKOS package you do not need to specify how many KNLs there +are per node; each KNL is simply treated as running some number of MPI +tasks. Examples of mpirun commands that follow these rules are shown below. @@ -223,57 +231,60 @@ tasks/node. The "-k on t Nt" command-line switch sets the number of threads/task as Nt. The product of these two values should be N, i.e. 256 or 264. -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both -pairwise and bonded interactions. When running on KNL, this -will typically be best for pair-wise potentials. For manybody potentials, -using "half" neighbor lists and setting the -Newton flag to "on" may be faster. It can also be faster to use non-threaded communication. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both +pairwise and bonded interactions. When running on KNL, this will +typically be best for pair-wise potentials. For manybody potentials, +using "half" neighbor lists and setting the Newton flag to "on" may be +faster. It can also be faster to use non-threaded communication. Use +the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to +change the default "package kokkos"_package.html options. See its doc +page for details and default settings. Experimenting with its options +can provide a speed-up for specific calculations. For example: mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj # Newton off, full neighbor list, non-threaded comm mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax # Newton on, half neighbor list, non-threaded comm :pre -NOTE: MPI tasks and threads should be bound to cores as described above for CPUs. +NOTE: MPI tasks and threads should be bound to cores as described +above for CPUs. -NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your -system must be configured to use them in "native" mode, not "offload" -mode like the USER-INTEL package supports. +NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors +such as Knight's Corner (KNC), your system must be configured to use +them in "native" mode, not "offload" mode like the USER-INTEL package +supports. [Running on GPUs:] -Use the "-k" "command-line switch"_Section_commands.html#start_7 to -specify the number of GPUs per node. Typically the -np setting -of the mpirun command should set the number of MPI -tasks/node to be equal to the # of physical GPUs on the node. -You can assign multiple MPI tasks to the same GPU with the -KOKKOS package, but this is usually only faster if significant portions -of the input script have not been ported to use Kokkos. Using CUDA MPS -is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number -of physical cores/node, then the number of MPI tasks/node should not exceed N. +Use the "-k" "command-line switch"_Section_start.html#start_7 to +specify the number of GPUs per node. Typically the -np setting of the +mpirun command should set the number of MPI tasks/node to be equal to +the # of physical GPUs on the node. You can assign multiple MPI tasks +to the same GPU with the KOKKOS package, but this is usually only +faster if significant portions of the input script have not been +ported to use Kokkos. Using CUDA MPS is recommended in this +scenario. As above for multi-core CPUs (and no GPU), if N is the +number of physical cores/node, then the number of MPI tasks/node +should not exceed N. -k on g Ng :pre -Here are examples of how to use the KOKKOS package for GPUs, -assuming one or more nodes, each with two GPUs: +Here are examples of how to use the KOKKOS package for GPUs, assuming +one or more nodes, each with two GPUs: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 2 GPUs/node mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre -NOTE: The default for the "package kokkos"_package.html command is -to use "full" neighbor lists and set the Newton flag to "off" for both +NOTE: The default for the "package kokkos"_package.html command is to +use "full" neighbor lists and set the Newton flag to "off" for both pairwise and bonded interactions, along with threaded communication. -When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs, -using "half" neighbor lists and setting the -Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize -equal to the ghost atom cutoff will give speedup. -Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to -change the default "package kokkos"_package.html -options. See its doc page for details and default settings. Experimenting with -its options can provide a speed-up for specific calculations. For example: +When running on Maxwell or Kepler GPUs, this will typically be +best. For Pascal GPUs, using "half" neighbor lists and setting the +Newton flag to "on" may be faster. For many pair styles, setting the +neighbor binsize equal to the ghost atom cutoff will give speedup. +Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 +to change the default "package kokkos"_package.html options. See its +doc page for details and default settings. Experimenting with its +options can provide a speed-up for specific calculations. For example: mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj # Set binsize = neighbor ghost cutoff mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre @@ -301,8 +312,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be duplicated by adding the "package kokkos"_package.html or "suffix kk"_suffix.html commands to your input script. -The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting -appropriate thread are the same. +The discussion above for building LAMMPS with the KOKKOS package, the +mpirun/mpiexec command, and setting appropriate thread are the same. You must still use the "-k on" "command-line switch"_Section_start.html#start_7 to enable the KOKKOS package, and @@ -320,17 +331,19 @@ wish to change any of its option defaults, as set by the "-k on" [Using OpenMP threading and CUDA together (experimental):] -With the KOKKOS package, both OpenMP multi-threading and GPUs can be used -together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must -include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi +With the KOKKOS package, both OpenMP multi-threading and GPUs can be +used together in a few special cases. In the Makefile, the +KOKKOS_DEVICES variable must include both "Cuda" and "OpenMP", as is +the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi KOKKOS_DEVICES=Cuda,OpenMP :pre The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA, -using the "-sf kk" in the command line gives the default CUDA version everywhere. -However, if the "/kk/host" suffix is added to a specific style in the input -script, the Kokkos OpenMP (CPU) version of that specific style will be used instead. -Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng" +using the "-sf kk" in the command line gives the default CUDA version +everywhere. However, if the "/kk/host" suffix is added to a specific +style in the input script, the Kokkos OpenMP (CPU) version of that +specific style will be used instead. Set the number of OpenMP threads +as "t Nt" and the number of GPUs as "g Ng" -k on t Nt g Ng :pre @@ -338,18 +351,20 @@ For example, the command to run with 1 GPU and 8 OpenMP threads is then: mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre -Conversely, if the "-sf kk/host" is used in the command line and then the -"/kk" or "/kk/device" suffix is added to a specific style in your input script, -then only that specific style will run on the GPU while everything else will -run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU -styles will NOT overlap, except for a special case: - -A kspace style and/or molecular topology (bonds, angles, etc.) running on -the host CPU can overlap with a pair style running on the GPU. First compile -with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile. -Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc. -in the input file and the "kk" suffix (equal to "kk/device") on the command line. -Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" +Conversely, if the "-sf kk/host" is used in the command line and then +the "/kk" or "/kk/device" suffix is added to a specific style in your +input script, then only that specific style will run on the GPU while +everything else will run on the CPU in OpenMP mode. Note that the +execution of the CPU and GPU styles will NOT overlap, except for a +special case: + +A kspace style and/or molecular topology (bonds, angles, etc.) running +on the host CPU can overlap with a pair style running on the +GPU. First compile with "--default-stream per-thread" added to CCFLAGS +in the Kokkos CUDA Makefile. Then explicitly use the "/kk/host" +suffix for kspace and bonds, angles, etc. in the input file and the +"kk" suffix (equal to "kk/device") on the command line. Also make +sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1" so CPU/GPU overlap can occur. [Speed-ups to expect:] @@ -386,9 +401,8 @@ hardware. There are other allowed options when building with the KOKKOS package. As above, they can be set either as variables on the make command line or in Makefile.machine. This is the full list of options, including -those discussed above. Each takes a value shown below. The -default value is listed, which is set in the -/lib/kokkos/Makefile.kokkos file. +those discussed above. Each takes a value shown below. The default +value is listed, which is set in the /lib/kokkos/Makefile.kokkos file. KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP} KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none} @@ -434,8 +448,8 @@ migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP provides alternative methods via environment variables for binding -threads to hardware cores. More info on binding threads to cores is -given in "Section 5.3"_Section_accelerate.html#acc_3. +threads to hardware cores. More info on binding threads to cores is +given on the "Speed omp"_Speed_omp.html doc page. KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism on most Unix platforms. This library is not available on all @@ -446,13 +460,14 @@ within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time debugging information that can be useful. It also enables runtime bounds checking on Kokkos data structures. -KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS. +KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when +building LAMMPS. -KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled -with the {enable_lambda} option when using GPUs. +KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS +package must be compiled with the {enable_lambda} option when using +GPUs. [Restrictions:] -Currently, there are no precision options with the KOKKOS -package. All compilation and computation is performed in double -precision. +Currently, there are no precision options with the KOKKOS package. All +compilation and computation is performed in double precision. diff --git a/doc/src/Speed_measure.txt b/doc/src/Speed_measure.txt new file mode 100644 index 0000000000000000000000000000000000000000..78dc220088d3873b241aae6237b84b8426f03776 --- /dev/null +++ b/doc/src/Speed_measure.txt @@ -0,0 +1,55 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Measuring performance :h3 + +Before trying to make your simulation run faster, you should +understand how it currently performs and where the bottlenecks are. + +The best way to do this is run the your system (actual number of +atoms) for a modest number of timesteps (say 100 steps) on several +different processor counts, including a single processor if possible. +Do this for an equilibrium version of your system, so that the +100-step timings are representative of a much longer run. There is +typically no need to run for 1000s of timesteps to get accurate +timings; you can simply extrapolate from short runs. + +For the set of runs, look at the timing data printed to the screen and +log file at the end of each LAMMPS run. "This +section"_Section_start.html#start_7 of the manual has an overview. + +Running on one (or a few processors) should give a good estimate of +the serial performance and what portions of the timestep are taking +the most time. Running the same problem on a few different processor +counts should give an estimate of parallel scalability. I.e. if the +simulation runs 16x faster on 16 processors, its 100% parallel +efficient; if it runs 8x faster on 16 processors, it's 50% efficient. + +The most important data to look at in the timing info is the timing +breakdown and relative percentages. For example, trying different +options for speeding up the long-range solvers will have little impact +if they only consume 10% of the run time. If the pairwise time is +dominating, you may want to look at GPU or OMP versions of the pair +style, as discussed below. Comparing how the percentages change as +you increase the processor count gives you a sense of how different +operations within the timestep are scaling. Note that if you are +running with a Kspace solver, there is additional output on the +breakdown of the Kspace time. For PPPM, this includes the fraction +spent on FFTs, which can be communication intensive. + +Another important detail in the timing info are the histograms of +atoms counts and neighbor counts. If these vary widely across +processors, you have a load-imbalance issue. This often results in +inaccurate relative timing data, because processors have to wait when +communication occurs for other processors to catch up. Thus the +reported times for "Communication" or "Other" may be higher than they +really are, due to load-imbalance. If this is an issue, you can +uncomment the MPI_Barrier() lines in src/timer.cpp, and recompile +LAMMPS, to obtain synchronized timings. + diff --git a/doc/src/accelerate_omp.txt b/doc/src/Speed_omp.txt similarity index 95% rename from doc/src/accelerate_omp.txt rename to doc/src/Speed_omp.txt index fa7bef1a520bd867b4d3cf610d50b5ea8614c865..bcfc406902d0947e2c6d9e0426b2fe8d7406dda3 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/Speed_omp.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section 5 overview"_Section_accelerate.html - -5.3.4 USER-OMP package :h5 +USER-OMP package :h3 The USER-OMP package was developed by Axel Kohlmeyer at Temple University. It provides multi-threaded versions of most pair styles, @@ -39,7 +37,8 @@ each MPI task running on a CPU. The lines above illustrate how to include/build with the USER-OMP package in two steps, using the "make" command. Or how to do it with -one command as described in "Section 4"_Section_packages.html of the manual. +one command as described on the "Packages +details"_Packages_details.html#USER-OMP doc page. Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must include "-fopenmp". Likewise, if you use an Intel compiler, the @@ -100,7 +99,7 @@ task, versus running standard LAMMPS with its standard un-accelerated styles (in serial or all-MPI parallelization with 1 task/core). This is because many of the USER-OMP styles contain similar optimizations to those used in the OPT package, described in "Section -5.3.5"_accelerate_opt.html. +5.3.5"_Speed_opt.html. With multiple threads/task, the optimal choice of number of MPI tasks/node and OpenMP threads/task can vary a lot and should always be diff --git a/doc/src/accelerate_opt.txt b/doc/src/Speed_opt.txt similarity index 85% rename from doc/src/accelerate_opt.txt rename to doc/src/Speed_opt.txt index 845264b5227ca31493cb582eac91ab5c216427ae..676a5d84182e90ea4f832c3938bab51e5a3011dc 100644 --- a/doc/src/accelerate_opt.txt +++ b/doc/src/Speed_opt.txt @@ -1,15 +1,13 @@ -"Previous Section"_Section_packages.html - "LAMMPS WWW Site"_lws - -"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -"Return to Section accelerate overview"_Section_accelerate.html - -5.3.5 OPT package :h5 +OPT package :h3 The OPT package was developed by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge @@ -34,7 +32,8 @@ None. The lines above illustrate how to build LAMMPS with the OPT package in two steps, using the "make" command. Or how to do it with one command -as described in "Section 4"_Section_packages.html of the manual. +as described on the "Packages details"_Packages_details.html#OPT doc +page. Note that if you use an Intel compiler to build with the OPT package, the CCFLAGS setting in your Makefile.machine must include "-restrict". diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt new file mode 100644 index 0000000000000000000000000000000000000000..f463ed91b85d28cf495db638a401f7c52a5326fe --- /dev/null +++ b/doc/src/Speed_packages.txt @@ -0,0 +1,192 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +Accelerator packages :h3 + +Accelerated versions of various "pair_style"_pair_style.html, +"fixes"_fix.html, "computes"_compute.html, and other commands have +been added to LAMMPS, which will typically run faster than the +standard non-accelerated versions. Some require appropriate hardware +to be present on your system, e.g. GPUs or Intel Xeon Phi +coprocessors. + +All of these commands are in packages provided with LAMMPS. An +overview of packages is give on the "Packages"_Packages.html doc +pages. + +These are the accelerator packages currently in LAMMPS, either as +standard or user packages: + +"GPU Package"_Speed_gpu.html : for NVIDIA GPUs as well as OpenCL support +"USER-INTEL Package"_Speed_intel.html : for Intel CPUs and Intel Xeon Phi +"KOKKOS Package"_Speed_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading +"USER-OMP Package"_Speed_omp.html : for OpenMP threading and generic CPU optimizations +"OPT Package"_Speed_opt.html : generic CPU optimizations :tb(s=:) + + + +Inverting this list, LAMMPS currently has acceleration support for +three kinds of hardware, via the listed packages: + +Many-core CPUs : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html, "USER-OMP"_Speed_omp.html, "OPT"_Speed_opt.html packages +NVIDIA GPUs : "GPU"_Speed_gpu.html, "KOKKOS"_Speed_kokkos.html packages +Intel Phi : "USER-INTEL"_Speed_intel.html, "KOKKOS"_Speed_kokkos.html packages :tb(s=:) + +Which package is fastest for your hardware may depend on the size +problem you are running and what commands (accelerated and +non-accelerated) are invoked by your input script. While these doc +pages include performance guidelines, there is no substitute for +trying out the different packages appropriate to your hardware. + +Any accelerated style has the same name as the corresponding standard +style, except that a suffix is appended. Otherwise, the syntax for +the command that uses the style is identical, their functionality is +the same, and the numerical results it produces should also be the +same, except for precision and round-off effects. + +For example, all of these styles are accelerated variants of the +Lennard-Jones "pair_style lj/cut"_pair_lj.html: + +"pair_style lj/cut/gpu"_pair_lj.html +"pair_style lj/cut/intel"_pair_lj.html +"pair_style lj/cut/kk"_pair_lj.html +"pair_style lj/cut/omp"_pair_lj.html +"pair_style lj/cut/opt"_pair_lj.html :ul + +To see what accelerate styles are currently available for a particular +style, find the style name in the "Commands_all"_Commands_all.html +style pages (fix,compute,pair,etc) and see what suffixes are listed +(g,i,k,o,t) with it. The doc pages for individual commands +(e.g. "pair lj/cut"_pair_lj.html or "fix nve"_fix_nve.html) also list +any accelerated variants available for that style. + +To use an accelerator package in LAMMPS, and one or more of the styles +it provides, follow these general steps. Details vary from package to +package and are explained in the individual accelerator doc pages, +listed above: + +build the accelerator library | + only for GPU package | +install the accelerator package | + make yes-opt, make yes-user-intel, etc | +add compile/link flags to Makefile.machine in src/MAKE | + only for USER-INTEL, KOKKOS, USER-OMP, OPT packages | +re-build LAMMPS | + make machine | +prepare and test a regular LAMMPS simulation | + lmp_machine -in in.script; mpirun -np 32 lmp_machine -in in.script | +enable specific accelerator support via '-k on' "command-line switch"_Section_start.html#start_6, | + only needed for KOKKOS package | +set any needed options for the package via "-pk" "command-line switch"_Section_start.html#start_6 or "package"_package.html command, | + only if defaults need to be changed | +use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu +:tb(c=2,s=|) + +Note that the first 4 steps can be done as a single command with +suitable make command invocations. This is discussed on the +"Packages"_Packages.html doc pages, and its use is illustrated in the +individual accelerator sections. Typically these steps only need to +be done once, to create an executable that uses one or more +accelerator packages. + +The last 4 steps can all be done from the command-line when LAMMPS is +launched, without changing your input script, as illustrated in the +individual accelerator sections. Or you can add +"package"_package.html and "suffix"_suffix.html commands to your input +script. + +NOTE: With a few exceptions, you can build a single LAMMPS executable +with all its accelerator packages installed. Note however that the +USER-INTEL and KOKKOS packages require you to choose one of their +hardware options when building for a specific platform. I.e. CPU or +Phi option for the USER-INTEL package. Or the OpenMP, Cuda, or Phi +option for the KOKKOS package. + +These are the exceptions. You cannot build a single executable with: + +both the USER-INTEL Phi and KOKKOS Phi options +the USER-INTEL Phi or Kokkos Phi option, and the GPU package :ul + +See the examples/accelerate/README and make.list files for sample +Make.py commands that build LAMMPS with any or all of the accelerator +packages. As an example, here is a command that builds with all the +GPU related packages installed (GPU, KOKKOS with Cuda), including +settings to build the needed auxiliary GPU libraries for Kepler GPUs: + +Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi \ + -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi :pre + +The examples/accelerate directory also has input scripts that can be +used with all of the accelerator packages. See its README file for +details. + +Likewise, the bench directory has FERMI and KEPLER and PHI +sub-directories with Make.py commands and input scripts for using all +the accelerator packages on various machines. See the README files in +those dirs. + +As mentioned above, the "Benchmark +page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives +performance results for the various accelerator packages for several +of the standard LAMMPS benchmark problems, as a function of problem +size and number of compute nodes, on different hardware platforms. + +Here is a brief summary of what the various packages provide. Details +are in the individual accelerator sections. + +Styles with a "gpu" suffix are part of the GPU package, and can be run +on NVIDIA GPUs. The speed-up on a GPU depends on a variety of +factors, discussed in the accelerator sections. :ulb,l + +Styles with an "intel" suffix are part of the USER-INTEL +package. These styles support vectorized single and mixed precision +calculations, in addition to full double precision. In extreme cases, +this can provide speedups over 3.5x on CPUs. The package also +supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) +coprocessors. This can result in additional speedup over 2x depending +on the hardware configuration. :l + +Styles with a "kk" suffix are part of the KOKKOS package, and can be +run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel +Xeon Phi in "native" mode. The speed-up depends on a variety of +factors, as discussed on the KOKKOS accelerator page. :l + +Styles with an "omp" suffix are part of the USER-OMP package and allow +a pair-style to be run in multi-threaded mode using OpenMP. This can +be useful on nodes with high-core counts when using less MPI processes +than cores is advantageous, e.g. when running with PPPM so that FFTs +are run on fewer MPI processors or when the many MPI tasks would +overload the available bandwidth for communication. :l + +Styles with an "opt" suffix are part of the OPT package and typically +speed-up the pairwise calculations of your simulation by 5-25% on a +CPU. :l +:ule + +The individual accelerator package doc pages explain: + +what hardware and software the accelerated package requires +how to build LAMMPS with the accelerated package +how to run with the accelerated package either via command-line switches or modifying the input script +speed-ups to expect +guidelines for best performance +restrictions :ul + diff --git a/doc/src/Speed_tips.txt b/doc/src/Speed_tips.txt new file mode 100644 index 0000000000000000000000000000000000000000..7c950779d5e4864db0802e90369c6acaaf8b6d36 --- /dev/null +++ b/doc/src/Speed_tips.txt @@ -0,0 +1,63 @@ +"Higher level section"_Speed.html - "LAMMPS WWW Site"_lws - "LAMMPS +Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +General tips :h3 + +NOTE: this section 5.2 is still a work in progress + +Here is a list of general ideas for improving simulation performance. +Most of them are only applicable to certain models and certain +bottlenecks in the current performance, so let the timing data you +generate be your guide. It is hard, if not impossible, to predict how +much difference these options will make, since it is a function of +problem size, number of processors used, and your machine. There is +no substitute for identifying performance bottlenecks, and trying out +various options. + +make individual pages for these, or one for PPPM +one for timestepping, etc +one for balancing +or proc layout + +rRESPA +2-FFT PPPM +Staggered PPPM +single vs double PPPM +partial charge PPPM +verlet/split run style +processor command for proc layout and numa layout +load-balancing: balance and fix balance :ul + +2-FFT PPPM, also called {analytic differentiation} or {ad} PPPM, uses +2 FFTs instead of the 4 FFTs used by the default {ik differentiation} +PPPM. However, 2-FFT PPPM also requires a slightly larger mesh size to +achieve the same accuracy as 4-FFT PPPM. For problems where the FFT +cost is the performance bottleneck (typically large problems running +on many processors), 2-FFT PPPM may be faster than 4-FFT PPPM. + +Staggered PPPM performs calculations using two different meshes, one +shifted slightly with respect to the other. This can reduce force +aliasing errors and increase the accuracy of the method, but also +doubles the amount of work required. For high relative accuracy, using +staggered PPPM allows one to half the mesh size in each dimension as +compared to regular PPPM, which can give around a 4x speedup in the +kspace time. However, for low relative accuracy, using staggered PPPM +gives little benefit and can be up to 2x slower in the kspace +time. For example, the rhodopsin benchmark was run on a single +processor, and results for kspace time vs. relative accuracy for the +different methods are shown in the figure below. For this system, +staggered PPPM (using ik differentiation) becomes useful when using a +relative accuracy of slightly greater than 1e-5 and above. + +:c,image(JPG/rhodo_staggered.jpg) + +NOTE: Using staggered PPPM may not give the same increase in accuracy +of energy and pressure as it does in forces, so some caution must be +used if energy and/or pressure are quantities of interest, such as +when using a barostat. diff --git a/doc/src/Section_tools.txt b/doc/src/Tools.txt similarity index 87% rename from doc/src/Section_tools.txt rename to doc/src/Tools.txt index 7cc07cbec55a5e7c4f3545c623875be8cc6919cc..85ee531cfd905371ebef6f17db26713c2a496d6c 100644 --- a/doc/src/Section_tools.txt +++ b/doc/src/Tools.txt @@ -1,40 +1,41 @@ -"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS +"Previous Section"_Examples.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next -Section"_Section_modify.html :c +Section"_Modify.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line -9. Additional tools :h2 +Auxiliary tools :h2 LAMMPS is designed to be a computational kernel for performing molecular dynamics computations. Additional pre- and post-processing -steps are often necessary to setup and analyze a simulation. A -list of such tools can be found on the LAMMPS home page -at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html +steps are often necessary to setup and analyze a simulation. A list +of such tools can be found on the "LAMMPS webpage"_lws at these links: -A few additional tools are provided with the LAMMPS distribution -and are described in this section. +"Pre/Post processing"_http://lammps.sandia.gov/prepost.html +"Offsite LAMMPS packages & tools"_http://lammps.sandia.gov/offsite.html +"Pizza.py toolkit"_pizza :ul -Our group has also written and released a separate toolkit called -"Pizza.py"_pizza which provides tools for doing setup, analysis, -plotting, and visualization for LAMMPS simulations. Pizza.py is -written in "Python"_python and is available for download from "the -Pizza.py WWW site"_pizza. +The last link for "Pizza.py"_pizza is a Python-based tool developed at +Sandia which provides tools for doing setup, analysis, plotting, and +visualization for LAMMPS simulations. -:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html) +:link(pizza,http://pizza.sandia.gov) :link(python,http://www.python.org) +Additional tools included in the LAMMPS distribution are described on +this page. + Note that many users write their own setup or analysis tools or use other existing codes and convert their output to a LAMMPS input format or vice versa. The tools listed here are included in the LAMMPS distribution as examples of auxiliary tools. Some of them are not -actively supported by Sandia, as they were contributed by LAMMPS -users. If you have problems using them, we can direct you to the -authors. +actively supported by the LAMMPS developers, as they were contributed +by LAMMPS users. If you have problems using them, we can direct you +to the authors. The source code for each of these codes is in the tools sub-directory of the LAMMPS distribution. There is a Makefile (which you may need @@ -71,11 +72,12 @@ own sub-directories with their own Makefiles and/or README files. "reax"_#reax_tool "smd"_#smd "vim"_#vim -"xmgrace"_#xmgrace +"xmgrace"_#xmgrace :ul +:line :line -amber2lmp tool :h3,link(amber) +amber2lmp tool :h4,link(amber) The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the @@ -90,7 +92,7 @@ necessary modifications yourself. :line -binary2txt tool :h3,link(binary) +binary2txt tool :h4,link(binary) The file binary2txt.cpp converts one or more binary LAMMPS dump file into ASCII text files. The syntax for running the tool is @@ -103,7 +105,7 @@ since binary files are not compatible across all platforms. :line -ch2lmp tool :h3,link(charmm) +ch2lmp tool :h4,link(charmm) The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS. @@ -128,7 +130,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London. :line -chain tool :h3,link(chain) +chain tool :h4,link(chain) The file chain.f creates a LAMMPS data file containing bead-spring polymer chains and/or monomer solvent atoms. It uses a text file @@ -140,12 +142,12 @@ The syntax for running the tool is chain < def.chain > data.file :pre See the def.chain or def.chain.ab files in the tools directory for -examples of definition files. This tool was used to create the -system for the "chain benchmark"_Section_perf.html. +examples of definition files. This tool was used to create the system +for the "chain benchmark"_Speed_bench.html. :line -colvars tools :h3,link(colvars) +colvars tools :h4,link(colvars) The colvars directory contains a collection of tools for postprocessing data produced by the colvars collective variable library. @@ -167,7 +169,7 @@ gmail.com) at ICTP, Italy. :line -createatoms tool :h3,link(createatoms) +createatoms tool :h4,link(createatoms) The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal @@ -180,7 +182,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov. :line -doxygen tool :h3,link(doxygen) +doxygen tool :h4,link(doxygen) The tools/doxygen directory contains a shell script called doxygen.sh which can generate a call graph and API lists using @@ -192,7 +194,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com. :line -drude tool :h3,link(drude) +drude tool :h4,link(drude) The tools/drude directory contains a Python script called polarizer.py which can add Drude oscillators to a LAMMPS @@ -205,7 +207,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr :line -eam database tool :h3,link(eamdb) +eam database tool :h4,link(eamdb) The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 @@ -221,7 +223,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, :line -eam generate tool :h3,link(eamgn) +eam generate tool :h4,link(eamgn) The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated "embedded atom @@ -234,7 +236,7 @@ The source files and potentials were provided by Gerolf Ziegenhain :line -eff tool :h3,link(eff) +eff tool :h4,link(eff) The tools/eff directory contains various scripts for generating structures and post-processing output for simulations using the @@ -245,18 +247,18 @@ These tools were provided by Andres Jaramillo-Botero at CalTech :line -emacs tool :h3,link(emacs) +emacs tool :h4,link(emacs) -The tools/emacs directory contains a Lips add-on file for Emacs that -enables a lammps-mode for editing of input scripts when using Emacs, -with various highlighting options setup. +The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs +that enables a lammps-mode for editing input scripts when using GNU Emacs, +with various highlighting options set up. These tools were provided by Aidan Thompson at Sandia (athomps at sandia.gov). :line -fep tool :h3,link(fep) +fep tool :h4,link(fep) The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation @@ -269,7 +271,7 @@ See README file in the tools/fep directory. :line -i-pi tool :h3,link(ipi) +i-pi tool :h4,link(ipi) The tools/i-pi directory contains a version of the i-PI package, with all the LAMMPS-unrelated files removed. It is provided so that it can @@ -286,7 +288,7 @@ calculations with LAMMPS. :line -ipp tool :h3,link(ipp) +ipp tool :h4,link(ipp) The tools/ipp directory contains a Perl script ipp which can be used to facilitate the creation of a complicated file (say, a lammps input @@ -300,7 +302,7 @@ tools/createatoms tool's input file. :line -kate tool :h3,link(kate) +kate tool :h4,link(kate) The file in the tools/kate directory is an add-on to the Kate editor in the KDE suite that allow syntax highlighting of LAMMPS input @@ -311,7 +313,7 @@ The file was provided by Alessandro Luigi Sellerio :line -lmp2arc tool :h3,link(arc) +lmp2arc tool :h4,link(arc) The lmp2arc sub-directory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly @@ -327,7 +329,7 @@ Greathouse at Sandia (jagreat at sandia.gov). :line -lmp2cfg tool :h3,link(cfg) +lmp2cfg tool :h4,link(cfg) The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the @@ -338,7 +340,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). :line -matlab tool :h3,link(matlab) +matlab tool :h4,link(matlab) The matlab sub-directory contains several "MATLAB"_matlabhome scripts for post-processing LAMMPS output. The scripts include readers for log @@ -356,7 +358,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ :line -micelle2d tool :h3,link(micelle) +micelle2d tool :h4,link(micelle) The file micelle2d.f creates a LAMMPS data file containing short lipid chains in a monomer solution. It uses a text file containing lipid @@ -369,11 +371,11 @@ micelle2d < def.micelle2d > data.file :pre See the def.micelle2d file in the tools directory for an example of a definition file. This tool was used to create the system for the -"micelle example"_Section_example.html. +"micelle example"_Examples.html. :line -moltemplate tool :h3,link(moltemplate) +moltemplate tool :h4,link(moltemplate) The moltemplate sub-directory contains a Python-based tool for building molecular systems based on a text-file description, and @@ -387,7 +389,7 @@ supports it. It has its own WWW page at :line -msi2lmp tool :h3,link(msi) +msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS template input and data files from BIOVIA's Materias Studio files (formerly Accelrys' @@ -404,7 +406,7 @@ See the README file in the tools/msi2lmp folder for more information. :line -phonon tool :h3,link(phonon) +phonon tool :h4,link(phonon) The phonon sub-directory contains a post-processing tool useful for analyzing the output of the "fix phonon"_fix_phonon.html command in @@ -419,7 +421,7 @@ University. :line -polybond tool :h3,link(polybond) +polybond tool :h4,link(polybond) The polybond sub-directory contains a Python-based tool useful for performing "programmable polymer bonding". The Python file @@ -433,7 +435,7 @@ This tool was written by Zachary Kraus at Georgia Tech. :line -pymol_asphere tool :h3,link(pymol) +pymol_asphere tool :h4,link(pymol) The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal @@ -451,7 +453,7 @@ This tool was written by Mike Brown at Sandia. :line -python tool :h3,link(pythontools) +python tool :h4,link(pythontools) The python sub-directory contains several Python scripts that perform common LAMMPS post-processing tasks, such as: @@ -467,7 +469,7 @@ README for more info on Pizza.py and how to use these scripts. :line -reax tool :h3,link(reax_tool) +reax tool :h4,link(reax_tool) The reax sub-directory contains stand-alond codes that can post-process the output of the "fix reax/bonds"_fix_reax_bonds.html @@ -478,7 +480,7 @@ These tools were written by Aidan Thompson at Sandia. :line -smd tool :h3,link(smd) +smd tool :h4,link(smd) The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output @@ -494,7 +496,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). :line -vim tool :h3,link(vim) +vim tool :h4,link(vim) The files in the tools/vim directory are add-ons to the VIM editor that allow easier editing of LAMMPS input scripts. See the README.txt @@ -505,7 +507,7 @@ ziegenhain.com) :line -xmgrace tool :h3,link(xmgrace) +xmgrace tool :h4,link(xmgrace) The files in the tools/xmgrace directory can be used to plot the thermodynamic data in LAMMPS log files via the xmgrace plotting @@ -517,4 +519,3 @@ simulation. See the README file for details. These files were provided by Vikas Varshney (vv0210 at gmail.com) - diff --git a/doc/src/angle_charmm.txt b/doc/src/angle_charmm.txt index 7ff7ef8fd417c1118951adcbc0f89b4c7d08540a..f72f0862348328bbd5c62a11d42274bb4f4c14d3 100644 --- a/doc/src/angle_charmm.txt +++ b/doc/src/angle_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,10 +51,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index d4330139c963c12c53dc50aa2312eca93ce068e6..3e5445d3a3c17200bd5e548791bdbfbb31f4dcbe 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,10 +83,9 @@ same value from the Ea formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -98,8 +97,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt index 37298ba14591ca28fe4a45952ec5ed80551a8178..4c217bae7d3905298202c2d48592e1bb045e49ef 100644 --- a/doc/src/angle_coeff.txt +++ b/doc/src/angle_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles is on the "Commands bond"_Commands_bond.html#angle doc +page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index c0ce3c9301f735fc69fb1b239d30ddce3150c3b0..5a1fe91c834271bfe883e1b2d5a410f3bb148a23 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,10 +38,9 @@ K (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 7182ffecc849e1c581793add231af6ed1fa03d57..63a451b7631456aa21b870eadf5808e92b052ec9 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_cosine_delta.txt b/doc/src/angle_cosine_delta.txt index 830fd6db584a67bf7c93082b971e3abb383e69d2..b6ac0ed8181ad55b183ab59962e9502c2cd5ab93 100644 --- a/doc/src/angle_cosine_delta.txt +++ b/doc/src/angle_cosine_delta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,9 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_periodic.txt b/doc/src/angle_cosine_periodic.txt index b5c53b1b0fb5a81d8ab33d2ebbc8e2087fd26fab..c5b184e0b46b1e5b14efb8b1dd0477740c59ae19 100644 --- a/doc/src/angle_cosine_periodic.txt +++ b/doc/src/angle_cosine_periodic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -21,10 +21,10 @@ angle_coeff * 75.0 1 6 :pre [Description:] The {cosine/periodic} angle style uses the following potential, which -is commonly used in the "DREIDING"_Section_howto.html#howto_4 force -field, particularly for organometallic systems where {n} = 4 might be -used for an octahedral complex and {n} = 3 might be used for a -trigonal center: +is commonly used in the "DREIDING"_Howto_bioFF.html force field, +particularly for organometallic systems where {n} = 4 might be used +for an octahedral complex and {n} = 3 might be used for a trigonal +center: :c,image(Eqs/angle_cosine_periodic.jpg) @@ -51,10 +51,9 @@ geometry. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 6ed9fe2150b7d7bdcda19e55bc7ca852ceed4a88..90ac61fe23c9d45f595c579e937d55bdea284909 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,10 +41,9 @@ theta (angle) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_shift_exp.txt b/doc/src/angle_cosine_shift_exp.txt index 44a68c1087582357c0d2b27a98ba21184a582531..f1c4c93c425e0ce8f51d12e39dd34c9493bf0426 100644 --- a/doc/src/angle_cosine_shift_exp.txt +++ b/doc/src/angle_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,10 +53,9 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_cosine_squared.txt b/doc/src/angle_cosine_squared.txt index 065cdad5421bf816fd6cb600a023d265e4bbfff8..ba5fd9d4139a4f1142c287e121d3e3e7f002a6d4 100644 --- a/doc/src/angle_cosine_squared.txt +++ b/doc/src/angle_cosine_squared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,9 @@ internally. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_dipole.txt b/doc/src/angle_dipole.txt index d91f260d51b5d208c8a2d3a182c6fb17fbc0545c..c001d9d9206c743222357f1cdcb345934f9a9ead 100644 --- a/doc/src/angle_dipole.txt +++ b/doc/src/angle_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -71,10 +71,9 @@ gamma0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] @@ -96,16 +95,17 @@ USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_2_3 section for more info on packages. NOTE: In the "Angles" section of the data file, the atom ID 'j' -corresponding to the dipole to restrain must come before the atom ID -of the reference atom 'i'. A third atom ID 'k' must also be provided, -although 'k' is just a 'dummy' atom which can be any atom; it may be -useful to choose a convention (e.g., 'k'='i') and adhere to it. For -example, if ID=1 for the dipolar atom to restrain, and ID=2 for the -reference atom, the corresponding line in the "Angles" section of the -data file would read: X X 1 2 2 +defining the direction of the dipole vector to restrain must come +before the atom ID of the reference atom 'i'. A third atom ID 'k' must +also be provided to comply with the requirement of a valid angle +definition. This atom ID k should be chosen to be that of an atom +bonded to atom 'i' to avoid errors with "lost angle atoms" when running +in parallel. Since the LAMMPS code checks for valid angle definitions, +cannot use the same atom ID of either 'i' or 'j' (this was allowed +and recommended with older LAMMPS versions). The "newton" command for intramolecular interactions must be "on" -(which is the default). +(which is the default except when using some accelerator packages). This angle style should not be used with SHAKE. diff --git a/doc/src/angle_fourier.txt b/doc/src/angle_fourier.txt index da39e7cf326b43afce171e0005c1ef93cde2d5c8..e0e32c1eed001fa0d6ecb70f2f2c69542d39d6c0 100644 --- a/doc/src/angle_fourier.txt +++ b/doc/src/angle_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,10 +39,9 @@ C2 (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -54,8 +53,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_fourier_simple.txt b/doc/src/angle_fourier_simple.txt index 5adda6cb32f85a00310f5dc62ada7838e84d5715..3c50536a2cbc0720ec69c4a4b02cdefa15bd48ff 100644 --- a/doc/src/angle_fourier_simple.txt +++ b/doc/src/angle_fourier_simple.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,10 +38,9 @@ n (real) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -53,8 +52,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_harmonic.txt b/doc/src/angle_harmonic.txt index 4c74763964832d98cfcae9443866e2db4293ca64..76c7a491e8943aa7cdd720750394818fc7460b9e 100644 --- a/doc/src/angle_harmonic.txt +++ b/doc/src/angle_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_hybrid.txt b/doc/src/angle_hybrid.txt index bdd3707ccb80130284817d86a3eec53a698c2a2a..26469034212fe359d66a965e216543404b2d1020 100644 --- a/doc/src/angle_hybrid.txt +++ b/doc/src/angle_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_none.txt b/doc/src/angle_none.txt index a4a9b07c78e0bf7616ffe4d0ae0dc4ee8c4c9061..1eca5cbbeca786991139f7af6a44547f86d9d821 100644 --- a/doc/src/angle_none.txt +++ b/doc/src/angle_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_quartic.txt b/doc/src/angle_quartic.txt index f7640bdfbc0f75af1170cb551220d846df1529a0..294be330b1faab22d868d16b1a78edb048be928c 100644 --- a/doc/src/angle_quartic.txt +++ b/doc/src/angle_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,10 +45,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 0cc535e543f878bba02b38b9a5fa18e65da0aea2..9c5630ef3adf62b7688dbbd021555283536b2cff 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index f687e9286c40ac37a84566a5ab904c65fb3d30bf..63295faf264d8fee8b2a75fb32143ae710d02586 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,9 @@ the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the angle section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +angle styles are is on the "Commands bond"_Commands_bond.html#angle +doc page. "angle_style none"_angle_none.html - turn off angle interactions "angle_style zero"_angle_zero.html - topology but no interactions diff --git a/doc/src/angle_table.txt b/doc/src/angle_table.txt index bd6e167bd8f4dfccc84412c6597e1d2568a1daec..31ab532be17c95598c2b54f3a34becbf3c966120 100644 --- a/doc/src/angle_table.txt +++ b/doc/src/angle_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -124,10 +124,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -139,8 +138,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/angle_zero.txt b/doc/src/angle_zero.txt index b8e8ebf953c6b6ba40a583bef0508ab9992f3a6d..c6c1958ec8f35f7d1335b5a9cafaf36b96049c9a 100644 --- a/doc/src/angle_zero.txt +++ b/doc/src/angle_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 1dc0fa6bfb6410df5eaef9abf35cebb3a66749fd..c882d1b0ba0f43a916ee3a954a4b85e41d6c2007 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -3,7 +3,7 @@ Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 49d9dde79119dee8b7b4ab7efa43519ac9910744..abf05885a3ee3d96846af804d6ef1caaf42643c6 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -15,12 +15,12 @@ atom_style style args :pre style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \ {dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \ {full} or {line} or {meso} or {molecular} or {peri} or {smd} or \ - {sphere} or {tri} or {template} or {hybrid} :ulb,l + {sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l args = none for any style except the following {body} args = bstyle bstyle-args bstyle = style of body particles bstyle-args = additional arguments specific to the bstyle - see the "body"_body.html doc page for details + see the "Howto body"_Howto_body.html doc page for details {tdpd} arg = Nspecies Nspecies = # of chemical species {template} arg = template-ID @@ -38,6 +38,7 @@ atom_style full atom_style body nparticle 2 10 atom_style hybrid charge bond atom_style hybrid charge body nparticle 2 5 +atom_style spin atom_style template myMols atom_style tdpd 2 :pre @@ -89,6 +90,7 @@ quantities. {peri} | mass, volume | mesocopic Peridynamic models | {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | +{spin} | magnetic moment | system with magnetic particles | {template} | template index, template atom | small molecules with fixed topology | {tri} | corner points, angular momentum | rigid bodies | {wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|) @@ -104,9 +106,9 @@ output the custom values. All of the above styles define point particles, except the {sphere}, {ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See "Section -6.14"_Section_howto.html#howto_14 for an overview of using finite-size -particle models with LAMMPS. +{body} styles, which define finite-size particles. See the "Howto +spherical"_Howto_spherical.html doc page for an overview of using +finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a per-type basis, using the "mass"_mass.html command, The finite-size @@ -175,6 +177,9 @@ used for calculating the field variables (e.g. stress and deformation) and a contact radius for calculating repulsive forces which prevent individual physical bodies from penetrating each other. +For the {spin} style, a magnetic spin is associated to each atom. +Those spins have a norm (their magnetic moment) and a direction. + The {wavepacket} style is similar to {electron}, but the electrons may consist of several Gaussian wave packets, summed up with coefficients cs= (cs_re,cs_im). Each of the wave packets is treated as a separate @@ -219,15 +224,16 @@ the {bstyle} argument. Body particles can represent complex entities, such as surface meshes of discrete points, collections of sub-particles, deformable objects, etc. -The "body"_body.html doc page describes the body styles LAMMPS -currently supports, and provides more details as to the kind of body -particles they represent. For all styles, each body particle stores -moments of inertia and a quaternion 4-vector, so that its orientation -and position can be time integrated due to forces and torques. +The "Howto body"_Howto_body.html doc page describes the body styles +LAMMPS currently supports, and provides more details as to the kind of +body particles they represent. For all styles, each body particle +stores moments of inertia and a quaternion 4-vector, so that its +orientation and position can be time integrated due to forces and +torques. Note that there may be additional arguments required along with the {bstyle} specification, in the atom_style body command. These -arguments are described in the "body"_body.html doc page. +arguments are described on the "Howto body"_Howto_body.html doc page. :line @@ -250,16 +256,16 @@ with another molecular style that stores bond,angle,etc info on a per-atom basis. LAMMPS can be extended with new atom styles as well as new body -styles; see "this section"_Section_modify.html. +styles; see the "Modify"_Modify.html doc page. :line Styles with a {kk} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +run faster, depending on your available hardware, as discussed in on +the "Speed packages"_Speed_packages.html doc page. The accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. Note that other acceleration packages in LAMMPS, specifically the GPU, USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom @@ -274,8 +280,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] @@ -312,6 +318,8 @@ The {meso} style is part of the USER-SPH package for smoothed particle hydrodynamics (SPH). See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. +The {spin} style is part of the SPIN package. + The {wavepacket} style is part of the USER-AWPMD package for the "antisymmetrized wave packet MD method"_pair_awpmd.html. diff --git a/doc/src/balance.txt b/doc/src/balance.txt index da6f59900d69fb784ee8cdf91cc3bef60921aaa8..06c4eca491d1bd6cdb3c68a5caa2381718159ea7 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_class2.txt b/doc/src/bond_class2.txt index 9687a6316805acb77298f74eeb84952e8f4243fe..3d8d5007bad145439de155227c8873fcfce616a9 100644 --- a/doc/src/bond_class2.txt +++ b/doc/src/bond_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,10 +44,9 @@ K4 (energy/distance^4) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt index d93c0b223b84a0da9d6f171d9e222847d905ee69..7485fa3d8d1da5da832cc832f69f7ffd6d593696 100644 --- a/doc/src/bond_coeff.txt +++ b/doc/src/bond_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,9 +61,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that here are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul diff --git a/doc/src/bond_fene.txt b/doc/src/bond_fene.txt index 9050c3bf5ccecdd8701f414ef0caea5e39a19c2c..e16307a71076c6c2c2b6aecd5c660eb4acda8f2a 100644 --- a/doc/src/bond_fene.txt +++ b/doc/src/bond_fene.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,10 +47,9 @@ sigma (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -62,8 +61,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_fene_expand.txt b/doc/src/bond_fene_expand.txt index ff687444a97378373514442bda71a614b74bd821..8edd325885e457e039765074ce14be6fe5fe2764 100644 --- a/doc/src/bond_fene_expand.txt +++ b/doc/src/bond_fene_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,10 +50,9 @@ delta (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_gromos.txt b/doc/src/bond_gromos.txt index cc3ff75878f36dd27f2d85b61ae3bfb522f52583..275036a421f618085eb25625f87a716cb28876c5 100644 --- a/doc/src/bond_gromos.txt +++ b/doc/src/bond_gromos.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,10 +40,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic.txt b/doc/src/bond_harmonic.txt index c18a7e0fd4d35a337a832255b64b4daf8f07392f..e4b2015fed2987dfe52a06e22021fff70bbb6ce6 100644 --- a/doc/src/bond_harmonic.txt +++ b/doc/src/bond_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -42,10 +42,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -57,8 +56,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift.txt b/doc/src/bond_harmonic_shift.txt index bf3b3c115adeb59fcbd0a7a51e36a4612e6c020d..b6dc18a5fd69453806968cebd189c4ca7c0d5dd3 100644 --- a/doc/src/bond_harmonic_shift.txt +++ b/doc/src/bond_harmonic_shift.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,9 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_harmonic_shift_cut.txt b/doc/src/bond_harmonic_shift_cut.txt index 1918ce00b6210468a119d332762ed85f8f2bad0e..b3054437d8e8b4a4bda593bb756e7721ff7ebe26 100644 --- a/doc/src/bond_harmonic_shift_cut.txt +++ b/doc/src/bond_harmonic_shift_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,9 @@ rc (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -58,8 +57,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_hybrid.txt b/doc/src/bond_hybrid.txt index 400c3e0be4c9e1b7fb1fd98936208ad19f384896..140fb723785476a1a09c67360b6865a898f8d1f5 100644 --- a/doc/src/bond_hybrid.txt +++ b/doc/src/bond_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_morse.txt b/doc/src/bond_morse.txt index 4f6a32e341b57a7977e4aaabc83d8dd1a1282137..9b64e8c5c1d2da41936def16578ba299160121a9 100644 --- a/doc/src/bond_morse.txt +++ b/doc/src/bond_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,10 +41,9 @@ r0 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_none.txt b/doc/src/bond_none.txt index 8cb262a50f939617011853d41fe416f1a6e3160a..cace1919e13ff668c51418063f6a2d4a30dbefbc 100644 --- a/doc/src/bond_none.txt +++ b/doc/src/bond_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_nonlinear.txt b/doc/src/bond_nonlinear.txt index 434af625061a45679e9f01630c3999743d6d77ee..08109bc699dfed95d7ad70cff09dbded043627f5 100644 --- a/doc/src/bond_nonlinear.txt +++ b/doc/src/bond_nonlinear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,10 +41,9 @@ lamda (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 927fea64031d5422615d1251b9332e4e66120d3a..a0e14a123abed8da2728ed13d3ad3b836fc3414b 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_quartic.txt b/doc/src/bond_quartic.txt index 4dc7ad4a3693e8d0ed492514fbaaf5f15deaecd0..87a21eff02ef4577638e44a5a6932ab181ec5a71 100644 --- a/doc/src/bond_quartic.txt +++ b/doc/src/bond_quartic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,10 +76,9 @@ delete_bonds all bond 0 remove :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -91,8 +90,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index 3bd8afda196a642c883f7321d7998ed70f98f09c..41fa1cabb213847c51aef2b7acef0b1bb6bee00e 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,9 +66,8 @@ the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. Note that there are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the bond section of "this -page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +bond styles is on the "Commands bond"_Commands_bond.html doc page. "bond_style none"_bond_none.html - turn off bonded interactions "bond_style zero"_bond_zero.html - topology but no interactions diff --git a/doc/src/bond_table.txt b/doc/src/bond_table.txt index 906d3e5d7639eb08e211554b2817195dd383bcf1..e53cbdfa9f626c0c36377d9ac56a8bea016f958b 100644 --- a/doc/src/bond_table.txt +++ b/doc/src/bond_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -121,10 +121,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -136,8 +135,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/bond_write.txt b/doc/src/bond_write.txt index 4797d06cb1b5a164a47805840ce38824ea78b6ce..711bd2c2968b7119d80539027feb9deefe991a16 100644 --- a/doc/src/bond_write.txt +++ b/doc/src/bond_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/bond_zero.txt b/doc/src/bond_zero.txt index b599f291b4cc5fef8b4a77beb893c3b99026d893..554f26e7f00d5eeee62343792b1b3b351ec9f92f 100644 --- a/doc/src/bond_zero.txt +++ b/doc/src/bond_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/boundary.txt b/doc/src/boundary.txt index ce638f11b3ffbe871d398762df4397114f147d76..f9685433b2c4ca35d6f5ebbdaf29b4071514a67f 100644 --- a/doc/src/boundary.txt +++ b/doc/src/boundary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,9 +82,9 @@ and xhi faces of the box are planes tilting in the +y direction as y increases. These tilted planes are shrink-wrapped around the atoms to determine the x extent of the box. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. [Restrictions:] diff --git a/doc/src/box.txt b/doc/src/box.txt index a6207ae9937e569277a9d5a9b001493297f991dc..38c874fb78bc68b93ddaf666c6f97c0c147794e4 100644 --- a/doc/src/box.txt +++ b/doc/src/box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,9 @@ For triclinic (non-orthogonal) simulation boxes, the {tilt} keyword allows simulation domains to be created with arbitrary tilt factors, e.g. via the "create_box"_create_box.html or "read_data"_read_data.html commands. Tilt factors determine how -skewed the triclinic box is; see "this -section"_Section_howto.html#howto_12 of the manual for a discussion of -triclinic boxes in LAMMPS. +skewed the triclinic box is; see the "Howto +triclinic"_Howto_triclinic.html doc page for a discussion of triclinic +boxes in LAMMPS. LAMMPS normally requires that no tilt factor can skew the box more than half the distance of the parallel box length, which is the 1st diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index 2c7a890d4cfb406abf018fb4787917f797fcc963..adc5d6bdcb42ee3c8b814ad21480e2ef9496e8d5 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,9 +75,9 @@ The "create_box"_create_box.html, "read data"_read_data.html, and simulation box is orthogonal or triclinic and their doc pages explain the meaning of the xy,xz,yz tilt factors. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. The keywords used in this command are applied sequentially to the @@ -140,8 +140,8 @@ transformation in the sequence. If skew is exceeded before the final transformation this can be avoided by changing the order of the sequence, or breaking the transformation into two or more smaller transformations. For more information on the allowed limits for box -skew see the discussion on triclinic boxes on "this -page"_Section_howto.html#howto_12. +skew see the discussion on triclinic boxes on "Howto +triclinic"_Howto_triclinic.html doc page. :line @@ -258,9 +258,7 @@ command. :line The {ortho} and {triclinic} keywords convert the simulation box to be -orthogonal or triclinic (non-orthogonal). See "this -section"_Section_howto#howto_13 for a discussion of how non-orthogonal -boxes are represented in LAMMPS. +orthogonal or triclinic (non-orthogonal). The simulation box is defined as either orthogonal or triclinic when it is created via the "create_box"_create_box.html, @@ -271,8 +269,8 @@ These keywords allow you to toggle the existing simulation box from orthogonal to triclinic and vice versa. For example, an initial equilibration simulation can be run in an orthogonal box, the box can be toggled to triclinic, and then a "non-equilibrium MD (NEMD) -simulation"_Section_howto.html#howto_13 can be run with deformation -via the "fix deform"_fix_deform.html command. +simulation"_Howto_nemd.html can be run with deformation via the "fix +deform"_fix_deform.html command. If the simulation box is currently triclinic and has non-zero tilt in xy, yz, or xz, then it cannot be converted to an orthogonal box. diff --git a/doc/src/clear.txt b/doc/src/clear.txt index 7ac4da5c8d93228e974c48d20b746a3abef2153c..c4ad4c4030ca601cc2c1fa9fde44ce71c21946d2 100644 --- a/doc/src/clear.txt +++ b/doc/src/clear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 3e8d0eca4ffe2d8c55e0998dd26384619fc712d6..489278523bde3a605053c565405732c55c905825 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 8248d654d32265924b3e25734fb19d40d2c3b0f5..39eb1d4ef5aece3e2d77f2b6bbd8d16940700ccc 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute.txt b/doc/src/compute.txt index c06735d28e3dbe0091b3426eebbf264f1e147ad0..7d9e443e7da7455de147ca1531daab58887e65f8 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute does not perform a computation. Instead computes are invoked by other LAMMPS commands as needed, e.g. to calculate a temperature needed for a thermostat fix or to generate thermodynamic or dump file output. -See this "howto section"_Section_howto.html#howto_15 for a summary of +See the "Howto output"_Howto_output.html doc page for a summary of various LAMMPS output options, many of which involve computes. The ID of a compute can only contain alphanumeric characters and @@ -153,21 +153,27 @@ via the "compute_modify"_compute_modify.html command. Computes can be deleted with the "uncompute"_uncompute.html command. -Code for new computes can be added to LAMMPS (see "this -section"_Section_modify.html of the manual) and the results of their +Code for new computes can be added to LAMMPS; see the +"Modify"_Modify.html doc page for details. The results of their calculations accessed in the various ways described above. :line Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles -available in LAMMPS. They are also given in more compact form in the -Compute section of "this page"_Section_commands.html#cmd_5. +available in LAMMPS. They are also listed in more compact form on the +"Commands compute"_Commands_compute.html doc page. There are also additional compute styles (not listed here) submitted -by users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the compute -section of "this page"_Section_commands.html#cmd_5. +by users which are included in the LAMMPS distribution. The full list +of all compute styles is on the "Commands +compute"_Commands_compute.html doc page. + +There are also additional accelerated compute styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +compute"_Commands_compute.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accerlerated styles exist. "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom "angle/local"_compute_bond_local.html - theta and energy of each angle @@ -243,16 +249,6 @@ section of "this page"_Section_commands.html#cmd_5. "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul -There are also additional compute styles submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the compute section of "this -page"_Section_commands.html#cmd_5. - -There are also additional accelerated compute styles included in the -LAMMPS distribution for faster performance on CPUs and GPUs. The list -of these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. - [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_ackland_atom.txt b/doc/src/compute_ackland_atom.txt index 3fd838d95775ae9e97f7ad8da792112b9890d80d..485c191313209e46eb2ac979d004f23314678190 100644 --- a/doc/src/compute_ackland_atom.txt +++ b/doc/src/compute_ackland_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,7 +60,7 @@ which computes this quantity.- This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. [Restrictions:] diff --git a/doc/src/compute_angle.txt b/doc/src/compute_angle.txt index 2c363ce8f63fcb4f181814399b47b1cf5f558435..64eb2f4bb1262828736bb342d3f9fe145f6c4f7b 100644 --- a/doc/src/compute_angle.txt +++ b/doc/src/compute_angle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "angle_style hybrid"_angle_style.html command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 0ee1d32d7dcf8e3611fb98a5b8f70774d8cb3334..3a321965ef71135104bdf12f8dc13111dd515564 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,8 +70,8 @@ array is the number of angles. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {theta} will be in degrees. The output for {eng} will diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 813da15eeadeed76c43a5f933f52e272d9653cbc..7e49ff302480a753cc5aacefe28b609931d56b06 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the angular momentum vector for each chunk, due to the velocity/momentum of the individual @@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index b59a3fd4c878789dfd13c3e60a40ef0fb682ec96..067a020c35ebec8da9acda96b21abb8c68724a30 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,9 +46,8 @@ in examples/USER/misc/basal. This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom vector values are unitless since the 3 columns represent components of a unit vector. diff --git a/doc/src/compute_body_local.txt b/doc/src/compute_body_local.txt index 12ce21885356da3541d1d3f2c9a0fcf23f35f198..8ac3f00c559345d1de1547542296a9f7b0469c00 100644 --- a/doc/src/compute_body_local.txt +++ b/doc/src/compute_body_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Define a computation that calculates properties of individual body sub-particles. The number of datums generated, aggregated across all processors, equals the number of body sub-particles plus the number of non-body particles in the system, modified by the group parameter as -explained below. See "Section 6.14"_Section_howto.html#howto_14 -of the manual and the "body"_body.html doc page for more details on -using body particles. +explained below. See the "Howto body"_Howto_body.html doc page for +more details on using body particles. The local data stored by this command is generated by looping over all the atoms. An atom will only be included if it is in the group. If @@ -58,8 +57,8 @@ group. For a body particle, the {integer} keywords refer to fields calculated by the body style for each sub-particle. The body style, as specified by the "atom_style body"_atom_style.html, determines how many fields -exist and what they are. See the "body"_body.html doc page for -details of the different styles. +exist and what they are. See the "Howto_body"_Howto_body.html doc +page for details of the different styles. Here is an example of how to output body information using the "dump local"_dump.html command with this compute. If fields 1,2,3 for the @@ -78,9 +77,9 @@ array is the number of datums as described above. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +command that uses local values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The "units"_units.html for output values depend on the body style. diff --git a/doc/src/compute_bond.txt b/doc/src/compute_bond.txt index 6c4384b0806c7436f9384fe9d043c3fd9cb33c51..a87c510538f6035bf90b75d61cbd886a78c19208 100644 --- a/doc/src/compute_bond.txt +++ b/doc/src/compute_bond.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "bond_style hybrid"_bond_style.html command, which can be accessed by indices 1-N. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 58d96f9ee4951f4517809a2e49f2fd6171941a16..c3dc1cc4afe92ae09118e8f56c0e678a380cee71 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ array is the number of bonds. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 4e4b03d16762c97eb44fb010f131d63ab0d1fd4f..183537690f43f61a5c5099ac3c76c3dd37b8223c 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a By default, this compute calculates the centrosymmetry value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. If the {axes} keyword setting is {yes}, then a per-atom array is diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 3a46f79d160013e96c177c3939454da9a6f4ecc7..95e6e6c0104a939af015cecc41a2c2ee3ea5c33c 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,14 +101,13 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix ave/chunk"_fix_ave_chunk.html command to sum and time average a variety of per-atom properties over the atoms in each chunk. Or they can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in "Section -6.15"_Section_howto.html#howto_15. +compute as input, as discussed on the "Howto output"_Howto_output.html +doc page. -See "Section 6.23"_Section_howto.html#howto_23 for an overview of -how this compute can be used with a variety of other commands to -tabulate properties of a simulation. The howto section gives several -examples of input script commands that can be used to calculate -interesting properties. +See the "Howto chunk"_Howto_chunk.html doc page for an overview of how +this compute can be used with a variety of other commands to tabulate +properties of a simulation. The page gives several examples of input +script commands that can be used to calculate interesting properties. Conceptually it is important to realize that this compute does two simple things. First, it sets the value of {Nchunk} = the number of @@ -167,11 +166,11 @@ or the bounds specified by the optional {bounds} keyword. For orthogonal simulation boxes, the bins are layers, pencils, or boxes aligned with the xyz coordinate axes. For triclinic (non-orthogonal) simulation boxes, the bin faces are parallel to the -tilted faces of the simulation box. See "this -section"_Section_howto.html#howto_12 of the manual for a discussion of -the geometry of triclinic boxes in LAMMPS. As described there, a -tilted simulation box has edge vectors a,b,c. In that nomenclature, -bins in the x dimension have faces with normals in the "b" cross "c" +tilted faces of the simulation box. See the "Howto +triclinic"_Howto_triclinic.html doc page for a discussion of the +geometry of triclinic boxes in LAMMPS. As described there, a tilted +simulation box has edge vectors a,b,c. In that nomenclature, bins in +the x dimension have faces with normals in the "b" cross "c" direction. Bins in y have faces normal to the "a" cross "c" direction. And bins in z have faces normal to the "a" cross "b" direction. Note that in order to define the size and position of @@ -275,7 +274,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. If the style begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed integer is @@ -285,7 +284,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with the timestep on which this compute accesses the fix, else an error results. Users can also write code for their own fix styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "v_", a variable name for an {atom} or {atomfile} style "variable"_variable.html must follow which has been @@ -626,7 +625,7 @@ cylinder, x for a y-axis cylinder, and x for a z-axis cylinder. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values are unitless chunk IDs, ranging from 1 to diff --git a/doc/src/compute_cluster_atom.txt b/doc/src/compute_cluster_atom.txt index 94113de5f2422a2628acc9f5bcb22a4940eefe21..e6138fe1e8eb80256cdc317120bcedb8fb7326cb 100644 --- a/doc/src/compute_cluster_atom.txt +++ b/doc/src/compute_cluster_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -84,7 +84,7 @@ the neighbor list. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be an ID > 0, as explained above. diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 23289b01325b4afac23c938788a8ef1e775ecc59..d69c5e9c467e626017381f6e96268c9ed8aa4b8f 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be a number from 0 to 5, as explained diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt index 16a51f5241f16ee058553a6e4634ec578219712c..44a77d23ca0fedade05df5f523302bcdaaa6215a 100644 --- a/doc/src/compute_cnp_atom.txt +++ b/doc/src/compute_cnp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,7 +78,7 @@ too frequently or to have multiple compute/dump commands, each with a This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be real positive numbers. Some typical CNP diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index b0e0c14e424ae0de3d043c2686bbc19be9e938f0..fdc631a263cb155e437a5f54aa368ffb40ee2d76 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,9 +41,8 @@ image"_set.html command. This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in distance "units"_units.html. diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index d497585cb036455b2cf199b6bc1098e34077b16e..b982f0d9017f4a501d56a9d1696cf6d4a5e51486 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the center-of-mass for each chunk, which includes all effects due to atoms passing thru @@ -71,9 +70,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass coordinates of each chunk. These values can be accessed by any command that uses global array values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in distance "units"_units.html. diff --git a/doc/src/compute_contact_atom.txt b/doc/src/compute_contact_atom.txt index f0bd62f4e87b9b5b1bfc85693ba0a028f95435ff..efe524263aa8c399e8771dd7348b52c9ae5cd42c 100644 --- a/doc/src/compute_contact_atom.txt +++ b/doc/src/compute_contact_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -36,7 +36,7 @@ specified compute group. This compute calculates a per-atom vector, whose values can be accessed by any command that uses per-atom values from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index a88f7ec729298c45b534ff8799d6c58896fbb793..66eecd195da4fb19851d5d84349c72391e51add6 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -109,9 +109,8 @@ array, with N columns. For {cstyle} orientorder, this compute calculates a per-atom vector. These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-atom vector or array values will be a number >= 0.0, as explained above. diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 918fbf65eff0c4172e92a8d551ce74e1a9f59cd1..74939e22806077fe5fb274cd17a7630954db9017 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,7 +44,7 @@ group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values are unitless numbers (damage) >= 0.0. diff --git a/doc/src/compute_dihedral.txt b/doc/src/compute_dihedral.txt index a3c3dff8d68f0bb2c36d6461ceb42d6f85fd238d..aa25f9dd1029af8d7f23ffb938bd7fd6a70e08c8 100644 --- a/doc/src/compute_dihedral.txt +++ b/doc/src/compute_dihedral.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "dihedral_style hybrid"_dihedral_style.html command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_dihedral_local.txt b/doc/src/compute_dihedral_local.txt index 865e86fddb1483ccf7a3b1c3d79fec912b90ea04..77812699d35fc826c95a344ddc7bf0207caf2ec4 100644 --- a/doc/src/compute_dihedral_local.txt +++ b/doc/src/compute_dihedral_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,8 +62,8 @@ array is the number of dihedrals. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {phi} will be in degrees. diff --git a/doc/src/compute_dilatation_atom.txt b/doc/src/compute_dilatation_atom.txt index ce00f7f12a5b9daae8a2b9ce9ae07a03188c41b4..498110cf99338e56fb24a2b9a362438f03f5f9f3 100644 --- a/doc/src/compute_dilatation_atom.txt +++ b/doc/src/compute_dilatation_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,8 +47,9 @@ compute group. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. +any command that uses per-atom values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-atom vector values are unitless numbers (theta) >= 0.0. diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index 75131ffbb113ad75802e88afb59c36f07f160ab5..d45fde9af2dbdd86aedc30abaa55c4b62e82b648 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,10 +32,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the dipole vector and the total dipole moment for each chunk, which includes all effects @@ -76,8 +75,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for the x,y,z dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global -array values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 00e5f696c118029431bf5a36395bcd906fe432ee..669ab9f7ca3ea74e4a3a8a0b5537c0b09cbd814d 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -118,9 +118,8 @@ would be empty. This compute calculates a per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom array values will be in distance "units"_units.html. diff --git a/doc/src/compute_dpd.txt b/doc/src/compute_dpd.txt index 0e43feb9d23195bced66f17990bd42022b86c1ee..1721456e35ab0da5a82d3965f676f35a3d4baa3b 100644 --- a/doc/src/compute_dpd.txt +++ b/doc/src/compute_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,9 +40,9 @@ where N is the number of particles in the system [Output info:] This compute calculates a global vector of length 5 (U_cond, U_mech, -U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. See -"this section"_Section_howto.html#howto_15 for an overview of LAMMPS -output options. +U_chem, dpdTheta, N_particles), which can be accessed by indices 1-5. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The vector values will be in energy and temperature "units"_units.html. diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index 0532fc60c64193f977ce7d74e84768709d6502cf..8e502d4a6060f297da9132013adf5e19d40b565a 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,9 +34,9 @@ particles. [Output info:] This compute calculates a per-particle array with 4 columns (u_cond, -u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command -that uses per-particle values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any +command that uses per-particle values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle array values will be in energy (u_cond, u_mech, u_chem) diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt index 5b8c8ebd67c371c20deb465941d4007008c60b35..f33398e03d68995dc18da4d73fd9537f5e75656d 100644 --- a/doc/src/compute_edpd_temp_atom.txt +++ b/doc/src/compute_edpd_temp_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,9 @@ For more details please see "(Espanol1997)"_#Espanol1997 and [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +any command that uses per-atom values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in temperature "units"_units.html. diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt new file mode 100644 index 0000000000000000000000000000000000000000..9c45fd287099ea6150621a177f55837bbc5855fb --- /dev/null +++ b/doc/src/compute_entropy_atom.txt @@ -0,0 +1,130 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute entropy/atom command :h3 + +[Syntax:] + +compute ID group-ID entropy/atom sigma cutoff keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :l +entropy/atom = style name of this compute command :l +sigma = width of gaussians used in the g(r) smoothening :l +cutoff = cutoff for the g(r) calculation :l +one or more keyword/value pairs may be appended :l +keyword = {avg} or {local} + {avg} values = {yes} or {no} cutoff2 + {yes} = average the pair entropy over neighbors + {no} = do not average the pair entropy over neighbors + cutoff2 = cutoff for the averaging over neighbors + {local} values = {yes} or {no} = use the local density around each atom to normalize the g(r) :pre +:ule + +[Examples:] + +compute 1 all entropy/atom 0.25 5. +compute 1 all entropy/atom 0.25 5. avg yes 5. +compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre + +[Description:] + +Define a computation that calculates the pair entropy fingerprint for +each atom in the group. The fingerprint is useful to distinguish between +ordered and disordered environments, for instance liquid and solid-like +environments, or glassy and crystalline-like environments. Some +applications could be the identification of grain boundaries, a +melt-solid interface, or a solid cluster emerging from the melt. +The advantage of this parameter over others is that no a priori +information about the solid structure is required. + +This parameter for atom i is computed using the following formula from +"(Piaggi)"_#Piaggi and "(Nettleton)"_#Nettleton , + +:c,image(Eqs/pair_entropy.jpg) + +where r is a distance, g(r) is the radial distribution function of atom +i and rho is the density of the system. The g(r) computed for each +atom i can be noisy and therefore it is smoothened using: + +:c,image(Eqs/pair_entropy2.jpg) + +where the sum in j goes through the neighbors of atom i, and sigma is a +parameter to control the smoothening. + +The input parameters are {sigma} the smoothening parameter, and the +{cutoff} for the calculation of g(r). + +If the keyword {avg} has the setting {yes}, then this compute also +averages the parameter over the neighbors of atom i according to: + +:c,image(Eqs/pair_entropy3.jpg) + +where the sum j goes over the neighbors of atom i and N is the number +of neighbors. This procedure provides a sharper distinction between +order and disorder environments. In this case the input parameter +{cutoff2} is the cutoff for the averaging over the neighbors and +must also be specified. + +If the {avg yes} option is used, the effective cutoff of the neighbor +list should be {cutoff}+{cutoff2} and therefore it might be necessary +to increase the skin of the neighbor list with: + +neighbor skin bin :pre + +See "neighbor"_neighbor.html for details. + +If the {local yes} option is used, the g(r) is normalized by the +local density around each atom, that is to say the density around each +atom is the number of neighbors within the neighbor list cutoff divided +by the corresponding volume. This option can be useful when dealing with +inhomogeneus systems such as those that have surfaces. + +Here are typical input parameters for fcc aluminum (lattice +constant 4.05 Angstroms), + +compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre + +and for bcc sodium (lattice constant 4.23 Angstroms), + +compute 1 all entropy/atom 0.25 7.3 avg yes 5.1 :pre + + +[Output info:] + +By default, this compute calculates the pair entropy value for each +atom as a per-atom vector, which can be accessed by any command that +uses per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. + +The pair entropy values have units of the Boltzmann constant. They are +always negative, and lower values (lower entropy) correspond to more +ordered environments. + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"compute cna/atom"_compute_cna_atom.html +"compute centro/atom"_compute_centro_atom.html + +[Default:] + +The default values for the optional keywords are avg = no and local = no. + +:line + +:link(Piaggi) +[(Piaggi)] Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017). + +:link(Nettleton) +[(Nettleton)] Nettleton and Green, J Chem Phys, 29, 6 (1958). diff --git a/doc/src/compute_erotate_asphere.txt b/doc/src/compute_erotate_asphere.txt index b9a486c32eab61c8399328e028d7eb6d59cdaa1c..5cdc0997826f3dfbfff0281e85efe3ebb4864bb0 100644 --- a/doc/src/compute_erotate_asphere.txt +++ b/doc/src/compute_erotate_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ will be the same as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_rigid.txt b/doc/src/compute_erotate_rigid.txt index dec0939a43375ebb3f082634f0d11e64b508b46c..5b9077870e1d25440827b5a6006b5c6e3233d830 100644 --- a/doc/src/compute_erotate_rigid.txt +++ b/doc/src/compute_erotate_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,9 +41,9 @@ calculation. This compute calculates a global scalar (the summed rotational energy of all the rigid bodies). This value can be used by any command that -uses a global scalar value from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +uses a global scalar value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output +options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/src/compute_erotate_sphere.txt b/doc/src/compute_erotate_sphere.txt index 41e80b0154dad4d1a073b9fdb4674365e0fe1033..d0c176b50eb264ff3431b6bbcdd71ad578092b1a 100644 --- a/doc/src/compute_erotate_sphere.txt +++ b/doc/src/compute_erotate_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,7 +35,7 @@ as in 3d. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_erotate_sphere_atom.txt b/doc/src/compute_erotate_sphere_atom.txt index a0081ff6a8cb8bc26106809817a108091026741e..fdd609a0e65ffd71a599a16310b9c1bacdd809b1 100644 --- a/doc/src/compute_erotate_sphere_atom.txt +++ b/doc/src/compute_erotate_sphere_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,7 +39,7 @@ in the specified compute group or for point particles with a radius = This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_event_displace.txt b/doc/src/compute_event_displace.txt index 5e3a0c8599d533af3313cbe711c5d64ab77c680d..561ded35c052ef3e99e53ea8cb0533e00d3f99e3 100644 --- a/doc/src/compute_event_displace.txt +++ b/doc/src/compute_event_displace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,7 +43,7 @@ local atom displacements and may generate "false positives." This compute calculates a global scalar (the flag). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 9bbae7b20f1c835c67d7808867d4a398a79b4541..8b4a92e16ea3a0486ca2c7113bf0b1ac87a47399 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +scalar or vector from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. For example, the computed values can be averaged using "fix ave/time"_fix_ave_time.html. diff --git a/doc/src/compute_global_atom.txt b/doc/src/compute_global_atom.txt index 3136b1fd18f849bcf6c69b328983b8aa135d5c50..a26dba72b008de7202aa880c2b6999be67dc56a8 100644 --- a/doc/src/compute_global_atom.txt +++ b/doc/src/compute_global_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,7 +67,7 @@ this command. This command will then assign the global chunk value to each atom in the chunk, producing a per-atom vector or per-atom array as output. The per-atom values can then be output to a dump file or used by any command that uses per-atom values from a compute as input, -as discussed in "Section 6.15"_Section_howto.html#howto_15. +as discussed on the "Howto output"_Howto_output.html doc page. As a concrete example, these commands will calculate the displacement of each atom from the center-of-mass of the molecule it is in, and @@ -130,7 +130,7 @@ page for details. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute -styles and "add them to LAMMPS"_Section_modify.html. See the +styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -143,7 +143,7 @@ references the values, else an error results. If no bracketed integer is appended, the per-atom vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -168,7 +168,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how +them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -181,7 +181,7 @@ global/atom references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their -own fix style and "add them to LAMMPS"_Section_modify.html. See the +own fix style and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -203,7 +203,7 @@ vector. If multiple inputs are specified, this compute produces a per-atom array values, where the number of columns is equal to the number of inputs specified. These values can be used by any command that uses per-atom vector or array values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector or array values will be in whatever units the diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt index f10547339d476eb44866be4dd596fd67b4657520..cff3687354589ab402cbe03114425ec9baf04985 100644 --- a/doc/src/compute_group_group.txt +++ b/doc/src/compute_group_group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -123,8 +123,8 @@ group-group calculations are performed. This compute calculates a global scalar (the energy) and a global vector of length 3 (force), which can be accessed by indices 1-3. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. Both the scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index dd71431527f6f985b4d0e64acb85d46881134390..4dc883ad0bd2f2737b4e547b05621da6f39a01d2 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,8 +55,8 @@ using the "set image"_set.html command. This compute calculates a global scalar (Rg) and a global vector of length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index 3e338213cf579f317e773374183b115bd327d697..dcbfc653938f13b147d5cd58ec85fb3ca392f163 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,10 +35,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the radius of gyration Rg for each chunk, which includes all effects due to atoms passing thru periodic @@ -93,8 +92,8 @@ calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword is specified, the global array has 6 columns. The vector or array can be accessed by any command that uses global values from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. All the vector or array values calculated by this compute are "intensive". The vector or array values will be in distance diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 39a1470201fc3f6705ee222e9719261aeae5dd4f..81a2a3f51711dc56e4b763de70421fecab1e4a4c 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,9 @@ or to calculate a thermal conductivity using the equilibrium Green-Kubo formalism. For other non-equilibrium ways to compute a thermal conductivity, see -"this section"_Section_howto.html#howto_20. These include use of the -"fix thermal/conductivity"_fix_thermal_conductivity.html command for -the Muller-Plathe method. Or the "fix heat"_fix_heat.html command +the "Howto kappa"_Howto_kappa.html doc page.. These include use of +the "fix thermal/conductivity"_fix_thermal_conductivity.html command +for the Muller-Plathe method. Or the "fix heat"_fix_heat.html command which can add or subtract heat from groups of atoms. The compute takes three arguments which are IDs of other @@ -99,8 +99,8 @@ result should be: average conductivity ~0.29 in W/mK. This compute calculates a global vector of length 6 (total heat flux vector, followed by convective heat flux vector), which can be accessed by indices 1-6. These values can be used by any command that -uses global vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values calculated by this compute are "extensive", meaning diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index cdf47e0894aeffffb7d4a83da178ee328a8d1eb2..082a3cad7a0e62195fa333fd15f5071c2810000c 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -95,10 +95,9 @@ This compute calculates a per-atom array with 2 columns, giving the real and imaginary parts {qn}, a complex number restricted to the unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 . -These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +These values can be accessed by any command that uses per-atom values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_improper.txt b/doc/src/compute_improper.txt index f0d2fa400e634ad40eccda5999f0bded55467eaf..867dd48cc16edc61f5b1cc8d64d4b80234120209 100644 --- a/doc/src/compute_improper.txt +++ b/doc/src/compute_improper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ This compute calculates a global vector of length N where N is the number of sub_styles defined by the "improper_style hybrid"_improper_style.html command. which can be accessed by indices 1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_improper_local.txt b/doc/src/compute_improper_local.txt index 0c289fbf0774fde0651d77d6a27b209621b5388e..f340d5a03fc472889b22f854480c0563eee0e6dc 100644 --- a/doc/src/compute_improper_local.txt +++ b/doc/src/compute_improper_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,8 +63,8 @@ array is the number of impropers. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {chi} will be in degrees. diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index b0dbb12aea8d5e7e1e5d982f0d4d656b9d0c2ffb..d6cdb3fe79eb950ce3aa3675c9a7d13986d1e957 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The @@ -72,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke.txt b/doc/src/compute_ke.txt index caee8971627231b080a680612017df790ef292df..64ab83db48b792aa0bc26dbd60ca0de7800166ae 100644 --- a/doc/src/compute_ke.txt +++ b/doc/src/compute_ke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,7 +44,7 @@ include different degrees of freedom (translational, rotational, etc). This compute calculates a global scalar (the summed KE). This value can be used by any command that uses a global scalar value from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_ke_atom.txt b/doc/src/compute_ke_atom.txt index f5431f0569fe48e82ec9ebbb48f77d3f9e1d7f17..d288ab0236d44a40c32805a94e8d1b04a181edd1 100644 --- a/doc/src/compute_ke_atom.txt +++ b/doc/src/compute_ke_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,7 +34,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_ke_atom_eff.txt b/doc/src/compute_ke_atom_eff.txt index 8228e13f07c697e32cf678c3e381082d21a653ea..f665f35055f36be914f26aa5c032b2b76233ccf2 100644 --- a/doc/src/compute_ke_atom_eff.txt +++ b/doc/src/compute_ke_atom_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,9 +57,9 @@ electrons) not in the specified compute group. [Output info:] This compute calculates a scalar quantity for each atom, which can be -accessed by any command that uses per-atom computes as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +accessed by any command that uses per-atom computes as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_ke_eff.txt b/doc/src/compute_ke_eff.txt index ac8d7e6c01d48b723484e9ff7ab7959e7b97b9e0..d6d7fdb10f5f3667a8443047505e80a775c3b1b6 100644 --- a/doc/src/compute_ke_eff.txt +++ b/doc/src/compute_ke_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,7 +61,7 @@ See "compute temp/eff"_compute_temp_eff.html. This compute calculates a global scalar (the KE). This value can be used by any command that uses a global scalar value from a compute as -input. See "Section 6.15"_Section_howto.html#howto_15 for an +input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt index f79696a77a1fe3692fad26fadbca9f47f765612e..45ba2673b0283a8106d55ee621103a7f8eb3a7fa 100644 --- a/doc/src/compute_ke_rigid.txt +++ b/doc/src/compute_ke_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,8 +40,8 @@ calculation. This compute calculates a global scalar (the summed KE of all the rigid bodies). This value can be used by any command that uses a -global scalar value from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +global scalar value from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_meso_e_atom.txt b/doc/src/compute_meso_e_atom.txt index 4e621b43018137817134f567efc0c550574e5737..9a9c7fae118d4b6a84636b94a9f83d582c6331c8 100644 --- a/doc/src/compute_meso_e_atom.txt +++ b/doc/src/compute_meso_e_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_meso_rho_atom.txt b/doc/src/compute_meso_rho_atom.txt index a017424dd01f0314e5155ac59e5b3dc50c652630..30b1142b6cdfef0afb329f7d3be5a360d9487465 100644 --- a/doc/src/compute_meso_rho_atom.txt +++ b/doc/src/compute_meso_rho_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in mass/volume "units"_units.html. diff --git a/doc/src/compute_meso_t_atom.txt b/doc/src/compute_meso_t_atom.txt index 9e81b038f452c901aeb5dc3d0747e4df6cafd215..ab92f05018a15b6f45edf30d4844b82b2c237493 100644 --- a/doc/src/compute_meso_t_atom.txt +++ b/doc/src/compute_meso_t_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ specified compute group. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in temperature "units"_units.html. diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index 9a2480ec0ac7fd7b584216a74355ed9b707c877e..192ea0bc9ec96d6c7691214f78f7cf2c080f4ddd 100644 --- a/doc/src/compute_modify.txt +++ b/doc/src/compute_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index f806c5e29266752bae1859a33bcf8eb1101eb99c..b54e05bc6498ffd450ce91ff9f5b4c959f9790fd 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,9 +93,8 @@ instead of many, which will change the values of msd somewhat. This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in distance^2 "units"_units.html. diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 7f31b61ed0bda808a94a5a45e3c4d165f4e3c1cf..264f38d5fde4a6f587ff97f22ed797b07f3b50bc 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the @@ -106,7 +105,7 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for dx,dy,dz and the total displacement. These values can be accessed by any command that uses global array values from a compute -as input. See "this section"_Section_howto.html#howto_15 for an +as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index 198da999e0a3c36af28e45f173dc9683aca3aa50..814159121d11781bf29850db7c8787ab5644b807 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,9 +57,8 @@ NOTEs, which also apply to this compute. This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The first vector value will be in distance^2 "units"_units.html, the second is in distance^4 units, and diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 46c72d3dcb3d15aed65805003bd419b30d098fb2..84b25ac6f26e014a2258715bf2e7d847642854df 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the angular velocity vector for each chunk, via the formula L = Iw where L is the angular @@ -73,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index adf11dcfcfa9822f4c736f1cb7203ca0e02c446c..7327a7b1d333a5375d033d5d8f88b9e74efc6237 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -115,10 +115,9 @@ Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}). This way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1) columns. -These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +These values can be accessed by any command that uses per-atom values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index 0602dab81bd5902838a01d52432a881db684f710..a2c25fcc8dc0dbe737e3efb76fd1ef57197dd765 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,9 +62,8 @@ This compute calculates a global scalar which is {epair} or {evdwl} or {ecoul}. If the pair style supports it, it also calculates a global vector of length >= 1, as determined by the pair style. These values can be used by any command that uses global scalar or vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are "extensive". diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 16aaba4667396dfc038c9f7625fdca532a8cd04b..7588e92527aa5d32157f4f94207226597a9966f4 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -119,8 +119,8 @@ array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The output for {dist} will be in distance "units"_units.html. The diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt index 15f27a8eff5f92cb97b215e8313b98429db8fef9..37655dfd480c8bb48b2b722436f5b6b0d15f5e6d 100644 --- a/doc/src/compute_pe.txt +++ b/doc/src/compute_pe.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,9 +64,8 @@ See the "thermo_style" command for more details. This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The scalar value will be in energy "units"_units.html. diff --git a/doc/src/compute_pe_atom.txt b/doc/src/compute_pe_atom.txt index c312c886a692f5a0ffcbb277e432acb34bcc88aa..400621f8df1d50b921c2ad870df98b8cdf578784 100644 --- a/doc/src/compute_pe_atom.txt +++ b/doc/src/compute_pe_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,7 +81,7 @@ global system energy. This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-atom vector values will be in energy "units"_units.html. diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index 788213fc65985cb86bee7a08b3e78f50adf423cc..50a51d99377899c3ed62a81059351ab494968567 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,8 +41,9 @@ compute group. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of LAMMPS output options. +any command that uses per-atom values from a compute as input. See +the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-atom vector values are unitless numbers (lambda) >= 0.0. diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index f0691ad20762758234828f976e7519ef47568d57..dea0a7f05b7f03d209077628f19a07172eb93e0f 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,10 +105,9 @@ where "thermo_temp" is the ID of a similarly defined compute of style Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -130,8 +129,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the pressure) and a global vector of length 6 (pressure tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar -or vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +or vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_pressure_uef.txt b/doc/src/compute_pressure_uef.txt index 5b252b369dd012691e62a3dcf267c6e00cca11c3..61cc85ad8097b3b43ac740cf186b7456f02db707 100644 --- a/doc/src/compute_pressure_uef.txt +++ b/doc/src/compute_pressure_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index bac19918ba7ccefedb982449b91db8cd086edae7..512009093c0e052e8e7b43f44455d1f61d7e6fb8 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,6 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, + sp, spx, spy, spz, fmx, fmy, fmz, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -46,6 +47,9 @@ input = one or more atom attributes :l q = atom charge mux,muy,muz = orientation of dipole moment of atom mu = magnitude of dipole moment of atom + sp = atomic magnetic spin moment + spx, spy, spz = direction of the atomic magnetic spin + fmx, fmy, fmz = magnetic force radius,diameter = radius,diameter of spherical particle omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle @@ -82,17 +86,18 @@ input = one or more atom attributes :l compute 1 all property/atom xs vx fx mux compute 2 all property/atom type -compute 1 all property/atom ix iy iz :pre +compute 1 all property/atom ix iy iz +compute 3 all property/atom sp spx spy spz :pre [Description:] Define a computation that simply stores atom attributes for each atom in the group. This is useful so that the values can be used by other -"output commands"_Section_howto.html#howto_15 that take computes as -inputs. See for example, the "compute reduce"_compute_reduce.html, -"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/chunk"_fix_ave_chunk.html, and "atom-style -variable"_variable.html commands. +"output commands"_Howto_output.html that take computes as inputs. See +for example, the "compute reduce"_compute_reduce.html, "fix +ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, "fix +ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html +commands. The list of possible attributes is the same as that used by the "dump custom"_dump.html command, which describes their meaning, with some @@ -144,14 +149,18 @@ on the number of input values. If a single input is specified, a per-atom vector is produced. If two or more inputs are specified, a per-atom array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses -per-atom values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values will be in whatever "units"_units.html the corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. +For the spin quantities, sp is in the units of the Bohr magneton, spx, +spy, and spz are adimentional quantities, and fmx, fmy and fmz are +given in rad.THz. + [Restrictions:] none [Related commands:] diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index b9d4944b30740cfcb28313811a6885296c65acf4..a30b5a1f0a5526421610cc06946328874c762115 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -36,15 +36,14 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates and stores the specified attributes of chunks as global data so they can be accessed by other "output -commands"_Section_howto.html#howto_15 and used in conjunction with -other commands that generate per-chunk data, such as "compute +commands"_Howto_output.html and used in conjunction with other +commands that generate per-chunk data, such as "compute com/chunk"_compute_com_chunk.html or "compute msd/chunk"_compute_msd_chunk.html. @@ -103,8 +102,8 @@ single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as -input. See "this section"_Section_howto.html#howto_15 for an overview -of LAMMPS output options. +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The vector or array values are "intensive". The values will be unitless or in the units discussed above. diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index 39106a39c890cae655d635216bbe93876f43fc74..b0ec088cf79d009e7c3062907d73dbfe3279e6da 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,10 +48,10 @@ compute 1 all property/local atype aatom2 :pre Define a computation that stores the specified attributes as local data so it can be accessed by other "output -commands"_Section_howto.html#howto_15. If the input attributes refer -to bond information, then the number of datums generated, aggregated -across all processors, equals the number of bonds in the system. -Ditto for pairs, angles, etc. +commands"_Howto_output.html. If the input attributes refer to bond +information, then the number of datums generated, aggregated across +all processors, equals the number of bonds in the system. Ditto for +pairs, angles, etc. If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the @@ -140,8 +140,8 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +that uses local values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the diff --git a/doc/src/compute_rdf.txt b/doc/src/compute_rdf.txt index e462e85fc038a10dfe9de0c701fecb103002a731..04b38682cc4957ac67459b18652249b1dfb75f14 100644 --- a/doc/src/compute_rdf.txt +++ b/doc/src/compute_rdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -152,7 +152,7 @@ coordinate (center of the bin), Each successive set of 2 columns has the g(r) and coord(r) values for a specific set of {itypeN} versus {jtypeN} interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values calculated by this compute are all "intensive". diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 07d3c3bda7b88e277f36cb2e839398763488ca40..ef3c7c6489e03ef3c1056edefd8d4dc419766cdf 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,7 +116,7 @@ per-atom or local quantities. See the individual is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own -compute styles and "add them to LAMMPS"_Section_modify.html. See the +compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -129,9 +129,9 @@ references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. See the discussion above for how -I can be specified with a wildcard asterisk to effectively specify -multiple values. +them to LAMMPS"_Modify.html. See the discussion above for how I can +be specified with a wildcard asterisk to effectively specify multiple +values. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an @@ -192,7 +192,7 @@ This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 077ad57d81b6bb1acd7d328e4e3f819867e71510..b5e6954ab99943f090a3153829ca08a6daa8f0b7 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,8 +49,8 @@ Define a computation that simply stores rigid body attributes for rigid bodies defined by the "fix rigid/small"_fix_rigid.html command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other "output -commands"_Section_howto.html#howto_15 that process local data, such as -the "compute reduce"_compute_reduce.html or "dump local"_dump.html +commands"_Howto_output.html that process local data, such as the +"compute reduce"_compute_reduce.html or "dump local"_dump.html commands. Note that this command only works with the "fix @@ -154,9 +154,9 @@ array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any -command that uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +command that uses local values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The vector or array values will be in whatever "units"_units.html the corresponding attribute is in: diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index 020f72f565c1009426ae22e891932aa648f6f1bd..8c17a30fcaf1acb403a936d4a15938206e89ad4d 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -143,10 +143,9 @@ the number of reciprocal lattice nodes that are explored by the mesh. The entries of the global vector are the computed diffraction intensities as described above. -The vector can be accessed by any command that uses global values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +The vector can be accessed by any command that uses global values from +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. All array values calculated by this compute are "intensive". diff --git a/doc/src/compute_slice.txt b/doc/src/compute_slice.txt index e89c05a0f95a0e2b39d2545a512fe158c4bd39e3..51031aeab3017a4bbfee683c0055165d74fd8c03 100644 --- a/doc/src/compute_slice.txt +++ b/doc/src/compute_slice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,7 +58,7 @@ page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -69,7 +69,7 @@ the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If an input value begins with "v_", a variable name must follow which has been previously defined in the input script. Only vector-style @@ -94,8 +94,8 @@ specified or a global array with N columns where N is the number of inputs. The length of the vector or the number of rows in the array is equal to the number of values extracted from each input vector. These values can be used by any command that uses global vector or -array values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The vector or array values calculated by this compute are simply diff --git a/doc/src/compute_smd_contact_radius.txt b/doc/src/compute_smd_contact_radius.txt index 69fe45334398fb60c77b4582074d0b2309c4f6ff..cd1381604788bfcd42f00653d2c5e9b46f98d25f 100644 --- a/doc/src/compute_smd_contact_radius.txt +++ b/doc/src/compute_smd_contact_radius.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ specified compute group. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle vector values will be in distance "units"_units.html. diff --git a/doc/src/compute_smd_damage.txt b/doc/src/compute_smd_damage.txt index b6c75a3b204532003231bad5f7a61089e9544199..afabe23d7cc1407496463c926ba8adcb9ddc7ff0 100644 --- a/doc/src/compute_smd_damage.txt +++ b/doc/src/compute_smd_damage.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -28,10 +28,10 @@ See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values are dimensionless an in the range of zero to one. diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt index a15b79e64e4490e51a9321d06206757589a5c06a..13fd20a5891cab8bdeeabb570d8343c063a705af 100644 --- a/doc/src/compute_smd_hourglass_error.txt +++ b/doc/src/compute_smd_hourglass_error.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,10 +37,10 @@ Mach Dynamics in LAMMPS. [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will are dimensionless. See "units"_units.html. diff --git a/doc/src/compute_smd_internal_energy.txt b/doc/src/compute_smd_internal_energy.txt index bc6f9e0f2068b440c731bbaa6a5710daa8d2c446..6585c3429f27a9c97d17c66a15dff959ebbbe5be 100644 --- a/doc/src/compute_smd_internal_energy.txt +++ b/doc/src/compute_smd_internal_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will be given in "units"_units.html of energy. diff --git a/doc/src/compute_smd_plastic_strain.txt b/doc/src/compute_smd_plastic_strain.txt index af5b1644534adcd3c624109aadf0f69205db78c6..fb3c5c9138cb5ae444320a5ff9f4a73878780a67 100644 --- a/doc/src/compute_smd_plastic_strain.txt +++ b/doc/src/compute_smd_plastic_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given dimensionless. See "units"_units.html. diff --git a/doc/src/compute_smd_plastic_strain_rate.txt b/doc/src/compute_smd_plastic_strain_rate.txt index ba7b3176dbf538f25802ec53eb0e4a12b2db3cff..b913ae90976009a7caf916352cbfe9475577d9db 100644 --- a/doc/src/compute_smd_plastic_strain_rate.txt +++ b/doc/src/compute_smd_plastic_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given in "units"_units.html of one over time. diff --git a/doc/src/compute_smd_rho.txt b/doc/src/compute_smd_rho.txt index ae50526725e091a21b80a1a1b0c8c39680fbf031..a1ee1d9c5b95a2971e64a52ad4416e74e54fc226 100644 --- a/doc/src/compute_smd_rho.txt +++ b/doc/src/compute_smd_rho.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,8 +33,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be in "units"_units.html of mass over volume. diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt index 68b5dffa1cf558df517156e61bc604604bbfa113..1663c84f65fd3b3c59daf427d4b15fe6a5d27ea9 100644 --- a/doc/src/compute_smd_tlsph_defgrad.txt +++ b/doc/src/compute_smd_tlsph_defgrad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS. This compute outputss a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-particle vector values will be given dimensionless. See "units"_units.html. The per-particle vector has 10 entries. The first diff --git a/doc/src/compute_smd_tlsph_dt.txt b/doc/src/compute_smd_tlsph_dt.txt index 560a9b6fd878386ff140cba30ecf879a62cdc047..c714f3266bceaf96ea1b86d487cf653cdeeeb47e 100644 --- a/doc/src/compute_smd_tlsph_dt.txt +++ b/doc/src/compute_smd_tlsph_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values will be given in "units"_units.html of time. diff --git a/doc/src/compute_smd_tlsph_num_neighs.txt b/doc/src/compute_smd_tlsph_num_neighs.txt index 0420d1903d82c6d4af44e519b309e0da27813293..af5b0741db6c0c964ab4a73b21bdb928b663fe42 100644 --- a/doc/src/compute_smd_tlsph_num_neighs.txt +++ b/doc/src/compute_smd_tlsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle values are dimensionless. See "units"_units.html. diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt index 02bd0c50ddb504d7effd71d7155e5cc39c7a4378..927cd7c7aecaa51cc45c095066586899bd37aefb 100644 --- a/doc/src/compute_smd_tlsph_shape.txt +++ b/doc/src/compute_smd_tlsph_shape.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,9 +33,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute -as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +as input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of diff --git a/doc/src/compute_smd_tlsph_strain.txt b/doc/src/compute_smd_tlsph_strain.txt index f25d1b77db2c32cc25a2d7a3dd64466db1370c20..4536f26c8ea364d40d306f1ac863f3fc4a278dff 100644 --- a/doc/src/compute_smd_tlsph_strain.txt +++ b/doc/src/compute_smd_tlsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The per-particle tensor values will be given dimensionless. See "units"_units.html. diff --git a/doc/src/compute_smd_tlsph_strain_rate.txt b/doc/src/compute_smd_tlsph_strain_rate.txt index 13ca57ac4df413e8348a37d34d49fa606239243e..ae2883e4bbedb0e698cac841601984de90af2031 100644 --- a/doc/src/compute_smd_tlsph_strain_rate.txt +++ b/doc/src/compute_smd_tlsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "How-to discussions, section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. diff --git a/doc/src/compute_smd_tlsph_stress.txt b/doc/src/compute_smd_tlsph_stress.txt index 5d707d4c2f6934cd0b630de1767a43f33b9de46c..50d6b7f4344ffb585cc27a00d644e803904e5fad 100644 --- a/doc/src/compute_smd_tlsph_stress.txt +++ b/doc/src/compute_smd_tlsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -29,11 +29,10 @@ Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute -as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. diff --git a/doc/src/compute_smd_triangle_mesh_vertices.txt b/doc/src/compute_smd_triangle_mesh_vertices.txt index 5b0f0afc4c84a93f0b1f31307da9d7a89197abbe..9e167924d1401fea40a6ac9b0d9bcc7d257d4355 100644 --- a/doc/src/compute_smd_triangle_mesh_vertices.txt +++ b/doc/src/compute_smd_triangle_mesh_vertices.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,9 +31,9 @@ Mach Dynamics in LAMMPS. [Output info:] This compute returns a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as -input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +accessed by any command that uses per-particle values from a compute +as input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding to the first, second, and third vertex of diff --git a/doc/src/compute_smd_ulsph_num_neighs.txt b/doc/src/compute_smd_ulsph_num_neighs.txt index adece9334361d154d3f7d7a62de19b0eaac01a93..202b8f15e1d95ec3441e272a23b618a0f57f443a 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.txt +++ b/doc/src/compute_smd_ulsph_num_neighs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,7 +32,7 @@ Mach Dynamics in LAMMPS. This compute returns a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle values will be given dimensionless, see "units"_units.html. diff --git a/doc/src/compute_smd_ulsph_strain.txt b/doc/src/compute_smd_ulsph_strain.txt index b7d425b12b7e1b0146ba321986e56470719b115f..76c47162a5c85e0def8c8231224ccda416ea6360 100644 --- a/doc/src/compute_smd_ulsph_strain.txt +++ b/doc/src/compute_smd_ulsph_strain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,7 +31,7 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle tensor, which can be accessed by any command that uses per-particle values from a compute as input. -See "Section 6.15"_Section_howto.html#howto_15 for an overview of +See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The per-particle vector has 6 entries, corresponding to the xx, yy, diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt index e2c349c2656de89aaa53534f3980e235caa17901..c851e767b34a418a614cfeb537638ec294ae489f 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.txt +++ b/doc/src/compute_smd_ulsph_strain_rate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,9 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt index 47f903d3b88effc7055084674b0866fe5ad4b596..a5692b2412ce589165a29514c6b199b7d0dd802d 100644 --- a/doc/src/compute_smd_ulsph_stress.txt +++ b/doc/src/compute_smd_ulsph_stress.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. diff --git a/doc/src/compute_smd_vol.txt b/doc/src/compute_smd_vol.txt index fc736a5bf5c2fd0e9c6d89b749acb11d6d79d1e1..fc4871d6f301157c45fcaf88e99301f20cdff31c 100644 --- a/doc/src/compute_smd_vol.txt +++ b/doc/src/compute_smd_vol.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,8 +31,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. -See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for -an overview of LAMMPS output options. +See the "Howto output"_Howto_output.html doc page for an overview of +LAMMPS output options. The per-particle vector values will be given in "units"_units.html of volume. diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 268e23ac2808d82f8750b95bd652cd4d50f6b9d2..3b302a0a71c65de87fee8ae571e866b3cc19653c 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -244,9 +244,8 @@ So the nesting order from inside to outside is bispectrum component, linear then quadratic, vector/tensor component, type. These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. [Restrictions:] diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..792706ecdfae311acd293546d899b51b2bf28d73 --- /dev/null +++ b/doc/src/compute_spin.txt @@ -0,0 +1,78 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +compute spin command :h3 + +[Syntax:] + +compute ID group-ID compute/spin :pre + +ID, group-ID are documented in "compute"_compute.html command +compute/spin = style name of this compute command :ul + +[Examples:] + +compute out_mag all compute/spin :pre + +[Description:] + +Define a computation that calculates magnetic quantities for a system +of atoms having spins. + +This compute calculates 6 magnetic quantities. + +The three first quantities are the x,y and z coordinates of the total magnetization. + +The fourth quantity is the norm of the total magnetization. + +The fifth quantity is the magnetic energy. + +The sixth one is referred to as the spin temperature, according +to the work of "(Nurdin)"_#Nurdin1. + +The simplest way to output the results of the compute spin calculation +is to define some of the quantities as variables, and to use the thermo and +thermo_style commands, for example: + +compute out_mag all compute/spin :pre + +variable mag_z equal c_out_mag\[3\] +variable mag_norm equal c_out_mag\[4\] +variable temp_mag equal c_out_mag\[6\] :pre + +thermo 10 +thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre + +This serie of commands evaluates the total magnetization along z, the norm of +the total magnetization, and the magnetic temperature. Three variables are +assigned to those quantities. The thermo and thermo_style commands print them +every 10 timesteps. + + +[Output info:] + +The array values are "intensive". The array values will be in +metal units ("units"_units.html). + +[Restrictions:] + +The {spin} compute is part of the SPIN package. +This compute is only enabled if LAMMPS was built with this package. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. +The atom_style has to be "spin" for this compute to be valid. + +[Related commands:] none + + +[Default:] none + +:line + +:link(Nurdin1) +[(Nurdin)] Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000) + diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 83b1df68e3555e4d74b4c0296845fc6a395148e7..222513da61d45e22238a38780c39977ec3900b68 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -142,9 +142,8 @@ global system pressure. This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The per-atom array values will be in pressure*volume "units"_units.html as discussed above. diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index 95ef4a553b8df78af94dd0d51a7fc48c12d313fb..23fac4309384bac044259f51d128726725fcd3f7 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt index a6a12dc52ccb31febe7a8bc5559b50913e0f242a..9ee4d3da3462fbed0bc3be6b66212d6988fd938d 100644 --- a/doc/src/compute_tdpd_cc_atom.txt +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,9 +33,9 @@ details see "(Li2015)"_#Li2015a. [Output info:] This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -"Section 6.15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +any command that uses per-atom values from a compute as input. See the +"Howto output"_Howto_output.html doc page for an overview of LAMMPS +output options. The per-atom vector values will be in the units of chemical species per unit mass. diff --git a/doc/src/compute_temp.txt b/doc/src/compute_temp.txt index b88be79e20704a41482ad444668ca8b81d0c4b32..9f3a1ca9061feeaab02ac197f5ab15c1844a709a 100644 --- a/doc/src/compute_temp.txt +++ b/doc/src/compute_temp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,8 +58,8 @@ compute thermo_temp all temp :pre See the "thermo_style" command for more details. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -67,10 +67,9 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -82,8 +81,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -92,8 +91,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index 495366b34501b65e785bff5ec6e442ff02e89b96..6766729ae0c463ce51c6470de27d6966102a0cff 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,8 +93,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -122,8 +122,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_body.txt b/doc/src/compute_temp_body.txt index f72b886cc47afa0b0f7badd75b39ef943375002d..4e3ce3e77f86db797f0222b62d403df6ef82c827 100644 --- a/doc/src/compute_temp_body.txt +++ b/doc/src/compute_temp_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,8 +75,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -104,8 +104,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index f877f6ece84b9a2429d64949eea298e20d98ef74..de8c850a7087329465e84544a2084309602a80d1 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,10 +52,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. The temperature is calculated by the formula KE = DOF/2 k T, where KE = total kinetic energy of all atoms assigned to chunks (sum of 1/2 m @@ -200,8 +199,8 @@ molecule. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. This compute also optionally calculates a global array, if one or more @@ -210,9 +209,8 @@ of the optional values are specified. The number of rows in the array "compute chunk/atom"_compute_chunk_atom.html command. The number of columns is the number of specified values (1 or more). These values can be accessed by any command that uses global array values from a -compute as input. Again, see "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +compute as input. Again, see the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The vector values are "extensive". The array values are "intensive". diff --git a/doc/src/compute_temp_com.txt b/doc/src/compute_temp_com.txt index c7cc5ec4e280db434892260b9b2d7d045515d765..12df694e382657c9424e8b0649a4dd677a2630d6 100644 --- a/doc/src/compute_temp_com.txt +++ b/doc/src/compute_temp_com.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -74,8 +74,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 561b787df637b48a69173f2f863ccec871e4855b..0236319f547a2a71e5f533f797ffb191e6e8254d 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -28,9 +28,9 @@ Define a computation that calculates the temperature of a system based on the center-of-mass velocity of atom pairs that are bonded to each other. This compute is designed to be used with the adiabatic core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham1. See -"Section 6.25"_Section_howto.html#howto_25 of the manual for an -overview of the model as implemented in LAMMPS. Specifically, this -compute enables correct temperature calculation and thermostatting of +the "Howto coreshell"_Howto_coreshell.html doc page for an overview of +the model as implemented in LAMMPS. Specifically, this compute +enables correct temperature calculation and thermostatting of core/shell pairs where it is desirable for the internal degrees of freedom of the core/shell pairs to not be influenced by a thermostat. A compute of this style can be used by any command that computes a @@ -83,8 +83,9 @@ langevin"_fix_langevin.html. The internal energy of core/shell pairs can be calculated by the "compute temp/chunk"_compute_temp_chunk.html command, if chunks are -defined as core/shell pairs. See "Section -6.25"_Section_howto.html#howto_25 for more discussion on how to do this. +defined as core/shell pairs. See the "Howto +coreshell"_Howto_coreshell.html doc page doc page for more discussion +on how to do this. [Output info:] diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt index 168b0b3880b2ec25e2040b17d135d874709dc68a..26d322589ed70d49d23a0ac8948fc4524e04daef 100644 --- a/doc/src/compute_temp_deform.txt +++ b/doc/src/compute_temp_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -104,8 +104,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -113,8 +113,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_deform_eff.txt b/doc/src/compute_temp_deform_eff.txt index d09a0ace2fbb449fd969dc63532402cfa2c3c06a..876d492f3446f7294ed295974e20c0f28a2369bd 100644 --- a/doc/src/compute_temp_deform_eff.txt +++ b/doc/src/compute_temp_deform_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,8 +48,8 @@ component of the electrons is not affected. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_drude.txt b/doc/src/compute_temp_drude.txt index 169b8d588086cefdac9aa0db42fc05ab95b18587..20d9a5c05670a66938a70bb85660cd6b79bc100a 100644 --- a/doc/src/compute_temp_drude.txt +++ b/doc/src/compute_temp_drude.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -22,10 +22,10 @@ compute TDRUDE all temp/drude :pre [Description:] Define a computation that calculates the temperatures of core-Drude -pairs. This compute is designed to be used with the -"thermalized Drude oscillator model"_tutorial_drude.html. Polarizable -models in LAMMPS are described in "this -Section"_Section_howto.html#howto_25. +pairs. This compute is designed to be used with the "thermalized Drude +oscillator model"_Howto_drude.html. Polarizable models in LAMMPS +are described on the "Howto polarizable"_Howto_polarizable.html doc +page. Drude oscillators consist of a core particle and a Drude particle connected by a harmonic bond, and the relative motion of these Drude @@ -57,8 +57,8 @@ kinetic energy of the centers of mass (energy units) kinetic energy of the dipoles (energy units) :ol These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. Both the scalar value and the first two values of the vector diff --git a/doc/src/compute_temp_eff.txt b/doc/src/compute_temp_eff.txt index 409319edcb9f3a89ffc38d43892a8539073c13ba..35ddb75b12c30ffac0d1d5fc249f9abe33617a0a 100644 --- a/doc/src/compute_temp_eff.txt +++ b/doc/src/compute_temp_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,8 +69,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] diff --git a/doc/src/compute_temp_partial.txt b/doc/src/compute_temp_partial.txt index fe2420b4e40d8d28e0b824d8022b8322596877f6..2769246532fd55f8cf36df3c076d6d822609d765 100644 --- a/doc/src/compute_temp_partial.txt +++ b/doc/src/compute_temp_partial.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,8 +65,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -74,10 +74,9 @@ thermostatting. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -89,8 +88,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -99,8 +98,8 @@ more instructions on how to use the accelerated styles effectively. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_profile.txt b/doc/src/compute_temp_profile.txt index 64a6abd283986747d01514a2e53d9fb3ca2cb1b3..4ed04ca67e0e0c07ebc3250829ad4f9486c791d2 100644 --- a/doc/src/compute_temp_profile.txt +++ b/doc/src/compute_temp_profile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -122,8 +122,8 @@ degrees-of-freedom adjustment described in the preceding paragraph, for fixes that constrain molecular motion. It does include the adjustment due to the {extra} option, which is applied to each bin. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. Using this compute in conjunction with a thermostatting fix, as explained there, will effectively implement a profile-unbiased thermostat (PUT), as described in "(Evans)"_#Evans1. @@ -145,8 +145,8 @@ indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10 indices are numbered from 1 to 10 in each dimension. These values can be used by any command that uses global scalar or -vector or array values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector or array values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_ramp.txt b/doc/src/compute_temp_ramp.txt index bc9283469cf2bda9e55f2ee29f95e25d92f68c69..15cad9c0cb814ed464f5c9210499a333f6cf576d 100644 --- a/doc/src/compute_temp_ramp.txt +++ b/doc/src/compute_temp_ramp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,8 +83,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -92,8 +92,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region.txt b/doc/src/compute_temp_region.txt index 3e4a80db8dd1ff4cf2c0cee248754bf2f2721158..f23901af9861633b83b33d5c172b62f8fe3f681c 100644 --- a/doc/src/compute_temp_region.txt +++ b/doc/src/compute_temp_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,8 +81,8 @@ If needed the number of subtracted degrees-of-freedom can be set explicitly using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -90,8 +90,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_region_eff.txt b/doc/src/compute_temp_region_eff.txt index 8baf2dd46cc01f57cbec0ede1d76265b3b8b113f..95892eb25778eac67c1042de5acf2ed97494c4f1 100644 --- a/doc/src/compute_temp_region_eff.txt +++ b/doc/src/compute_temp_region_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -39,8 +39,8 @@ temp/eff"_compute_temp_eff.html command. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_rotate.txt b/doc/src/compute_temp_rotate.txt index 34feca7b6fd014ee4792126aed5c9277e1b4c203..189246d3e47e734b00a63da770e83a0333c9c85e 100644 --- a/doc/src/compute_temp_rotate.txt +++ b/doc/src/compute_temp_rotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,8 +64,8 @@ atoms that include these constraints will be computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. [Output info:] @@ -73,8 +73,8 @@ thermostatting. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_sphere.txt b/doc/src/compute_temp_sphere.txt index 9e9dff2cb6dc149e5834043a7f420f968666f15a..5a55126d121755a60f9705e52189f28dbcca70cf 100644 --- a/doc/src/compute_temp_sphere.txt +++ b/doc/src/compute_temp_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -79,8 +79,8 @@ computed correctly. If needed, the subtracted degrees-of-freedom can be altered using the {extra} option of the "compute_modify"_compute_modify.html command. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. :line @@ -108,8 +108,8 @@ rotational degrees of freedom. This compute calculates a global scalar (the temperature) and a global vector of length 6 (KE tensor), which can be accessed by indices 1-6. These values can be used by any command that uses global scalar or -vector values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index acd3a6218d9e39d25a73be4d7562ee8127ae9cfa..a94d5db8ed767604c3dd6edac9bf81723d02da1b 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 733954d146bc9ec9b90c821f45432115638db7fc..e79b594e3f32a252a1ea352a1b3fc113324ebb3d 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,9 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike. This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +a compute as input. See the "Howto output"_Howto_output.html doc page +for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index b9f832dd03afe36960509535c348973a46e83e01..6484076b37619db625ea585480d1d00b73c455ed 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the 3 components of the torque vector for eqch chunk, due to the forces on the individual atoms in the chunk around @@ -72,7 +71,7 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the torque for each chunk. These values can be accessed by any command that uses global array values from a -compute as input. See "Section 6.15"_Section_howto.html#howto_15 +compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_vacf.txt b/doc/src/compute_vacf.txt index a0d9a3c5f702ea42c77d8a18f433743f73500f77..70f1e99490586badb949d7fe6bec0b791a0ebc1c 100644 --- a/doc/src/compute_vacf.txt +++ b/doc/src/compute_vacf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -55,9 +55,8 @@ correctly with time=0 atom velocities from the restart file. This compute calculates a global vector of length 4, which can be accessed by indices 1-4 by any command that uses global vector values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. +from a compute as input. See the "Howto output"_Howto_output.html doc +page for an overview of LAMMPS output options. The vector values are "intensive". The vector values will be in velocity^2 "units"_units.html. diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt index de02c586bf9d0d052f7e9421e4f52372b5b8e3c4..7e8ad712086fe17931a8676179865117aaf41c1f 100644 --- a/doc/src/compute_vcm_chunk.txt +++ b/doc/src/compute_vcm_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,10 +30,9 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be -defined and examples of how they can be used to measure properties of -a system. +chunk/atom"_compute_chunk_atom.html and "Howto chunk"_Howto_chunk.html +doc pages for details of how chunks can be defined and examples of how +they can be used to measure properties of a system. This compute calculates the x,y,z components of the center-of-mass velocity for each chunk. This is done by summing mass*velocity for @@ -63,8 +62,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index a280b2b151d7e7656a421e8007f04c1eed464c90..a8ce77882ad42069d32d51864cb06ce3566c8bba 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -122,18 +122,16 @@ to locate vacancies (the coordinates are given by the atom coordinates at the time step when the compute was first invoked), while column two data can be used to identify interstitial atoms. -If the {neighbors} value is set to yes, then -this compute creates a local array with 3 columns. There -is one row for each face of each Voronoi cell. The -3 columns are the atom ID of the atom that owns the cell, -the atom ID of the atom in the neighboring cell -(or zero if the face is external), and the area of the face. -The array can be accessed by any command that -uses local values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. More specifically, the array can be accessed by a -"dump local"_dump.html command to write a file containing -all the Voronoi neighbors in a system: +If the {neighbors} value is set to yes, then this compute creates a +local array with 3 columns. There is one row for each face of each +Voronoi cell. The 3 columns are the atom ID of the atom that owns the +cell, the atom ID of the atom in the neighboring cell (or zero if the +face is external), and the area of the face. The array can be +accessed by any command that uses local values from a compute as +input. See the "Howto output"_Howto_output.html doc page for an +overview of LAMMPS output options. More specifically, the array can be +accessed by a "dump local"_dump.html command to write a file +containing all the Voronoi neighbors in a system: compute 6 all voronoi/atom neighbors yes dump d2 all local 1 dump.neighbors index c_6\[1\] c_6\[2\] c_6\[3\] :pre @@ -186,8 +184,8 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the {occupation} keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section -6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See the "Howto +output"_Howto_output.html doc page for an overview of LAMMPS output options. If the {peratom} keyword is set to "no", the per-atom array is still created, but it is not accessible. diff --git a/doc/src/compute_xrd.txt b/doc/src/compute_xrd.txt index 1a151d63f9157380349a55d2f4a49d2ac806a4a2..609fde3582d9efd03bd9c0ae6fbb63ac3d54db20 100644 --- a/doc/src/compute_xrd.txt +++ b/doc/src/compute_xrd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -162,7 +162,7 @@ or degrees) provided with the {2Theta} values. The second column contains the computed diffraction intensities as described above. The array can be accessed by any command that uses global values from -a compute as input. See "this section"_Section_howto.html#howto_15 +a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. All array values calculated by this compute are "intensive". diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 1b64e2e5b46393313fc74099ef9bbf04da946b74..46dd30f7570f7a87d9874367f67f1d4af85a2fca 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -31,6 +31,7 @@ Computes :h1 compute_dpd compute_dpd_atom compute_edpd_temp_atom + compute_entropy_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere @@ -95,6 +96,7 @@ Computes :h1 compute_smd_ulsph_stress compute_smd_vol compute_sna_atom + compute_spin compute_stress_atom compute_tally compute_tdpd_cc_atom diff --git a/doc/src/create_atoms.txt b/doc/src/create_atoms.txt index 5d824ae1ef2e57815bba64e8596d069048a46f12..d80e2d45f1473d2a4a084b35af0140e6a3e0605a 100644 --- a/doc/src/create_atoms.txt +++ b/doc/src/create_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index 6af69214d3c4523318945c3bf70ac0547621dd64..8596cab51d24c6f0283d5d070192153d6d218534 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,8 +37,8 @@ keyword = {special} :l create_bonds many all all 1 1.0 1.2 create_bonds many surf solvent 3 2.0 2.4 -create_bond single/bond 1 1 2 -create_bond single/angle 5 52 98 107 special no :pre +create_bonds single/bond 1 1 2 +create_bonds single/angle 5 52 98 107 special no :pre [Description:] diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index f4ef13654c6eaf3f13a1795862879b6642e7734b..0993b4f927d49a02b8a93328f564c72e16e3fbdb 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,9 +73,9 @@ factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. When a prism region is used, the simulation domain should normally be diff --git a/doc/src/delete_atoms.txt b/doc/src/delete_atoms.txt index 1aa71d341f83a34a25017b4d123996f22a6fcd16..57faf97ad1bf1d213135707989985a1f866a8f8d 100644 --- a/doc/src/delete_atoms.txt +++ b/doc/src/delete_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/delete_bonds.txt b/doc/src/delete_bonds.txt index b1137a22881213506c8921b9e422d0d9f2e33253..b29fa82f2d0d16c9b1a252073080aba43332605c 100644 --- a/doc/src/delete_bonds.txt +++ b/doc/src/delete_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dielectric.txt b/doc/src/dielectric.txt index e98badf87b72c94b3a308c806044499966d76463..f93be8cc25823c691b108dce6d8e41b5d6367775 100644 --- a/doc/src/dielectric.txt +++ b/doc/src/dielectric.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 06abe054e4819e7c7e9ea9e248e7f2285e423572..8adef6cf4b5ed1ee5f25ab1d72c7fc12f43078fc 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,10 +116,9 @@ computed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -131,8 +130,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_class2.txt b/doc/src/dihedral_class2.txt index cb9fc72c223b2293990764db4b0dffb59dc249b5..1a2f37abbbd0352fd04bc6e958912c0b17966627 100644 --- a/doc/src/dihedral_class2.txt +++ b/doc/src/dihedral_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -141,10 +141,9 @@ r3 (distance) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -156,8 +155,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt index 5b43cbbe7f36d937fcb60334bde83a5911a2e61d..1db69e40d5739320b57139e56494749f6661e8d2 100644 --- a/doc/src/dihedral_coeff.txt +++ b/doc/src/dihedral_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,9 +74,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul diff --git a/doc/src/dihedral_cosine_shift_exp.txt b/doc/src/dihedral_cosine_shift_exp.txt index 715682affc010e657556ba9221ca68a093b5259a..7ef27e6bc966b129156159c9714e27a2cc050853 100644 --- a/doc/src/dihedral_cosine_shift_exp.txt +++ b/doc/src/dihedral_cosine_shift_exp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -52,10 +52,9 @@ A (real number) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -67,8 +66,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_fourier.txt b/doc/src/dihedral_fourier.txt index 0accbb22bf80bfb89e1b77bd7fa8760e56ad3e55..f51cbc9c8cd8e1aeed0248730d7b633a3d636f74 100644 --- a/doc/src/dihedral_fourier.txt +++ b/doc/src/dihedral_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,10 +44,9 @@ dm (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -59,8 +58,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_harmonic.txt b/doc/src/dihedral_harmonic.txt index d9a48ff384d9df3dd9228a05be3c523302b80362..1eda0c5d02b8f1a7bbba646ad26d684cff7e7806 100644 --- a/doc/src/dihedral_harmonic.txt +++ b/doc/src/dihedral_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,10 +53,9 @@ Some force fields let {n} be positive or negative which corresponds to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_helix.txt b/doc/src/dihedral_helix.txt index 1e907557b28564f74e3f080160997a107941d4b5..3af4b410bcd24e4469ccdc50e9576fb81cc9539c 100644 --- a/doc/src/dihedral_helix.txt +++ b/doc/src/dihedral_helix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,10 +46,9 @@ C (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -61,8 +60,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_hybrid.txt b/doc/src/dihedral_hybrid.txt index 8cb40eff44a66189d2ff37aadbd0c25ccd5a00c3..c9ca86680c175aca2188891523265ca4d2203f81 100644 --- a/doc/src/dihedral_hybrid.txt +++ b/doc/src/dihedral_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_multi_harmonic.txt b/doc/src/dihedral_multi_harmonic.txt index 7d3c2ea083d0ef78b7e275caa9ca51e1305e8e49..7c22391923b37a065369b53c0871d20cd90710fe 100644 --- a/doc/src/dihedral_multi_harmonic.txt +++ b/doc/src/dihedral_multi_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,10 +40,9 @@ A5 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_nharmonic.txt b/doc/src/dihedral_nharmonic.txt index 8392d83899de8c41cd855e6a038f3e7a585ec08a..aa8f1e0d7fdc646fa6c06009909b750294e06613 100644 --- a/doc/src/dihedral_nharmonic.txt +++ b/doc/src/dihedral_nharmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,10 +40,9 @@ An (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -55,8 +54,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_none.txt b/doc/src/dihedral_none.txt index 3ce2aa1729c6dfb31ad8924b20554f974cbc73b5..4c1ff2ea5d30fadd25949e613b6ec29e4cfa3fdb 100644 --- a/doc/src/dihedral_none.txt +++ b/doc/src/dihedral_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_opls.txt b/doc/src/dihedral_opls.txt index d1a6ba3ff2865db905b97bf72b70d343f509e06e..f0cf91f30ad67fe914b376aef1c0c94ef5145955 100644 --- a/doc/src/dihedral_opls.txt +++ b/doc/src/dihedral_opls.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,10 +48,9 @@ K4 (energy) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_quadratic.txt b/doc/src/dihedral_quadratic.txt index ca2f5aed40f2f67512a255813689a50e35a4c7d7..e65cf2dee86a2b108513f1d83a5cbfe29c8a0034 100644 --- a/doc/src/dihedral_quadratic.txt +++ b/doc/src/dihedral_quadratic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -41,10 +41,9 @@ phi0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -56,8 +55,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 7c17fbf5ef1c50aa939642c0eb224835c3721f0d..10a757e8986d6d9c5f450a84bfffc6be81221078 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index ca592b29b55415fde7c4306fa231ea35e0c5f40a..6aff3f0994777390eba737e8273524f770fd5e8e 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,9 +81,9 @@ the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the dihedral section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral +doc page. "dihedral_style none"_dihedral_none.html - turn off dihedral interactions "dihedral_style zero"_dihedral_zero.html - topology but no interactions diff --git a/doc/src/dihedral_table.txt b/doc/src/dihedral_table.txt index 0b88f26a61076c6b10750ea419b947fb88a0dd8f..d722ef7c82a76c67ac0353a02b1656b8a8de73c0 100644 --- a/doc/src/dihedral_table.txt +++ b/doc/src/dihedral_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -174,10 +174,9 @@ that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -189,8 +188,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index 1c83d4ffa09f7221ac8c3859594abc754b9b28c4..cc7df8cdf9de397a6a91d9ec89bef542f5b5002a 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dihedral_zero.txt b/doc/src/dihedral_zero.txt index 4d33126eeb76330e830fced4f9c55d7b47c86fdf..0c9995a5637c84571297f7b6a28a7162dc75b2fd 100644 --- a/doc/src/dihedral_zero.txt +++ b/doc/src/dihedral_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dimension.txt b/doc/src/dimension.txt index 0531e92acf60d439c22848fc3d2a94b653a1c52d..b7dde7652443a10a7199ddc46f9e7e70a21b3a09 100644 --- a/doc/src/dimension.txt +++ b/doc/src/dimension.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ prior to setting up a simulation box via the "create_box"_create_box.html or "read_data"_read_data.html commands. Restart files also store this setting. -See the discussion in "Section 6"_Section_howto.html for +See the discussion on the "Howto 2d"_Howto_2d.html doc page for additional instructions on how to run 2d simulations. NOTE: Some models in LAMMPS treat particles as finite-size spheres or diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt index 634add196b78fe249d4c42177482b69b05f5719e..b4afd5c3a9b9eb4af9666fc4b57f0b0df85810be 100644 --- a/doc/src/displace_atoms.txt +++ b/doc/src/displace_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 438ff1d4e074779f22217e851799a81f1f7ff857..5b478b7301960bd536ef29158086c0c8b0f34023 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -1,8 +1,8 @@ - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -184,10 +184,10 @@ file and in what format. Settings made via the individual values and the file itself. The {atom}, {local}, and {custom} styles create files in a simple text -format that is self-explanatory when viewing a dump file. Many of the -LAMMPS "post-processing tools"_Section_tools.html, including -"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this -format, as does the "rerun"_rerun.html command. +format that is self-explanatory when viewing a dump file. Some of the +LAMMPS post-processing tools described on the "Tools"_Tools.html doc +page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, +work with this format, as does the "rerun"_rerun.html command. For post-processing purposes the {atom}, {local}, and {custom} text files are self-describing in the following sense. @@ -224,12 +224,12 @@ This bounding box is convenient for many visualization programs. The meaning of the 6 character flags for "xx yy zz" is the same as above. Note that the first two numbers on each line are now xlo_bound instead -of xlo, etc, since they represent a bounding box. See "this -section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic boxes, as defined by LAMMPS, simple formulas -for how the 6 bounding box extents (xlo_bound,xhi_bound,etc) are -calculated from the triclinic parameters, and how to transform those -parameters to and from other commonly used triclinic representations. +of xlo, etc, since they represent a bounding box. See the "Howto +triclinic"_Howto_triclinic.html doc page for a geometric description +of triclinic boxes, as defined by LAMMPS, simple formulas for how the +6 bounding box extents (xlo_bound,xhi_bound,etc) are calculated from +the triclinic parameters, and how to transform those parameters to and +from other commonly used triclinic representations. The "ITEM: ATOMS" line in each snapshot lists column descriptors for the per-atom lines that follow. For example, the descriptors would be @@ -413,10 +413,10 @@ If the filename ends with ".bin", the dump file (or files, if "*" or will be about the same size as a text version, but will typically write out much faster. Of course, when post-processing, you will need to convert it back to text format (see the "binary2txt -tool"_Section_tools.html#binary) or write your own code to read the -binary file. The format of the binary file can be understood by -looking at the tools/binary2txt.cpp file. This option is only -available for the {atom} and {custom} styles. +tool"_Tools.html#binary) or write your own code to read the binary +file. The format of the binary file can be understood by looking at +the tools/binary2txt.cpp file. This option is only available for the +{atom} and {custom} styles. If the filename ends with ".gz", the dump file (or files, if "*" or "%" is also used) is written in gzipped format. A gzipped dump file will @@ -530,7 +530,7 @@ so that each value is 0.0 to 1.0. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are the non-orthogonal vectors of the simulation box edges, as discussed -in "Section 6.12"_Section_howto.html#howto_12. +on the "Howto triclinic"_Howto_triclinic.html doc page. Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has @@ -625,9 +625,9 @@ The {d_name} and {i_name} attributes allow to output custom per atom floating point or integer properties that are managed by "fix property/atom"_fix_property_atom.html. -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index e257f9c4f16d2f768ee4e688f3d71e0a0dd0c1cd..665be14be1330e0b902c73686d430f3ce904a315 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index 93c87d85b7a6064140b6cf320199d3cd99114e10..fbd682dad9cac9c112fc10ee30c31c922e00f4a0 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index 3fa267d2b099a252bce78e49d24c69609dffac2a..06332b5dcf92a593ba084c50f9daaacfd7fb4ae3 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -356,16 +356,16 @@ is used to define body particles with internal state body style. If this keyword is not used, such particles will be drawn as spheres, the same as if they were regular atoms. -The "body"_body.html doc page describes the body styles LAMMPS -currently supports, and provides more details as to the kind of body -particles they represent and how they are drawn by this dump image -command. For all the body styles, individual atoms can be either a -body particle or a usual point (non-body) particle. Non-body +The "Howto body"_Howto_body.html doc page describes the body styles +LAMMPS currently supports, and provides more details as to the kind of +body particles they represent and how they are drawn by this dump +image command. For all the body styles, individual atoms can be +either a body particle or a usual point (non-body) particle. Non-body particles will be drawn the same way they would be as a regular atom. The {bflag1} and {bflag2} settings are numerical values which are passed to the body style to affect how the drawing of a body particle -is done. See the "body"_body.html doc page for a description of what -these parameters mean for each body style. +is done. See the "Howto body"_Howto_body.html doc page for a +description of what these parameters mean for each body style. The only setting currently allowed for the {color} value is {type}, which will color the body particles according to the atom type of the @@ -606,9 +606,9 @@ supported. :l :line -See "Section 10"_Section_modify.html of the manual for information -on how to add new compute and fix styles to LAMMPS to calculate -per-atom quantities which could then be output into dump files. +See the "Modify"_Modify.html doc page for information on how to add +new compute and fix styles to LAMMPS to calculate per-atom quantities +which could then be output into dump files. :line diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 3230507dc3eaebc8bce634acf6a7ac2e3c2c7707..73107d07f786e40d60407423551ba839033d7948 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -486,7 +486,7 @@ to respond to the call from the dump command, and update the appropriate reference positions. This is done be defining an "atom-style variable"_variable.html, {check} in this example, which calculates a Boolean value (0 or 1) for each atom, based on the same -criterion used by dump_modify thresh. +criterion used by dump_modify thresh. See the "compute displace/atom"_compute_displace_atom.html command for more details, including an example of how to produce output that @@ -600,13 +600,13 @@ included.) region foo sphere 10 20 10 15 variable inregion atom rmask(foo) -dump_modify ... thresh v_inregion |^ LAST +dump_modify ... thresh v_inregion |^ LAST :pre This will dump atoms which crossed the boundary of the spherical region since the last dump. variable charge atom "(q > 0.5) || (q < -0.5)" -dump_modify ... thresh v_charge |^ LAST +dump_modify ... thresh v_charge |^ LAST :pre This will dump atoms whose charge has changed from an absolute value less than 1/2 to greater than 1/2 (or vice versa) since the last dump. diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt index 7e68490a68e013c42f13883d9b7d1f9044929ce8..9fa04bd1aeed0de92d8fac59dfe3e8e0d83bee3e 100644 --- a/doc/src/dump_molfile.txt +++ b/doc/src/dump_molfile.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 70111a36a8b28d9654db6779426090b7e37b507d..b1c63736514d00e4c35e1056aebab49d18f1cc54 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt index d4d28c81fca69cea2fb65d72e940acf4de0fdcb0..afc6099534eb5c80ffb18461f0f8426ea50bcc67 100644 --- a/doc/src/dump_vtk.txt +++ b/doc/src/dump_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/echo.txt b/doc/src/echo.txt index 3141c7a719bcb0de5d39366183a269f761bd0230..dc6918dc8981af7b971e3e3cd406d29c6aa2e8b7 100644 --- a/doc/src/echo.txt +++ b/doc/src/echo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix.txt b/doc/src/fix.txt index e54a918cd0e2d876088f9cc76a4a52136df71a7e..fd966b5bd9916407648f6db1ea7f01d293faef10 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -30,9 +30,9 @@ Set a fix that will be applied to a group of atoms. In LAMMPS, a timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary -conditions, computing diagnostics, etc. There are dozens of fixes -defined in LAMMPS and new ones can be added; see "this -section"_Section_modify.html for a discussion. +conditions, computing diagnostics, etc. There are hundredes of fixes +defined in LAMMPS and new ones can be added; see the +"Modify"_Modify.html doc page for details. Fixes perform their operations at different stages of the timestep. If 2 or more fixes operate at the same stage of the timestep, they are @@ -133,7 +133,7 @@ reduce"_compute_reduce.html command, or histogrammed by the "fix ave/histo"_fix_ave_histo.html command. :l :ule -See this "howto section"_Section_howto.html#howto_15 for a summary of +See the "Howto output"_Howto_output.html doc page for a summary of various LAMMPS output options, many of which involve fixes. The results of fixes that calculate global quantities can be either @@ -151,16 +151,20 @@ for further info. :line -Each fix style has its own documentation page which describes its -arguments and what it does, as listed below. Here is an alphabetic -list of fix styles available in LAMMPS. They are also given in more -compact form in the Fix section of "this -page"_Section_commands.html#cmd_5. +Each fix style has its own doc page which describes its arguments and +what it does, as listed below. Here is an alphabetic list of fix +styles available in LAMMPS. They are also listed in more compact form +on the "Commands fix"_Commands_fix.html doc page. There are also additional fix styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the fix section -of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all fix styles is on the "Commands fix"_Commands_fix.html doc page. + +There are also additional accelerated fix styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands fix"_Commands_fix.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accerlerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time "addforce"_fix_addforce.html - add a force to each atom diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 19d1009b8a838829c0dfee1adde7526134d29053..0ca28fb8694c6c5c4d4c2d39ab649dc79a9152a3 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -205,6 +205,14 @@ a bond coefficient over time, very similar to how the {pair} keyword operates. The only difference is that now a bond coefficient for a given bond type is adapted. +A wild-card asterisk can be used in place of or in conjunction with +the bond type argument to set the coefficients for multiple bond types. +This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of +atom types, then an asterisk with no numeric values means all types +from 1 to N. A leading asterisk means all types from 1 to n (inclusive). +A trailing asterisk means all types from n to N (inclusive). A middle +asterisk means all types from m to n (inclusive). + Currently {bond} does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are working with fix_adapt are @@ -262,10 +270,10 @@ fix 1 center adapt 10 atom diameter v_size :pre No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. For "rRESPA time integration"_run_style.html, this fix changes parameters on the outermost rRESPA level. diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 5dd58bc39adb83c1994bf847bcaf4e878ea34fb4..7e30a1d29d5b4354b7fae0761f50fc7d8d6e8dd3 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -243,10 +243,10 @@ parameters on the outermost rRESPA level. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt index b2ac95eabb0f4e2e49e4af226ae6cc98ea0d0358..51be39fdb2b72156560b0d85c56b6fc1a517056f 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,12 +103,12 @@ converge properly. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -150,11 +150,11 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the potential -energy discussed above. The vector is the total force on the group of -atoms before the forces on individual atoms are changed by the fix. -The scalar and vector values calculated by this fix are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the potential energy discussed above. The vector is the +total force on the group of atoms before the forces on individual +atoms are changed by the fix. The scalar and vector values calculated +by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt index 793ec0e0157121a404a6991a2e67d9c01444ae21..c80fad26da1c5e40d8a96f42c034f2f8b18cdb86 100644 --- a/doc/src/fix_addtorque.txt +++ b/doc/src/fix_addtorque.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,11 +70,11 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its torque. Default is the outermost level. This fix computes a global scalar and a global 3-vector, which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The scalar is the potential energy discussed above. The vector is the -total torque on the group of atoms before the forces on individual -atoms are changed by the fix. The scalar and vector values calculated -by this fix are "extensive". +accessed by various "output commands"_Howto_output.html. The scalar +is the potential energy discussed above. The vector is the total +torque on the group of atoms before the forces on individual atoms are +changed by the fix. The scalar and vector values calculated by this +fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt index 27070c9be53f3d725e5f4492a1d35ce1deffead2..c6af361afcfe24a5da8cc97c4e917238fe981ab0 100644 --- a/doc/src/fix_append_atoms.txt +++ b/doc/src/fix_append_atoms.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -87,10 +87,10 @@ define the lattice spacings. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_atc.txt b/doc/src/fix_atc.txt index 49014f0591ff08e6f6e636067eed11ee9c8aab43..6de917e5714e6b68537b1180a7f7c5b9769cec81 100644 --- a/doc/src/fix_atc.txt +++ b/doc/src/fix_atc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,7 +102,13 @@ Note coupling and post-processing can be combined in the same simulations using [Restart, fix_modify, output, run start/stop, minimize info:] -No information about this fix is written to "binary restart files"_restart.html. The "fix_modify"_fix_modify.html options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. +No information about this fix is written to "binary restart +files"_restart.html. The "fix_modify"_fix_modify.html options +relevant to this fix are listed below. No global scalar or vector or +per-atom quantities are stored by this fix for access by various +"output commands"_Howto_output.html. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_atom_swap.txt b/doc/src/fix_atom_swap.txt index bf56277214bf78ac10270d40ea2fcd56c1391aa7..c1d84dade1954b2a8d1ec15bb699cb99a5d1e1ae 100644 --- a/doc/src/fix_atom_swap.txt +++ b/doc/src/fix_atom_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,8 +150,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global vector of length 2, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The vector -values are the following global cumulative quantities: +by various "output commands"_Howto_output.html. The vector values are +the following global cumulative quantities: 1 = swap attempts 2 = swap successes :ul diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index 3251125a5d2f21e8f9cdeea958112a5a23b59506..10deaf64cd2900ee76be741c7a835ed2d0e04175 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,7 +38,7 @@ fix 1 all ave/atom 10 20 1000 c_my_stress\[*\] :pre Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting per-atom averages can be used by other "output -commands"_Section_howto.html#howto_15 such as the "fix +commands"_Howto_output.html such as the "fix ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands. The group specified with the command means only atoms within the group @@ -124,7 +124,7 @@ appended, the per-atom vector calculated by the compute is used. If a bracketed term containing an index I is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can +LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -136,8 +136,8 @@ the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. See the discussion above for how I can -be specified with a wildcard asterisk to effectively specify multiple +LAMMPS"_Modify.html. See the discussion above for how I can be +specified with a wildcard asterisk to effectively specify multiple values. If a value begins with "v_", a variable name must follow which has @@ -155,14 +155,14 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. +commands"_Howto_output.html. This fix produces a per-atom vector or array which can be accessed by -various "output commands"_Section_howto.html#howto_15. A vector is -produced if only a single quantity is averaged by this fix. If two or -more quantities are averaged, then an array of values is produced. -The per-atom values can only be accessed on timesteps that are -multiples of {Nfreq} since that is when averaging is performed. +various "output commands"_Howto_output.html. A vector is produced if +only a single quantity is averaged by this fix. If two or more +quantities are averaged, then an array of values is produced. The +per-atom values can only be accessed on timesteps that are multiples +of {Nfreq} since that is when averaging is performed. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index a8691d376772f458d5c0ed82376fcd0154b7a69a..d331e512953b8c32817f0aef973ca99d4289216a 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,17 +85,17 @@ fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre Use one or more per-atom vectors as inputs every few timesteps, sum the values over the atoms in each chunk at each timestep, then average the per-chunk values over longer timescales. The resulting chunk -averages can be used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style -custom"_thermo_style.html, and can also be written to a file. +averages can be used by other "output commands"_Howto_output.html such +as "thermo_style custom"_thermo_style.html, and can also be written to +a file. In LAMMPS, chunks are collections of atoms defined by a "compute chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and "Section -6.23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and the "Howto +chunk"_Howto_chunk.html doc page for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -263,7 +263,7 @@ previously defined in the input script. If no bracketed integer is appended, the per-atom vector calculated by the compute is used. If a bracketed integer is appended, the Ith column of the per-atom array calculated by the compute is used. Users can also write code for -their own compute styles and "add them to LAMMPS"_Section_modify.html. +their own compute styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -274,7 +274,7 @@ bracketed integer is appended, the Ith column of the per-atom array calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error results. Users can also write code for their -own fix styles and "add them to LAMMPS"_Section_modify.html. See the +own fix styles and "add them to LAMMPS"_Modify.html. See the discussion above for how I can be specified with a wildcard asterisk to effectively specify multiple values. @@ -456,20 +456,19 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -the number of chunks {Nchunk} as calculated by the specified "compute +various "output commands"_Howto_output.html. The values can only be +accessed on timesteps that are multiples of {Nfreq} since that is when +averaging is performed. The global array has # of rows = the number +of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The # of columns = M+1+Nvalues, where M = 1 to 4, depending on whether the optional -columns for OrigID and CoordN are used, as explained above. -Following the optional columns, the next column contains the count of -atoms in the chunk, and the remaining columns are the Nvalue -quantities. When the array is accessed with a row I that exceeds the -current number of chunks, than a 0.0 is returned by the fix instead of -an error, since the number of chunks can vary as a simulation runs -depending on how that value is computed by the compute chunk/atom -command. +columns for OrigID and CoordN are used, as explained above. Following +the optional columns, the next column contains the count of atoms in +the chunk, and the remaining columns are the Nvalue quantities. When +the array is accessed with a row I that exceeds the current number of +chunks, than a 0.0 is returned by the fix instead of an error, since +the number of chunks can vary as a simulation runs depending on how +that value is computed by the compute chunk/atom command. The array values calculated by this fix are treated as "intensive", since they are typically already normalized by the count of atoms in diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 371f2f66a88f5394bac76c74e18a811939eb6961..22e8768f1d04444df665513b4d5651c1e31cdbde 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,7 +68,7 @@ calculate time correlations between them at varying time intervals, and average the correlation data over longer timescales. The resulting correlation values can be time integrated by "variables"_variable.html or used by other "output -commands"_Section_howto.html#howto_15 such as "thermo_style +commands"_Howto_output.html such as "thermo_style custom"_thermo_style.html, and can also be written to a file. See the "fix ave/correlate/long"_fix_ave_correlate_long.html command for an alternate method for computing correlation functions efficiently over @@ -176,7 +176,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -189,7 +189,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style or @@ -313,16 +313,15 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The values can -only be accessed on timesteps that are multiples of {Nfreq} since that -is when averaging is performed. The global array has # of rows = -{Nrepeat} and # of columns = Npair+2. The first column has the time -delta (in timesteps) between the pairs of input values used to -calculate the correlation, as described above. The 2nd column has the -number of samples contributing to the correlation average, as -described above. The remaining Npair columns are for I,J pairs of the -N input values, as determined by the {type} keyword, as described -above. +various "output commands"_Howto_output.html. The values can only be +accessed on timesteps that are multiples of {Nfreq} since that is when +averaging is performed. The global array has # of rows = {Nrepeat} +and # of columns = Npair+2. The first column has the time delta (in +timesteps) between the pairs of input values used to calculate the +correlation, as described above. The 2nd column has the number of +samples contributing to the correlation average, as described above. +The remaining Npair columns are for I,J pairs of the N input values, +as determined by the {type} keyword, as described above. For {type} = {auto}, the Npair = N columns are ordered: C11, C22, ..., CNN. :ulb,l diff --git a/doc/src/fix_ave_correlate_long.txt b/doc/src/fix_ave_correlate_long.txt index 7b4bc53701cf9232ca87cd6cec1ceee38ac67690..ac0ef873aac6ae3cd90fca5077a3cc86e3160645 100644 --- a/doc/src/fix_ave_correlate_long.txt +++ b/doc/src/fix_ave_correlate_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 043f0e22be3c7dda7b85209b9b6c53c3578c5b30..f1da130ff7e25c84528bda44cc2e582a8e910274 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,10 +69,9 @@ fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD\[1\] c_XRD\[2\] :pre Use one or more values as inputs every few timesteps to create a single histogram. The histogram can then be averaged over longer timescales. The resulting histogram can be used by other "output -commands"_Section_howto.html#howto_15, and can also be written to a -file. The fix ave/histo/weight command has identical syntax to fix -ave/histo, except that exactly two values must be specified. See -details below. +commands"_Howto_output.html, and can also be written to a file. The +fix ave/histo/weight command has identical syntax to fix ave/histo, +except that exactly two values must be specified. See details below. The group specified with this command is ignored for global and local input values. For per-atom input values, only atoms in the group @@ -183,11 +182,11 @@ Note that there is a "compute reduce"_compute_reduce.html command which can sum per-atom quantities into a global scalar or vector which can thus be accessed by fix ave/histo. Or it can be a compute defined not in your input script, but by "thermodynamic -output"_thermo_style.html or other fixes such as "fix -nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See -the doc pages for these commands which give the IDs of these computes. -Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html +or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for +these commands which give the IDs of these computes. Users can also +write code for their own compute styles and "add them to +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -204,7 +203,7 @@ values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then @@ -320,10 +319,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector and global array which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The values can only be accessed on timesteps that are multiples of -{Nfreq} since that is when a histogram is generated. The global -vector has 4 values: +accessed by various "output commands"_Howto_output.html. The values +can only be accessed on timesteps that are multiples of {Nfreq} since +that is when a histogram is generated. The global vector has 4 +values: 1 = total counts in the histogram 2 = values that were not histogrammed (see {beyond} keyword) diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 266e3f0e38488694dfce0b442a607a6851483377..a53e318d3fd83a3aab0382876b305681ed17ee0b 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -64,7 +64,7 @@ fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre Use one or more global values as inputs every few timesteps, and average them over longer timescales. The resulting averages can be -used by other "output commands"_Section_howto.html#howto_15 such as +used by other "output commands"_Howto_output.html such as "thermo_style custom"_thermo_style.html, and can also be written to a file. Note that if no time averaging is done, this command can be used as a convenient way to simply output one or more global values to @@ -168,7 +168,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them -to LAMMPS"_Section_modify.html. +to LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If {mode} = scalar, then if @@ -184,7 +184,7 @@ specify multiple values. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. If {mode} = scalar, then @@ -305,10 +305,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global scalar or global vector or global array -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The values can only be -accessed on timesteps that are multiples of {Nfreq} since that is when -averaging is performed. +which can be accessed by various "output commands"_Howto_output.html. +The values can only be accessed on timesteps that are multiples of +{Nfreq} since that is when averaging is performed. A scalar is produced if only a single input value is averaged and {mode} = scalar. A vector is produced if multiple input values are diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 5d7dec3e6aef7bb804f312546cb15bbe85b0e639..1fc7e4a18dd8f5efd1b84a21c0a785797be692a1 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,12 +63,12 @@ to it. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -80,8 +80,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -95,10 +95,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index f148e6f99663fe6028e83a246f334b5160ddb470..2de17cdd2a992344886a3eec4d92bc8e3d15b893 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -357,8 +357,8 @@ number of particles (or total weight) on any processor to the average number of particles (or total weight) per processor. These quantities can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar and vector values -calculated by this fix are "intensive". +commands"_Howto_output.html. The scalar and vector values calculated +by this fix are "intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index f53b7c785c251240a0d325b820545f342ce21c06..f5bbc8a2519dcef980bdce8e3d08eb22a8789867 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 83364b9efbbb0b6b9135707c15cae7353ca5b0da..bdb2f2a8624869a8552992b246a111cb3396e7c5 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ are relevant to this fix. This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive". +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive". These are the 2 quantities: diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index c0045ac0f081e4df37c9fd6cf201d43238aea88f..ab34433cecf631fbb8b9cff9fb87d43b87d7c07d 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -211,8 +211,8 @@ are relevant to this fix. This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive". +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive". These are the 2 quantities: diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index f85ef9bc1aa6ea034364e5358ac1eafa2824f0d6..883968e012557e2ee8d13eddef15b8bc1f6873ef 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -298,9 +298,8 @@ relevant to this fix. This fix computes one statistic for each {react} argument that it stores in a global vector, of length 'number of react arguments', that -can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated by -this fix are "intensive". +can be accessed by various "output commands"_Howto_output.html. The +vector values calculated by this fix are "intensive". These is 1 quantity for each react argument: diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index ca7069e2478de279e063b5e43f1a82d29fe1f9b1..a829171f333aa3aa850fbc04c659eae6ac61ad40 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,13 +150,13 @@ the Boltzmann criterion. This fix computes two statistical quantities as a global 2-vector of output, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The first component of the -vector is the cumulative number of swaps performed by all processors. -The second component of the vector is the cumulative number of swaps -attempted (whether accepted or rejected). Note that a swap "attempt" -only occurs when swap partners meeting the criteria described above -are found on a particular timestep. The vector values calculated by -this fix are "intensive". +commands"_Howto_output.html. The first component of the vector is the +cumulative number of swaps performed by all processors. The second +component of the vector is the cumulative number of swaps attempted +(whether accepted or rejected). Note that a swap "attempt" only +occurs when swap partners meeting the criteria described above are +found on a particular timestep. The vector values calculated by this +fix are "intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index e3d75ee858ea82013a59441cbc1fe016fcd19670..8e21ec2c748963302db1fd9876cc855d0d1e35d8 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -315,17 +315,15 @@ specified by the {press} keyword will be unaffected by the {temp} setting. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -pressure-volume energy, plus the strain energy, if it exists, -as described above. -The energy values reported at the -end of a minimization run under "Minimization stats" include this -energy, and so differ from what LAMMPS normally reports as potential -energy. This fix does not support the "fix_modify"_fix_modify.html -{energy} option, because that would result in double-counting of the -fix energy in the minimization energy. Instead, the fix energy can be -explicitly added to the potential energy using one of these two -variants: +"output commands"_Howto_output.html. The scalar is the pressure-volume +energy, plus the strain energy, if it exists, as described above. The +energy values reported at the end of a minimization run under +"Minimization stats" include this energy, and so differ from what +LAMMPS normally reports as potential energy. This fix does not support +the "fix_modify"_fix_modify.html {energy} option, because that would +result in double-counting of the fix energy in the minimization +energy. Instead, the fix energy can be explicitly added to the +potential energy using one of these two variants: variable emin equal pe+f_1 :pre diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index f8de2b4efec469736a067faa51fd4ac5a7d863eb..6f3769fafe6a634770dcdedb8908540972ee5d70 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,9 +103,9 @@ the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index e48dedacd9e17c54b7f4a28d588d173a821ad289..4a1d84de64a458dbc56999885ca8246a03ba21ed 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -99,9 +99,9 @@ to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_controller.txt b/doc/src/fix_controller.txt index cfb26138fdaa468c3074b1ef6fa1f1dfe6c6eb8c..7458f1bcfa015985158cbb3a1148fe625eb964e4 100644 --- a/doc/src/fix_controller.txt +++ b/doc/src/fix_controller.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,7 +139,7 @@ for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates a global @@ -150,7 +150,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. +them to LAMMPS"_Modify.html. If {pvar} begins with "v_", a variable name must follow which has been previously defined in the input script. Only equal-style variables @@ -180,9 +180,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector with 3 values which can be accessed -by various "output commands"_Section_howto.html#howto_15. The values -can be accessed on any timestep, though they are only updated on -timesteps that are a multiple of {Nevery}. +by various "output commands"_Howto_output.html. The values can be +accessed on any timestep, though they are only updated on timesteps +that are a multiple of {Nevery}. The three values are the most recent updates made to the control variable by each of the 3 terms in the PID equation above. The first diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index c870c73bdccf918288589c5141ba4dbafcc60434..e92d1e6b19c5943d4de785c916738fdd10dc8ef0 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -94,7 +94,7 @@ nvt/sllod"_fix_nvt_sllod.html and "compute temp/deform"_compute_temp_deform.html commands for more details. Note that simulation of a continuously extended system (extensional flow) can be modeled using the "USER-UEF -package"_Section_packages.html#USER-UEF and its "fix +package"_Packages_details.html#USER-UEF and its "fix commands"_fix_nh_uef.html. For the {x}, {y}, {z} parameters, the associated dimension cannot be @@ -550,10 +550,9 @@ command if you want to include lattice spacings in a variable formula. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -565,18 +564,17 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] This fix will restore the initial box settings from "binary restart files"_restart.html, which allows the fix to be properly continue deformation, when using the start/stop options of the "run"_run.html -command. None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. +command. None of the "fix_modify"_fix_modify.html options are +relevant to this fix. No global or per-atom quantities are stored by +this fix for access by various "output commands"_Howto_output.html. This fix can perform deformation over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index 477c14ea8955ed45763bb1dd27d1242898e22ff5..277ca8777ad7409e586eb16344df34168786c165 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ side = {in}. NOTE: LAMMPS checks that the specified region is wholly inside the simulation box. It can do this correctly for orthonormal simulation -boxes. However for "triclinic boxes"_Section_howto.html#howto_12, it -only tests against the larger orthonormal box that bounds the tilted +boxes. However for "triclinic boxes"_Howto_triclinic.html, it only +tests against the larger orthonormal box that bounds the tilted simulation box. If the specified region includes volume outside the tilted box, then an insertion will likely fail, leading to a "lost atoms" error. Thus for triclinic boxes you should insure the @@ -263,9 +263,9 @@ operation of the fix continues in an uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_dpd_energy.txt b/doc/src/fix_dpd_energy.txt index 1c10d954d6eb910f5863120a405ace281b12e6da..f539bc534e76b7e667938ce4dcd78a2f9501ed4e 100644 --- a/doc/src/fix_dpd_energy.txt +++ b/doc/src/fix_dpd_energy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,10 +50,9 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -65,8 +64,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_dpd_source.txt b/doc/src/fix_dpd_source.txt index b6decc657cea412ac80a96ff4bcf7d8d84bb6348..04af9a28a184676e1ebc51f67dc13eb5340787a0 100644 --- a/doc/src/fix_dpd_source.txt +++ b/doc/src/fix_dpd_source.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,10 +63,10 @@ cuboid domain to apply the source flux to. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt index 235d3d38b5f97d91dae8a4fa3122e77486fbf7cd..92e68d13a447e07f9f83c4f5c2a1d1666cbdef53 100644 --- a/doc/src/fix_drag.txt +++ b/doc/src/fix_drag.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -47,9 +47,9 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms by the drag force. The vector -values calculated by this fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms by the drag force. The vector values +calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_drude.txt b/doc/src/fix_drude.txt index faa354b31439dbecf3dc8e04a3b31e47d1011757..80eb79201b2a8e5e0222337209bbacb074c6c78e 100644 --- a/doc/src/fix_drude.txt +++ b/doc/src/fix_drude.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -25,10 +25,10 @@ fix 1 all drude C C N C N D D D :pre [Description:] Assign each atom type in the system to be one of 3 kinds of atoms -within the Drude polarization model. This fix is designed to be -used with the "thermalized Drude oscillator -model"_tutorial_drude.html. Polarizable models in LAMMPS -are described in "this Section"_Section_howto.html#howto_25. +within the Drude polarization model. This fix is designed to be used +with the "thermalized Drude oscillator model"_Howto_drude.html. +Polarizable models in LAMMPS are described on the "Howto +polarizable"_Howto_polarizable.html doc page. The three possible types can be designated with an integer (0,1,2) or capital letter (N,C,D): diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 2e094d528c368ca35e59eb09d67abe2e2eb6198e..8864cc4eb66242f220bbc50a3e87e2e9abb5385a 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,8 +34,8 @@ Transform the coordinates of Drude oscillators from real to reduced and back for thermalizing the Drude oscillators as described in "(Lamoureux)"_#Lamoureux1 using a Nose-Hoover thermostat. This fix is designed to be used with the "thermalized Drude oscillator -model"_tutorial_drude.html. Polarizable models in LAMMPS are -described in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html. Polarizable models in LAMMPS are described +on the "Howto polarizable"_Howto_polarizable.html doc page. Drude oscillators are a pair of atoms representing a single polarizable atom. Ideally, the mass of Drude particles would vanish diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 1bed4f9e89271f367dd68257f78f33b76c42f11f..be4fbd255b58983cd52ac8a9fbb1e4144b5a2f6c 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -19,7 +19,9 @@ Tmin = minimum dt allowed which can be NULL (time units) Tmax = maximum dt allowed which can be NULL (time units) Xmax = maximum distance for an atom to move in one timestep (distance units) zero or more keyword/value pairs may be appended -keyword = {units} :ul +keyword = {emax} or {units} :ul + {emax} value = Emax + Emax = maximum kinetic energy change for an atom in one timestep (energy units) {units} value = {lattice} or {box} lattice = Xmax is defined in lattice units box = Xmax is defined in simulation box units :pre @@ -27,12 +29,17 @@ keyword = {units} :ul [Examples:] fix 5 all dt/reset 10 1.0e-5 0.01 0.1 -fix 5 all dt/reset 10 0.01 2.0 0.2 units box :pre +fix 5 all dt/reset 10 0.01 2.0 0.2 units box +fix 5 all dt/reset 5 NULL 0.001 0.5 emax 30 units box :pre [Description:] Reset the timestep size every N steps during a run, so that no atom -moves further than Xmax, based on current atom velocities and forces. +moves further than the specified {Xmax} distance, based on current +atom velocities and forces. Optionally an additional criterion is +imposed by the {emax} keyword, so that no atom's kinetic energy +changes by more than the specified {Emax}. + This can be useful when starting from a configuration with overlapping atoms, where forces will be large. Or it can be useful when running an impact simulation where one or more high-energy atoms collide with @@ -48,7 +55,12 @@ current velocity and force. Since performing this calculation exactly would require the solution to a quartic equation, a cheaper estimate is generated. The estimate is conservative in that the atom's displacement is guaranteed not to exceed {Xmax}, though it may be -smaller. +smaller. + +In addition if the {emax} keyword is used, the specified {Emax} value +is enforced as a limit on how much an atom's kinetic energy can +change. If the timestep required is even smaller than for the {Xmax} +displacement, then the smaller timestep is used. Given this putative timestep for each atom, the minimum timestep value across all atoms is computed. Then the {Tmin} and {Tmax} bounds are @@ -70,8 +82,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar stores -the last timestep on which the timestep was reset to a new value. +"output commands"_Howto_output.html. The scalar stores the last +timestep on which the timestep was reset to a new value. The scalar value calculated by this fix is "intensive". @@ -87,4 +99,5 @@ minimization"_minimize.html. [Default:] -The option defaults is units = lattice. +The option defaults are units = lattice, and no emax kinetic energy +limit. diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt index 5d2b86fe4b9c1dcc3cc3b8ae5fd25802d5d1c1bd..b5a43f68aa76b5a205f50df3e6ff9325099711bb 100644 --- a/doc/src/fix_efield.txt +++ b/doc/src/fix_efield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -134,11 +134,10 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix adding its forces. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the potential -energy discussed above. The vector is the total force added to the -group of atoms. The scalar and vector values calculated by this fix -are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the potential energy discussed above. The vector is the +total force added to the group of atoms. The scalar and vector values +calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index 40752a811fdabe06285d0f980ee9cdd253ac10e6..cfcc917d012ba1dca5ff08afd75fb718bb101f82 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_enforce2d.txt b/doc/src/fix_enforce2d.txt index 4bbf41d25d13122c15f3da14ad8764e85d8346d9..2925e44bda17ef8cf023a9e41c0513694d4c50fa 100644 --- a/doc/src/fix_enforce2d.txt +++ b/doc/src/fix_enforce2d.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,10 +31,9 @@ not move from their initial z coordinate. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -46,8 +45,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -56,9 +55,9 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_eos_cv.txt b/doc/src/fix_eos_cv.txt index 4c973043353c307790aa15447d70ffe77f375e7d..b94e2c64a97ebd8373b3a3dafcee2ab9ecad6ed5 100644 --- a/doc/src/fix_eos_cv.txt +++ b/doc/src/fix_eos_cv.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 42778d79781c80ced6c90855f7fefe78f62d7207..743c51f4157cfeffc8c59840f9f95ab3132a3d74 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index 0c878743471ae03c5bd76fec05f16dbc7631f01e..f9deab61c8acebfb5ffe69966b1880e7cacff369 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,10 +156,9 @@ no 0.93 0.00 0.000 -1.76 :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index ed6c6d03775d5fe11195b3c3d6ccfc7eb365c909..6237a137fd0aa8c719d5f96f7791ebb176b669da 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,9 +73,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar, which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative number of deleted atoms. The scalar value calculated by -this fix is "intensive". +"output commands"_Howto_output.html. The scalar is the cumulative +number of deleted atoms. The scalar value calculated by this fix is +"intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_external.txt b/doc/src/fix_external.txt index b28d33446fe6df61d6efd46017dc37c4cf6f61ee..1dec226414c9f7e62b13b3d60a2f34efc6326ccd 100644 --- a/doc/src/fix_external.txt +++ b/doc/src/fix_external.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,11 +31,10 @@ fix 1 all external pf/array 10 :pre [Description:] This fix allows external programs that are running LAMMPS through its -"library interface"_Section_howto.html#howto_19 to modify certain -LAMMPS properties on specific timesteps, similar to the way other -fixes do. The external driver can be a "C/C++ or Fortran -program"_Section_howto.html#howto_19 or a "Python -script"_Section_python.html. +"library interface"_Howto_library.html to modify certain LAMMPS +properties on specific timesteps, similar to the way other fixes do. +The external driver can be a "C/C++ or Fortran +program"_Howto_library.html or a "Python script"_Python.html. :line @@ -137,9 +136,8 @@ external program to the system's virial as part of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar stored by this fix -is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar stored by this fix is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index b782d285c768ec6f4b25eaf29037cef6695e7613..d1e5e12f3ef1b764d4d2d9cc35a5d8f504c27a4e 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,10 +63,9 @@ No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. These fixes are not invoked during "energy -minimization"_minimize.html. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. These +fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_flow_gauss.txt b/doc/src/fix_flow_gauss.txt index efa58ea65fa8b71a940d707dbbabb5119ad90759..843c2a66a5505d5b3c7051fd9d84897a99ea4138 100644 --- a/doc/src/fix_flow_gauss.txt +++ b/doc/src/fix_flow_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -128,11 +128,11 @@ integrator the fix computes and adds the external acceleration. Default is the outermost level. This fix computes a global scalar and a global 3-vector of forces, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is the negative of the -work done on the system, see above discussion. The vector is the total force -that this fix applied to the group of atoms on the current timestep. -The scalar and vector values calculated by this fix are "extensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the negative of the work done on the system, see above +discussion. The vector is the total force that this fix applied to +the group of atoms on the current timestep. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_freeze.txt b/doc/src/fix_freeze.txt index a63ee4cb32688c286797292acbaa140fbed18101..76a9fd3b1a2d3f3ffc8372a2cebac2ac85f9fb6f 100644 --- a/doc/src/fix_freeze.txt +++ b/doc/src/fix_freeze.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -31,12 +31,12 @@ using "fix setforce"_fix_setforce.html. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -48,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -60,10 +60,10 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 38f0fb95ce0530d425689b0daa9052e6a6995074..394690ea5d173b898b51acc6ee9b2094aa5d26b1 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -349,7 +349,7 @@ in the context of NVT dynamics. NOTE: If the density of the cell is initially very small or zero, and increases to a much larger density after a period of equilibration, then certain quantities that are only calculated once at the start -(kspace parameters, tail corrections) may no longer be accurate. The +(kspace parameters) may no longer be accurate. The solution is to start a new simulation after the equilibrium density has been reached. @@ -382,8 +382,8 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global vector of length 8, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The vector -values are the following global cumulative quantities: +by various "output commands"_Howto_output.html. The vector values are +the following global cumulative quantities: 1 = translation attempts 2 = translation successes diff --git a/doc/src/fix_gld.txt b/doc/src/fix_gld.txt index 1425f62e13374d3c6f0feb14d624c63a1e2128cf..1c5db6157ddaca593ffc5fc70ebc59613038ae88 100644 --- a/doc/src/fix_gld.txt +++ b/doc/src/fix_gld.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -126,7 +126,7 @@ sense, a restarted simulation should produce the same behavior. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. +access by various "output commands"_Howto_output.html. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index 6568060f0c2482c99607b1af93022a20ec0d6fe6..9fdc72bf9f206f9b5a6e55267638af159810beeb 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,9 +116,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". [Restrictions:] diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index dae8ac5ed0910fc2c91b776339de840707bf5500..832c677f81559e3893e643dc32330d0e9699a1f7 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,10 +90,9 @@ field. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -125,11 +124,11 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. This scalar is the -gravitational potential energy of the particles in the defined field, -namely mass * (g dot x) for each particles, where x and mass are the -particles position and mass, and g is the gravitational field. The -scalar value calculated by this fix is "extensive". +"output commands"_Howto_output.html. This scalar is the gravitational +potential energy of the particles in the defined field, namely mass * +(g dot x) for each particles, where x and mass are the particles +position and mass, and g is the gravitational field. The scalar value +calculated by this fix is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 661f68ed99cf21d5c5a08514d78dff411a28880e..506e266505a54248fee381d4135802122fd86aba 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_halt.txt b/doc/src/fix_halt.txt index 08043eb5fb76659bf851d59444eeec56548b11cd..ec117518d285d488b28a78e552280f1ac7b81c17 100644 --- a/doc/src/fix_halt.txt +++ b/doc/src/fix_halt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,10 +133,10 @@ files. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt index 23db87dac27d8fc51d958bb1df857a0b6539e426..6db75926091bf4aac4e7fafa5679dab9e58231f4 100644 --- a/doc/src/fix_heat.txt +++ b/doc/src/fix_heat.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,12 +108,11 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. This scalar is the -most recent value by which velocites were scaled. The scalar value -calculated by this fix is "intensive". If {eflux} is specified as -an atom-style variable, this fix computes the average value by which -the velocities were scaled for all of the atoms that had their -velocities scaled. +"output commands"_Howto_output.html. This scalar is the most recent +value by which velocites were scaled. The scalar value calculated by +this fix is "intensive". If {eflux} is specified as an atom-style +variable, this fix computes the average value by which the velocities +were scaled for all of the atoms that had their velocities scaled. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt index b2756128191740d86ec6a9be5a18a831e48a0627..8e21a1619b8647b0ba6c497540ac2b7c4973b36a 100644 --- a/doc/src/fix_imd.txt +++ b/doc/src/fix_imd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -136,9 +136,9 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This +fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index c9a791ae4ece3069805ac86172ffae4805361076..9931793c0bffbc1398bee31bf7a5c87cda692d7d 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -180,8 +180,8 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global 3-vector of forces (on the indenter), which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar and vector values -calculated by this fix are "extensive". +commands"_Howto_output.html. The scalar and vector values calculated +by this fix are "extensive". The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. Note that if you diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index 07e8025d77061db6e41fd3c3e765898664f2ffcd..eba30ef08821d7c55ab06270d18a4300da293de5 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index 93c73f5a5dd2390f93d80dfe7ce2d4efc7f53e69..4d7728cdba4b918d1cc8926f2aaef266bc20a42b 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,7 +101,7 @@ should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for +See the "Howto thermostat"_Howto_thermostat.html doc page for a discussion of different ways to compute temperature and perform thermostatting. @@ -264,10 +264,9 @@ generates an average temperature of 220 K, instead of 300 K. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -279,8 +278,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -306,10 +305,10 @@ output"_thermo_style.html. Note that use of this option requires setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the {tally} keyword to {yes}. +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". Note that calculation of this quantity requires +setting the {tally} keyword to {yes}. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index c85ff24c96d2982439d67c4ac52fd3bea5083044..19a3f87ffc0a20fb66038671e6a76529c5a1db6d 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -44,8 +44,9 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes :pre Apply two Langevin thermostats as described in "(Jiang)"_#Jiang1 for thermalizing the reduced degrees of freedom of Drude oscillators. This link describes how to use the "thermalized Drude oscillator -model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS -are discussed in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS +are discussed on the "Howto polarizable"_Howto_polarizable.html doc +page. Drude oscillators are a way to simulate polarizables atoms, by splitting them into a core and a Drude particle bound by a harmonic @@ -99,8 +100,8 @@ Likewise, this fix should not normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostating. :line diff --git a/doc/src/fix_langevin_eff.txt b/doc/src/fix_langevin_eff.txt index 4a50bfae54d1a058b3b31bf86159e838163ff87f..cf42f9c036b2dc4da5a9f2afb98296d8a78862d4 100644 --- a/doc/src/fix_langevin_eff.txt +++ b/doc/src/fix_langevin_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -79,10 +79,10 @@ output"_thermo_style.html. Note that use of this option requires setting the {tally} keyword to {yes}. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". Note that calculation of this -quantity requires setting the {tally} keyword to {yes}. +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". Note that calculation of this quantity requires +setting the {tally} keyword to {yes}. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b1936376de0fe29450cf9b4c2db7e298e6d64ab --- /dev/null +++ b/doc/src/fix_langevin_spin.txt @@ -0,0 +1,102 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix langevin/spin command :h3 + +[Syntax:] + +fix ID group-ID langevin/spin T Tdamp seed :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +langevin/spin = style name of this fix command :l +T = desired temperature of the bath (temperature units, K in metal units) :l +Tdamp = transverse magnetic damping parameter (adim) :l +seed = random number seed to use for white noise (positive integer) :l +:ule + +[Examples:] + +fix 2 all langevin/spin 300.0 0.01 21 :pre + +[Description:] + +Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the +magnetic spins associated to the atoms. +Used with "fix nve/spin"_fix_nve_spin.html, this command performs +Brownian dynamics (BD). +A random torque and a transverse dissipation are applied to each spin i according to +the following stochastic differential equation: + +:c,image(Eqs/fix_langevin_spin_sLLG.jpg) + +with lambda the transverse damping, and eta a random verctor. +This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) +equation. + +The components of eta are drawn from a Gaussian probability law. Their amplitude +is defined as a proportion of the temperature of the external thermostat T (in K +in metal units). + +More details about this implementation are reported in "(Tranchida)"_#Tranchida2. + +Note: due to the form of the sLLG equation, this fix has to be defined just +before the nve/spin fix (and after all other magnetic fixes). +As an example: + +fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 +fix 2 all langevin/spin 300.0 0.01 21 +fix 3 all nve/spin lattice yes :pre + +is correct, but defining a force/spin command after the langevin/spin command +would give an error message. + +Note: The random # {seed} must be a positive integer. A Marsaglia random +number generator is used. Each processor uses the input seed to +generate its own unique seed and its own stream of random numbers. +Thus the dynamics of the system will not be identical on two runs on +different numbers of processors. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. Because the state of the random number generator +is not saved in restart files, this means you cannot do "exact" +restarts with this fix, where the simulation continues on the same as +if no restart had taken place. However, in a statistical sense, a +restarted simulation should produce the same behavior. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +The {langevin/spin} fix is part of the SPIN package. +This style is only enabled if LAMMPS was built with this package. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +The numerical integration has to be performed with {fix nve/spin} +when {fix langevin/spin} is enabled. + +This fix has to be the last defined magnetic fix before the time +integration fix (e.g. {fix nve/spin}). + +[Related commands:] + +"fix nve/spin"_fix_nve_spin.html, "fix precession/spin"_fix_precession_spin.html + +[Default:] none + +:line + +:link(Mayergoyz1) +[(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009) + +:link(Tranchida2) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index 4edd610546350ac082789fb517af918c7167c1f3..9bc589520bc3689a4ad4370f99e92b9977bb209c 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -118,9 +118,9 @@ of "thermodynamic output"_thermo_style.html. The default is {virial yes} This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy discussed above. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy discussed above. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_lb_fluid.txt b/doc/src/fix_lb_fluid.txt index fc6203b0f2c1967613e81b694977c9dd26accfcf..5347f0147f4be26b5e3b61877084925003c4fbf4 100644 --- a/doc/src/fix_lb_fluid.txt +++ b/doc/src/fix_lb_fluid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -299,9 +299,9 @@ is written to the main LAMMPS "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_lb_momentum.txt b/doc/src/fix_lb_momentum.txt index 97965e870d95b70688428bd17304bdb83dce43e5..a58c5d257eabeb012284a3fd2dd3e2eecd20c1d7 100644 --- a/doc/src/fix_lb_momentum.txt +++ b/doc/src/fix_lb_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,10 +49,10 @@ dimension. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_lb_pc.txt b/doc/src/fix_lb_pc.txt index d2b6aafaab84a38d890abba5d5125ca5327f9687..bd121b7813253cb3b9e547235db88cdc85e5e472 100644 --- a/doc/src/fix_lb_pc.txt +++ b/doc/src/fix_lb_pc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,10 +34,10 @@ algorithm if the force coupling constant has been set by default. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can be -used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_lb_rigid_pc_sphere.txt b/doc/src/fix_lb_rigid_pc_sphere.txt index 468ebe1ff5d31e8b224e6b864b3a8949eafd7c22..bc8fa2ea257212f588dabe01b824d98ff4289a1b 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.txt +++ b/doc/src/fix_lb_rigid_pc_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,12 +80,12 @@ assumes the constituent atoms are point particles); see No information about the {rigid} and {rigid/nve} fixes are written to "binary restart files"_restart.html. -Similar to the "fix rigid"_fix_rigid.html command: The rigid -fix computes a global scalar which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "intensive". The scalar is the current temperature of -the collection of rigid bodies. This is averaged over all rigid -bodies and their translational and rotational degrees of freedom. The +Similar to the "fix rigid"_fix_rigid.html command: The rigid fix +computes a global scalar which can be accessed by various "output +commands"_Howto_output.html. The scalar value calculated by these +fixes is "intensive". The scalar is the current temperature of the +collection of rigid bodies. This is averaged over all rigid bodies +and their translational and rotational degrees of freedom. The translational energy of a rigid body is 1/2 m v^2, where m = total mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment @@ -94,17 +94,17 @@ of freedom constrained by the {force} and {torque} keywords are removed from this calculation. All of these fixes compute a global array of values which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The number of rows in the array is equal to the number of rigid -bodies. The number of columns is 15. Thus for each rigid body, 15 -values are stored: the xyz coords of the center of mass (COM), the xyz -components of the COM velocity, the xyz components of the force acting -on the COM, the xyz components of the torque acting on the COM, and -the xyz image flags of the COM, which have the same meaning as image -flags for atom positions (see the "dump" command). The force and -torque values in the array are not affected by the {force} and -{torque} keywords in the fix rigid command; they reflect values before -any changes are made by those keywords. +accessed by various "output commands"_Howto_output.html. The number +of rows in the array is equal to the number of rigid bodies. The +number of columns is 15. Thus for each rigid body, 15 values are +stored: the xyz coords of the center of mass (COM), the xyz components +of the COM velocity, the xyz components of the force acting on the +COM, the xyz components of the torque acting on the COM, and the xyz +image flags of the COM, which have the same meaning as image flags for +atom positions (see the "dump" command). The force and torque values +in the array are not affected by the {force} and {torque} keywords in +the fix rigid command; they reflect values before any changes are made +by those keywords. The ordering of the rigid bodies (by row in the array) is as follows. For the {single} keyword there is just one rigid body. For the diff --git a/doc/src/fix_lb_viscous.txt b/doc/src/fix_lb_viscous.txt index fcc69d2b4315bd9a6695260efc0da5bafe27a0c2..7bbdd204e34d1a4fae91fcf2f4bb2aa4c32fefbf 100644 --- a/doc/src/fix_lb_viscous.txt +++ b/doc/src/fix_lb_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,9 +57,9 @@ As described in the "fix viscous"_fix_viscous.html documentation: "No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. This fix should only diff --git a/doc/src/fix_lineforce.txt b/doc/src/fix_lineforce.txt index 65672fc5a5bdce5ca34fbff81f1c5fb0b94d6c07..3114ed62501e3c3c3581ae06a154c45de0d92996 100644 --- a/doc/src/fix_lineforce.txt +++ b/doc/src/fix_lineforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ it should continue to move along the line thereafter. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt index 5fc25167a7c7218097606cbbd77031a1cff0b709..aa32a875bfe2f77de00cdbee7f87085af8443a94 100644 --- a/doc/src/fix_manifoldforce.txt +++ b/doc/src/fix_manifoldforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -36,10 +36,10 @@ I have found that only {hftn} and {quickmin} with a very small time step perform No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is invoked during "energy +minimization"_minimize.html. :line diff --git a/doc/src/fix_meso.txt b/doc/src/fix_meso.txt index 85f5838dd261fbd232a8fa570aaa20fc1391ef8a..8f5ad29929313fc6d1b31169b140b5dad0d46959 100644 --- a/doc/src/fix_meso.txt +++ b/doc/src/fix_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,10 +34,10 @@ LAMMPS. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_meso_stationary.txt b/doc/src/fix_meso_stationary.txt index 5b83573bc8bcc58d2ad6aedc1d8b18c7d46f9368..38d26b34d67ad7d0a38eec70c7f28583394778eb 100644 --- a/doc/src/fix_meso_stationary.txt +++ b/doc/src/fix_meso_stationary.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,10 +35,10 @@ LAMMPS. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 308bba1ac31fdf9a7cbd45ec1da50122cd46bcb9..ddb5f9a4cd4346e6f0d3195a101445c15eaedfde 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_momentum.txt b/doc/src/fix_momentum.txt index bcf4465fb8f5c9bc30626cc3275f422fd2158e9e..f7fe35be2a9fd3825b82db9a0cd3d3cca76dfb56 100644 --- a/doc/src/fix_momentum.txt +++ b/doc/src/fix_momentum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -61,10 +61,9 @@ initial velocities with zero aggregate linear and/or angular momentum. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -76,18 +75,18 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 7cb40ad1320e365153d3d3165df06a8a1f064750..08f38d0ed65f2dec91bfec38fd572b8e82e75770 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -203,10 +203,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a per-atom array which can be accessed by various -"output commands"_Section_howto.html#howto_15. The number of columns -for each atom is 3, and the columns store the original unwrapped x,y,z -coords of each atom. The per-atom values can be accessed on any -timestep. +"output commands"_Howto_output.html. The number of columns for each +atom is 3, and the columns store the original unwrapped x,y,z coords +of each atom. The per-atom values can be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 7d16967955d1d9988636092d721fe40902386054..aadc3caf5aa909c8ff32f23d51bcac2d3f0919ab 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index 310692669abb39aaebb7e3596ee7f0b9e8cdf865..91ffbbb0fa147ea6e520ac75658d114198654da6 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,8 +156,8 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_ These fixes compute a global scalar and a global vector of 4 quantities, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar values calculated -by this fix are "extensive"; the vector values are "intensive". +commands"_Howto_output.html. The scalar values calculated by this fix +are "extensive"; the vector values are "intensive". [Restrictions:] diff --git a/doc/src/fix_mvv_dpd.txt b/doc/src/fix_mvv_dpd.txt index fb3c6fe8885ce8a23b58897cd05a94269a20e5d7..1e9bf631fde813d95546bcc6638b3c24172a0e79 100644 --- a/doc/src/fix_mvv_dpd.txt +++ b/doc/src/fix_mvv_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,10 +69,10 @@ addition to position and velocity, and must be used with the No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 5d18c39d994de3d58b752f7d595dfa4eb55e0019..5341d6999c4e6b0f5220af5d5d77ebd331176fbb 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,9 +43,9 @@ Add nudging forces to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged elastic band (NEB) calculation for finding the transition state. Hi-level explanations of NEB are given with the "neb"_neb.html command -and in "Section_howto 5"_Section_howto.html#howto_5 of the manual. -The fix neb command must be used with the "neb" command and defines -how inter-replica nudging forces are computed. A NEB calculation is +and on the "Howto replica"_Howto_replica.html doc page. The fix neb +command must be used with the "neb" command and defines how +inter-replica nudging forces are computed. A NEB calculation is divided in two stages. In the first stage n replicas are relaxed toward a MEP until convergence. In the second stage, the climbing image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the @@ -192,9 +192,9 @@ target energy. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, as invoked by the "minimize"_minimize.html command via the diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 41d0e6438fc9e05d08aa43d1548a98c0856ffd90..f6b155e2db2c66bad86e479a8d1ee67d86fd51a7 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -386,9 +386,10 @@ have their temperature controlled by another fix - e.g. by "fix langevin"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. +See the "Howto thermostat"_Howto_thermostat.html and "Howto +barostat"_Howto_barostat.html doc pages for a discussion of different +ways to compute temperature and perform thermostatting and +barostatting. :line @@ -484,10 +485,9 @@ the various ways to do this. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -499,8 +499,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -538,9 +538,9 @@ and barostatting to the system's potential energy as part of "thermodynamic output"_thermo_style.html. These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar value calculated by these fixes is "extensive"; the vector +values are "intensive". The scalar is the cumulative energy change due to the fix. diff --git a/doc/src/fix_nh_eff.txt b/doc/src/fix_nh_eff.txt index 1731f1f3317a6f982a564c256e593439a8f73423..afb319bfa51f6c518b213f63f75cbab14741e0bc 100644 --- a/doc/src/fix_nh_eff.txt +++ b/doc/src/fix_nh_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index bde1818371f2c4bcab0bafe11e19c4b04df107b8..0e73c57e089b44643834f1b78fad2c1f046281f4 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nph_asphere.txt b/doc/src/fix_nph_asphere.txt index 8c35b6a1a7a4b8bbd2fc98573764f99f0995249c..6bfd9d3fe26085cff9f1d3c5c0b32fbbd5c5948a 100644 --- a/doc/src/fix_nph_asphere.txt +++ b/doc/src/fix_nph_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -81,10 +81,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -96,8 +95,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nph_body.txt b/doc/src/fix_nph_body.txt index 1e590f1cb3f3d5a46724d86e657d805a6a1906e3..377e1980eb3cf8c9c46b41baa6a14b2e379c7816 100644 --- a/doc/src/fix_nph_body.txt +++ b/doc/src/fix_nph_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,10 +80,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nph_sphere.txt b/doc/src/fix_nph_sphere.txt index 62b45edfd7cd5ffbd8fe8ab48d5aefc29d3417ee..8b7639c4c6a7467e9107db127699efabea8a8993 100644 --- a/doc/src/fix_nph_sphere.txt +++ b/doc/src/fix_nph_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,10 +90,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -105,8 +104,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nphug.txt b/doc/src/fix_nphug.txt index 292e46f94af6fcfe8e8c8b5b1e04908c2c55c9bc..0bd5153152b4afdcd8a0048b0472df81ad63ed08 100644 --- a/doc/src/fix_nphug.txt +++ b/doc/src/fix_nphug.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -140,10 +140,9 @@ It also means that changing attributes of {thermo_temp} or Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -155,8 +154,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -193,9 +192,9 @@ included in the definition of internal energy E when calculating the value of Delta in the above equation. These fixes compute a global scalar and a global vector of quantities, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar value calculated by -these fixes is "extensive"; the vector values are "intensive". +which can be accessed by various "output commands"_Howto_output.html. +The scalar value calculated by these fixes is "extensive"; the vector +values are "intensive". The scalar is the cumulative energy change due to the fix. diff --git a/doc/src/fix_npt_asphere.txt b/doc/src/fix_npt_asphere.txt index 5f3979e36ed9e586f2eee15750364641348c040c..9c95a80d3310a08e3e8ddecd12af471419340773 100644 --- a/doc/src/fix_npt_asphere.txt +++ b/doc/src/fix_npt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,10 +105,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -120,8 +119,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_npt_body.txt b/doc/src/fix_npt_body.txt index d89bf19db24fa7a988923a8cb5822cccc9641ed9..0d2b797299dd4d3c803e96cbfb1f4030ac13c032 100644 --- a/doc/src/fix_npt_body.txt +++ b/doc/src/fix_npt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -104,10 +104,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -119,8 +118,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_npt_sphere.txt b/doc/src/fix_npt_sphere.txt index c4cf2cb08de85d8fe892f240473a0a90daa56de0..dcb25d1c737b39f3a2bcea9a4e01eb1a011fbb60 100644 --- a/doc/src/fix_npt_sphere.txt +++ b/doc/src/fix_npt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -115,10 +115,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -130,8 +129,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nve.txt b/doc/src/fix_nve.txt index c04c17858ebdf9b4166827a9cf5f52ed0f43e597..e446b273977b4dd05865de697b3d10af144bb149 100644 --- a/doc/src/fix_nve.txt +++ b/doc/src/fix_nve.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -34,10 +34,9 @@ ensemble. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -49,8 +48,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -59,10 +58,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_nve_asphere.txt b/doc/src/fix_nve_asphere.txt index 1f31fb96792239de806f99e78744106b0b08c1f7..b7fb3e922ce418d666b0cfe9b87170daa7c195ed 100644 --- a/doc/src/fix_nve_asphere.txt +++ b/doc/src/fix_nve_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,20 +35,19 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -60,8 +59,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_nve_asphere_noforce.txt b/doc/src/fix_nve_asphere_noforce.txt index 5f1b2715464c01468494f8fb0da33bd46c1c5ec4..e57417bda5e1657ca69a621840ea82f2199b14b1 100644 --- a/doc/src/fix_nve_asphere_noforce.txt +++ b/doc/src/fix_nve_asphere_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -38,10 +38,10 @@ Dynamics, since the velocity and angular momentum are updated by the No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 604b5391cd180e064207ca3cd5a02d2335470ac7..d072bfa1611770921b5e97f7f1fb2bce2128c748 100644 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,9 +24,9 @@ fix 1 all nve/body :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See "Section -6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html -doc page for more details on using body particles. +consistent with the microcanonical ensemble. See the "Howto +body"_Howto_body.html doc page for more details on using body +particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 0e0c8f8ecf5d9d02f3a6982ee1ae3e5cd8aa3746..1041a248d8784a0cfae575f1d5a515a4e2c76e35 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index 93d875bca5436127526cdb5f1dad6b170d6c46b3..68c1b4232830fe1a2eaaadaf8ce832474a394f13 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nve_eff.txt b/doc/src/fix_nve_eff.txt index 156f184daceb6ee31c14168e65deecc43d7a9bc1..7343ddc4292df0f02e7eadef7829ec8041ccae5b 100644 --- a/doc/src/fix_nve_eff.txt +++ b/doc/src/fix_nve_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,10 +35,10 @@ of electrons are also updated. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_limit.txt b/doc/src/fix_nve_limit.txt index 2ecec83e9ce8bf5886a1d66dc4c50046a7f74882..8c8c66a0dac92424d08b577ee3957277e81e6ce2 100644 --- a/doc/src/fix_nve_limit.txt +++ b/doc/src/fix_nve_limit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,14 +63,14 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -count of how many updates of atom's velocity/position were limited by -the maximum distance criterion. This should be roughly the number of -atoms so affected, except that updates occur at both the beginning and -end of a timestep in a velocity Verlet timestepping algorithm. This -is a cumulative quantity for the current run, but is re-initialized to -zero each time a run is performed. The scalar value calculated by -this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the count of how +many updates of atom's velocity/position were limited by the maximum +distance criterion. This should be roughly the number of atoms so +affected, except that updates occur at both the beginning and end of a +timestep in a velocity Verlet timestepping algorithm. This is a +cumulative quantity for the current run, but is re-initialized to zero +each time a run is performed. The scalar value calculated by this fix +is "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_nve_line.txt b/doc/src/fix_nve_line.txt index ac5206aa5ce4ad1f9047bed437d96318498362d0..dd5101489b00d27a707ac4c044bed5f4a84be643 100644 --- a/doc/src/fix_nve_line.txt +++ b/doc/src/fix_nve_line.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -24,9 +24,9 @@ fix 1 all nve/line :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for line segment particles in the group each timestep. V is volume; E is energy. This creates a system -trajectory consistent with the microcanonical ensemble. See -"Section 6.14"_Section_howto.html#howto_14 of the manual for an -overview of using line segment particles. +trajectory consistent with the microcanonical ensemble. See "Howto +spherical"_Howto_spherical.html doc page for an overview of using line +segment particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_manifold_rattle.txt b/doc/src/fix_nve_manifold_rattle.txt index e032a7e1cc76408f8db42a9108662997a47e440d..b333d093fb8eec0ce08d16c8affb3a2cf481c802 100644 --- a/doc/src/fix_nve_manifold_rattle.txt +++ b/doc/src/fix_nve_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,7 +40,7 @@ the dynamics of particles constrained to curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates Brownian motion of particles constrained to a curved surface. For a list of currently supported manifolds and their -parameters, see "manifolds"_manifolds.html. +parameters, see the "Howto manifold"_Howto_manifold.html doc page. Note that the particles must initially be close to the manifold in question. If not, RATTLE will not be able to iterate until the @@ -68,10 +68,10 @@ conserved. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line diff --git a/doc/src/fix_nve_noforce.txt b/doc/src/fix_nve_noforce.txt index a0dbcc80f18f0fc7d15f7b4503031fa80aaaa50c..da8d16bbb7c1c49bdee6af72dc4c1bcc2f355a1e 100644 --- a/doc/src/fix_nve_noforce.txt +++ b/doc/src/fix_nve_noforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -40,10 +40,10 @@ fcm() group function to compute the total force on the group of atoms. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index 21dc6cba8a4aa7e067bcb9b0c066879e60b23479..6e259bdb8e7803482ee894d68d2a354dcefc0e6f 100644 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,10 +65,9 @@ moment of inertia, as used in the time integration. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -80,8 +79,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -90,10 +89,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..e31185bc889e785030dbef61a36019a7ba086af0 --- /dev/null +++ b/doc/src/fix_nve_spin.txt @@ -0,0 +1,76 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix nve/spin command :h3 + +[Syntax:] + +fix ID group-ID nve/spin keyword values :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +nve/spin = style name of this fix command :l +keyword = {lattice} :l + {lattice} value = {no} or {yes} :pre +:ule + +[Examples:] + +fix 3 all nve/spin lattice yes +fix 1 all nve/spin lattice no :pre + +[Description:] + +Perform a symplectic integration for the spin or spin-lattice system. + +The {lattice} keyword defines if the spins are integrated on a lattice +of fixed atoms (lattice = no), or if atoms are moving (lattice = yes). + +By default (lattice = yes), a spin-lattice integration is performed. + +The {nve/spin} fix applies a Suzuki-Trotter decomposition to +the equations of motion of the spin lattice system, following the scheme: + +:c,image(Eqs/fix_integration_spin_stdecomposition.jpg) + +according to the implementation reported in "(Omelyan)"_#Omelyan1. + +A sectoring method enables this scheme for parallel calculations. +The implementation of this sectoring algorithm is reported +in "(Tranchida)"_#Tranchida1. + +:line + +[Restrictions:] + +This fix style can only be used if LAMMPS was built with the +SPIN package. See the "Making LAMMPS"_Section_start.html#start_3 +section for more info on packages. + +To use the spin algorithm, it is necessary to define a map with +the atom_modify command. Typically, by adding the command: + +atom_modify map array :pre + +before you create the simulation box. Note that the keyword "hash" +instead of "array" is also valid. + +[Related commands:] + +"atom_style spin"_atom_style.html, "fix nve"_fix_nve.html + +[Default:] none + +:line + +:link(Omelyan1) +[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. +86(5), 898. (2001). + +:link(Tranchida1) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/fix_nve_tri.txt b/doc/src/fix_nve_tri.txt index cee27e2fa43087a2b6847a6f119fcb3792252259..ebdda19e36428828bdbeb6558b3202cc00982a80 100644 --- a/doc/src/fix_nve_tri.txt +++ b/doc/src/fix_nve_tri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -23,10 +23,10 @@ fix 1 all nve/tri :pre Perform constant NVE integration to update position, velocity, orientation, and angular momentum for triangular particles in the -group each timestep. V is volume; E is energy. This creates a -system trajectory consistent with the microcanonical ensemble. See -"Section 6.14"_Section_howto.html#howto_14 of the manual for an -overview of using triangular particles. +group each timestep. V is volume; E is energy. This creates a system +trajectory consistent with the microcanonical ensemble. See the +"Howto spherical"_Howto_spherical.html doc page for an overview of +using triangular particles. This fix differs from the "fix nve"_fix_nve.html command, which assumes point particles and only updates their position and velocity. @@ -36,10 +36,10 @@ assumes point particles and only updates their position and velocity. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt index 49fd8217ab7a88b90c23afc7ca56295e906ec245..e3189f8e8a3981b76f848f64080b6baa50500738 100644 --- a/doc/src/fix_nvk.txt +++ b/doc/src/fix_nvk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -42,10 +42,10 @@ energy prior to this fix. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_nvt_asphere.txt b/doc/src/fix_nvt_asphere.txt index 21b900f16ac69d3ef28b7b39fa90f232f43eb290..7b9763717574062e64b9e812bd201d8174cb4880 100644 --- a/doc/src/fix_nvt_asphere.txt +++ b/doc/src/fix_nvt_asphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -86,10 +86,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -101,8 +100,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_body.txt b/doc/src/fix_nvt_body.txt index 6a5e09ba7fb57ef45a91b9bf764e1f2e821fc34f..4493a892777221ee5c4375769438f8c02cfaf570 100644 --- a/doc/src/fix_nvt_body.txt +++ b/doc/src/fix_nvt_body.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,10 +85,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_manifold_rattle.txt b/doc/src/fix_nvt_manifold_rattle.txt index a620648a460682c26780b67f9a4eddb3f21738ce..1b4ad7916626ea3550b69c4aef84514318acb30e 100644 --- a/doc/src/fix_nvt_manifold_rattle.txt +++ b/doc/src/fix_nvt_manifold_rattle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,9 +37,13 @@ fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0 [Description:] -This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the -canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt). -For a list of currently supported manifolds and their parameters, see "manifolds"_manifolds.html +This fix combines the RATTLE-based "(Andersen)"_#Andersen2 time +integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html +"(Paquay)"_#Paquay3 with a Nose-Hoover-chain thermostat to sample the +canonical ensemble of particles constrained to a curved surface +(manifold). This sampling does suffer from discretization bias of +O(dt). For a list of currently supported manifolds and their +parameters, see the "Howto manifold"_Howto_manifold.html doc page. :line @@ -48,10 +52,10 @@ For a list of currently supported manifolds and their parameters, see "manifolds No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 392dbc281c6f5eee0fc164f4ed8eb6670bfbcbef..9eb506536910f574867121e26d6dee23ff8071a0 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -109,10 +109,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_nvt_sllod_eff.txt b/doc/src/fix_nvt_sllod_eff.txt index 408eb1da01f99bc026a4581bedbb4ecff2a91b6a..0200d5cb002312980fb21344687676dd06d74fee 100644 --- a/doc/src/fix_nvt_sllod_eff.txt +++ b/doc/src/fix_nvt_sllod_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_nvt_sphere.txt b/doc/src/fix_nvt_sphere.txt index ecf0922b7901a154f0728579b41d6e9502b2f3d0..a87e4abe677ed4c44d6b54470e5d2ee9539d8f7c 100644 --- a/doc/src/fix_nvt_sphere.txt +++ b/doc/src/fix_nvt_sphere.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -96,10 +96,9 @@ thermal degrees of freedom, and the bias is added back in. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -111,8 +110,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_oneway.txt b/doc/src/fix_oneway.txt index 2d85c581ebd95ec5cfdf27129ee39ae1c73532d5..433ceb50f244e7570b83979dffed7c5b34d7a8ca 100644 --- a/doc/src/fix_oneway.txt +++ b/doc/src/fix_oneway.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -43,10 +43,10 @@ membrane, or as an implementation of Maxwell's demon. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt index 20ff94866ea3ad0c92fde75042cad455494bcc92..7552bea8c5bcfb73867322c90f502887276aacf9 100644 --- a/doc/src/fix_orient.txt +++ b/doc/src/fix_orient.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -135,14 +135,14 @@ fixes. This allows to set at which level of the "r-RESPA"_run_style.html integrator a fix is adding its forces. Default is the outermost level. This fix calculates a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -potential energy change due to this fix. The scalar value calculated -by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the potential +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix also calculates a per-atom array which can be accessed by -various "output commands"_Section_howto.html#howto_15. The array -stores the order parameter Xi and normalized order parameter (0 to 1) -for each atom. The per-atom values can be accessed on any timestep. +various "output commands"_Howto_output.html. The array stores the +order parameter Xi and normalized order parameter (0 to 1) for each +atom. The per-atom values can be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index aad6c2bfaa401bcb0af6e76851f849cb67c1af0c..30e5864e3d16af76cdc86ea021c0cf80fda6b2ff 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -150,7 +150,7 @@ fix. You can use it to change the temperature compute from thermo_temp to the one that reflects the true temperature of atoms in the group. No global scalar or vector or per-atom quantities are stored by this -fix for access by various "output commands"_Section_howto.html#howto_15. +fix for access by various "output commands"_Howto_output.html. Instead, this fix outputs its initialization information (including mapping information) and the calculated dynamical matrices to the file diff --git a/doc/src/fix_pimd.txt b/doc/src/fix_pimd.txt index 38022e4c7dd3d6d2e2bb1b0a56177fae2918604c..b61b3f3065a7c0c57f5994a2a2a23d6ed8778407 100644 --- a/doc/src/fix_pimd.txt +++ b/doc/src/fix_pimd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -103,14 +103,13 @@ is appropriate for most situations. The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme as described in "(Calhoun)"_#Calhoun. In LAMMPS this is done by using -"multi-replica feature"_Section_howto.html#howto_5 in LAMMPS, where -each quasi-particle system is stored and simulated on a separate -partition of processors. The following diagram illustrates this -approach. The original system with 2 ring polymers is shown in red. -Since each ring has 4 quasi-beads (imaginary time slices), there are 4 -replicas of the system, each running on one of the 4 partitions of -processors. Each replica (shown in green) owns one quasi-bead in each -ring. +"multi-replica feature"_Howto_replica.html in LAMMPS, where each +quasi-particle system is stored and simulated on a separate partition +of processors. The following diagram illustrates this approach. The +original system with 2 ring polymers is shown in red. Since each ring +has 4 quasi-beads (imaginary time slices), there are 4 replicas of the +system, each running on one of the 4 partitions of processors. Each +replica (shown in green) owns one quasi-bead in each ring. :c,image(JPG/pimd.jpg) diff --git a/doc/src/fix_planeforce.txt b/doc/src/fix_planeforce.txt index 67956c8b6ddfdcf7c3cfe0520f0fa888b4c9c87c..ffe1952e31a2f412ce23edf7b36a891b42f70f38 100644 --- a/doc/src/fix_planeforce.txt +++ b/doc/src/fix_planeforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -35,9 +35,9 @@ should continue to move in the plane thereafter. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 03abc058b8b0d6e982f6291e1fecbb887cf2ad9a..1a79c2a048fb75dc04935e978fdc50ae84ab9e69 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -114,9 +114,9 @@ early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively. No global or per-atom quantities are stored by this fix for access by -various "output commands"_Section_howto.html#howto_15. No parameter -of this fix can be used with the {start/stop} keywords of the -"run"_run.html command. This fix is not invoked during "energy +various "output commands"_Howto_output.html. No parameter of this fix +can be used with the {start/stop} keywords of the "run"_run.html +command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_pour.txt b/doc/src/fix_pour.txt index 54f78287e01d98368f1938122b1c9317e8446659..e58d8ebc3ad90069a45cfd92ae504ce4656305dc 100644 --- a/doc/src/fix_pour.txt +++ b/doc/src/fix_pour.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -237,9 +237,9 @@ appropriately. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt new file mode 100644 index 0000000000000000000000000000000000000000..fafe78448be133680f5b22711403262f1f28086b --- /dev/null +++ b/doc/src/fix_precession_spin.txt @@ -0,0 +1,87 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix precession/spin command :h3 + +[Syntax:] + +fix ID group precession/spin style args :pre + +ID, group are documented in "fix"_fix.html command :ulb,l +precession/spin = style name of this fix command :l +style = {zeeman} or {anisotropy} :l + {zeeman} args = H x y z + H = intensity of the magnetic field (in Tesla) + x y z = vector direction of the field + {anisotropy} args = K x y z + K = intensity of the magnetic anisotropy (in eV) + x y z = vector direction of the anisotropy :pre +:ule + +[Examples:] + +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 +fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre + +[Description:] + +Impose a force torque to each magnetic spin in the group. + +Style {zeeman} is used for the simulation of the interaction +between the magnetic spins in the defined group and an external +magnetic field: + +:c,image(Eqs/force_spin_zeeman.jpg) + +with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T +in metal units). + +Style {anisotropy} is used to simulate an easy axis or an easy plane +for the magnetic spins in the defined group: + +:c,image(Eqs/force_spin_aniso.jpg) + +with n defining the direction of the anisotropy, and K (in eV) its intensity. +If K>0, an easy axis is defined, and if K<0, an easy plane is defined. + +In both cases, the choice of (x y z) imposes the vector direction for the force. +Only the direction of the vector is important; it's length is ignored. + +Both styles can be combined within one single command line. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +By default, the energy associated to this fix is not added to the potential +energy of the system. +The "fix_modify"_fix_modify.html {energy} option is supported by this fix +to add this magnetic potential energy to the potential energy of the system, + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes :pre + +This fix computes a global scalar which can be accessed by various +"output commands"_Howto_output.html. + +No information about this fix is written to "binary restart +files"_restart.html. + +[Restrictions:] + +The {precession/spin} style is part of the SPIN package. +This style is only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html + +[Default:] none diff --git a/doc/src/fix_press_berendsen.txt b/doc/src/fix_press_berendsen.txt index 9c9da8ec7b052f9e91651fa6adca5ee3ae675166..7f47a29ba35fa0a1ca9cc0c3aebd51917131564d 100644 --- a/doc/src/fix_press_berendsen.txt +++ b/doc/src/fix_press_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,9 +58,8 @@ to control the temperature, such as "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html or "fix temp/berendsen"_fix_temp_berendsen.html. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform -thermostatting and barostatting. +See the "Howto baroostat"_Howto_barostat.html doc page for a +discussion of different ways to perform barostatting. :line @@ -196,7 +195,7 @@ pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms. No global or per-atom quantities are stored by this fix for access by -various "output commands"_Section_howto.html#howto_15. +various "output commands"_Howto_output.html. This fix can ramp its target pressure over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_print.txt b/doc/src/fix_print.txt index cf3b542833b6d951e2b160797998e28406867758..d23c1103d3000963e8efcf4600080f79bf3eac20 100644 --- a/doc/src/fix_print.txt +++ b/doc/src/fix_print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -73,10 +73,10 @@ where ID is replaced with the fix-ID. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 10bb89c94cad5b28414578f621cab34c31266165..136ed6c15e6ecb9de65599eb41a821d6487bbf69 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -194,24 +194,23 @@ dump 1 all custom 100 tmp.dump id x y z c_1\[1\] c_1\[2\] :pre If you wish to add new "pair styles"_pair_style.html, "fixes"_fix.html, or "computes"_compute.html that use the per-atom -properties defined by this fix, see "Section -modify"_Section_modify.html#mod_1 of the manual which has some details -on how the properties can be accessed from added classes. +properties defined by this fix, see the "Modify atom"_Modify_atom.html +doc page which has details on how the properties can be accessed from +added classes. :line -:link(isotopes) -Example for using per-atom masses with TIP4P water to study isotope -effects. When setting up simulations with the "TIP4P pair -styles"_Section_howto.html#howto_8 for water, you have to provide -exactly one atom type each to identify the water oxygen and hydrogen +:link(isotopes) Example for using per-atom masses with TIP4P water to +study isotope effects. When setting up simulations with the "TIP4P +pair styles"_Howto_tip4p.html for water, you have to provide exactly +one atom type each to identify the water oxygen and hydrogen atoms. Since the atom mass is normally tied to the atom type, this makes it impossible to study multiple isotopes in the same simulation. With {fix property/atom rmass} however, the per-type masses are replaced by per-atom masses. Asumming you have a working input deck -for regular TIP4P water, where water oxygen is atom type 1 and -water hydrogen is atom type 2, the following lines of input script -convert this to using per-atom masses: +for regular TIP4P water, where water oxygen is atom type 1 and water +hydrogen is atom type 2, the following lines of input script convert +this to using per-atom masses: fix Isotopes all property/atom rmass ghost yes set type 1 mass 15.9994 @@ -247,12 +246,12 @@ command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the "fix_modify"_fix_modify.html options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] none diff --git a/doc/src/fix_python_invoke.txt b/doc/src/fix_python_invoke.txt index 787940d9ebc4de8cd334a21454fe58dd6fa7b341..5e0c0369a54b62f81c5c14c6360d182c1f655df0 100644 --- a/doc/src/fix_python_invoke.txt +++ b/doc/src/fix_python_invoke.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt index f10f607a9bc29ca630445664b844d9c1fce36fe5..a4e0eb39376ea0945bd667ce6625c406b697534a 100644 --- a/doc/src/fix_python_move.txt +++ b/doc/src/fix_python_move.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -83,10 +83,10 @@ Examples for how to do this are in the {examples/python} folder. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_qbmsst.txt b/doc/src/fix_qbmsst.txt index 2c116fb0f8cf34f6e29143035d0c9cc7414e2750..e96bd97f4587cfa7446b5adc5606a6f4e13df09d 100644 --- a/doc/src/fix_qbmsst.txt +++ b/doc/src/fix_qbmsst.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,10 +179,10 @@ thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_ The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of etot. This global scalar and the vector of 5 quantities can be accessed by various "output -commands"_Section_howto.html#howto_15. It is worth noting that the -temp keyword under the "thermo_style"_thermo_style.html command print -the instantaneous classical temperature Tcl as -described in the command "fix qtb"_fix_qtb.html. +commands"_Howto_output.html. It is worth noting that the temp keyword +under the "thermo_style"_thermo_style.html command print the +instantaneous classical temperature Tcl as described +in the command "fix qtb"_fix_qtb.html. :line diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index 194361e990afdedbfccecf47be254c71df4623b7..27fb613ef957fc91f280f5eccf7328afcc1cdb35 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,9 +179,8 @@ parameters. See the examples/qeq directory for some examples. No information about these fixes is written to "binary restart files"_restart.html. No global scalar or vector or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. Thexe fixes are invoked during "energy minimization"_minimize.html. diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index 7f82404127fc61f6c3225f1c0d9b960bad470e27..99e86df030fb80215b1dfceab6d521fd8f4167f8 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,10 +62,9 @@ equilibration calculation is written to the specified file. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -93,9 +92,9 @@ integrator the fix is performing charge equilibration. Default is the outermost level. This fix produces a per-atom vector which can be accessed by various -"output commands"_Section_howto.html#howto_15. The vector stores the -gradient of the charge on each atom. The per-atom values be accessed -on any timestep. +"output commands"_Howto_output.html. The vector stores the gradient +of the charge on each atom. The per-atom values be accessed on any +timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index 18450c7cd5c0852c30e2324f3c683d84a2b63479..cf16daf84731096ec617c9abce809de80764ee73 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -70,8 +70,8 @@ the {qeq/reax/omp} style. Otherwise they are processed separately. No information about this fix is written to "binary restart files"_restart.html. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This fix is invoked during "energy minimization"_minimize.html. @@ -80,10 +80,9 @@ This fix is invoked during "energy minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 1b4a850a42f7740ba4649d0a5cd8e494537987b3..657ee841810a25338390cb7c14d6218691dfd6c1 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,9 +46,9 @@ No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +commands"_Howto_output.html. No parameter of this fix can be used +with the {start/stop} keywords of the "run"_run.html command. This +fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_qtb.txt b/doc/src/fix_qtb.txt index 07a6af39ba2f81db6ed16cce0eb93d39ac98b65b..5b212934a94780b1d6e34c8c90873519b1bcc543 100644 --- a/doc/src/fix_qtb.txt +++ b/doc/src/fix_qtb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index 3f8f237de1c7d574bfc214b9dfec2892e11b3793..49d61f4db80d45f1993bec664a07bc249f259ca1 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,17 +62,17 @@ version, but will also take longer to write. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -87,7 +87,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt index 7c920791f7b10bd923da0402c35a8215a15bf650..5be1c46230b477e62f07ff70c9dcf02c03ef7da3 100644 --- a/doc/src/fix_reaxc_species.txt +++ b/doc/src/fix_reaxc_species.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -116,8 +116,8 @@ are relevant to this fix. This fix computes both a global vector of length 2 and a per-atom vector, either of which can be accessed by various "output -commands"_Section_howto.html#howto_15. The values in the global -vector are "intensive". +commands"_Howto_output.html. The values in the global vector are +"intensive". The 2 values in the global vector are as follows: @@ -139,7 +139,7 @@ minimization"_minimize.html. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section_accelerate"_Section_accelerate.html +hardware, as discussed in "Speed"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -154,7 +154,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section_accelerate"_Section_accelerate.html of the manual for +See "Speed"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt index 342bed42515f8b827cc18a1cd228480480bd70f0..cfac756cd1659f9d8e7fcc6abc2922104a6b7bb0 100644 --- a/doc/src/fix_recenter.txt +++ b/doc/src/fix_recenter.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -94,13 +94,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -distance the group is moved by fix recenter. +"output commands"_Howto_output.html. The scalar is the distance the +group is moved by fix recenter. This fix also computes global 3-vector which can be accessed by -various "output commands"_Section_howto.html#howto_15. The 3 -quantities in the vector are xyz components of displacement applied to -the group of atoms by the fix. +various "output commands"_Howto_output.html. The 3 quantities in the +vector are xyz components of displacement applied to the group of +atoms by the fix. The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 9de63defb700fb0f713187d87f4077fd35b86e0f..2edc7e32963bb94c3bd60158bd21f94ba123e0a4 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -187,8 +187,8 @@ added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the "fix_modify"_fix_modify.html {energy} option for this fix. -This fix computes a global scalar and a global vector of length 3, which -can be accessed by various "output commands"_Section_howto.html#howto_15. +This fix computes a global scalar and a global vector of length 3, +which can be accessed by various "output commands"_Howto_output.html. The scalar is the total potential energy for {all} the restraints as discussed above. The vector values are the sum of contributions to the following individual categories: diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt index 2db920ac4bef02c60f95604beb5e6feeb9cb7de6..68cce694e9b46eb71275eb61b5af3ad877eb1fa5 100644 --- a/doc/src/fix_rhok.txt +++ b/doc/src/fix_rhok.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index ec7ed4f2b1e16374b0dd318a75cf31b3618711ce..d5e3b0166810dd39613d4a9105d9ac0ed43e86b9 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -241,19 +241,17 @@ molecule ID = 0) surrounding rigid bodies, this may not be what you want. Thus you should be careful to use a fix group that only includes atoms you want to be part of rigid bodies. -Bodystyle {custom} is similar to bodystyle {molecule}, however some -custom properties are used to group atoms into rigid bodies. The -special case for molecule/body ID = 0 is not available. Possible -custom properties are an integer property associated with atoms through -"fix property/atom"_fix_property_atom.html or an atom style variable -or an atomfile style variable. For the latter two, the variable value -will be rounded to an integer and then rigid bodies defined from -those values. - -For bodystyle {group}, each of the listed groups is treated as a -separate rigid body. Only atoms that are also in the fix group are -included in each rigid body. This option is only allowed for the -{rigid} styles. +Bodystyle {custom} is similar to bodystyle {molecule} except that it +is more flexible in using other per-atom properties to define the sets +of atoms that form rigid bodies. An integer vector defined by the +"fix property/atom"_fix_property_atom.txt command can be used. Or an +"atom-style or atomfile-style variable"_variable.html can be used; the +floating-point value produced by the variable is rounded to an +integer. As with bondstyle {molecule}, each set of atoms in the fix +groups with the same integer value is treated as a different rigid +body. Since fix property/atom vectors and atom-style variables +produce values for all atoms, you should be careful to use a fix group +that only includes atoms you want to be part of rigid bodies. NOTE: To compute the initial center-of-mass position and other properties of each rigid body, the image flags for each atom in the @@ -692,10 +690,9 @@ rigid/nvt. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -707,8 +704,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -748,29 +745,29 @@ computed early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage or the timestep, respectively. The 2 NVE rigid fixes compute a global scalar which can be accessed by -various "output commands"_Section_howto.html#howto_15. The scalar -value calculated by these fixes is "intensive". The scalar is the -current temperature of the collection of rigid bodies. This is -averaged over all rigid bodies and their translational and rotational -degrees of freedom. The translational energy of a rigid body is 1/2 m -v^2, where m = total mass of the body and v = the velocity of its -center of mass. The rotational energy of a rigid body is 1/2 I w^2, -where I = the moment of inertia tensor of the body and w = its angular -velocity. Degrees of freedom constrained by the {force} and {torque} -keywords are removed from this calculation, but only for the {rigid} -and {rigid/nve} fixes. +various "output commands"_Howto_output.html. The scalar value +calculated by these fixes is "intensive". The scalar is the current +temperature of the collection of rigid bodies. This is averaged over +all rigid bodies and their translational and rotational degrees of +freedom. The translational energy of a rigid body is 1/2 m v^2, where +m = total mass of the body and v = the velocity of its center of mass. +The rotational energy of a rigid body is 1/2 I w^2, where I = the +moment of inertia tensor of the body and w = its angular velocity. +Degrees of freedom constrained by the {force} and {torque} keywords +are removed from this calculation, but only for the {rigid} and +{rigid/nve} fixes. The 6 NVT, NPT, NPH rigid fixes compute a global scalar which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The scalar value calculated by these fixes is "extensive". The scalar -is the cumulative energy change due to the thermostatting and -barostatting the fix performs. +accessed by various "output commands"_Howto_output.html. The scalar +value calculated by these fixes is "extensive". The scalar is the +cumulative energy change due to the thermostatting and barostatting +the fix performs. All of the {rigid} styles (not the {rigid/small} styles) compute a global array of values which can be accessed by various "output -commands"_Section_howto.html#howto_15. Similar information about the -bodies defined by the {rigid/small} styles can be accessed via the -"compute rigid/local"_compute_rigid_local.html command. +commands"_Howto_output.html. Similar information about the bodies +defined by the {rigid/small} styles can be accessed via the "compute +rigid/local"_compute_rigid_local.html command. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 diff --git a/doc/src/fix_rx.txt b/doc/src/fix_rx.txt index 0810a347408f33cf20586448cf2141fb4c037275..d39e41e922d16158b2f643e4b0d4eb60e900493a 100644 --- a/doc/src/fix_rx.txt +++ b/doc/src/fix_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,10 +186,9 @@ read_data data.dpd fix foo_SPECIES NULL Species Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_saed_vtk.txt b/doc/src/fix_saed_vtk.txt index 814e17b8e952ad71d3ffe918c99596a0d10dc575..60708cd6962cfa57823d1a3c3d33ba1b50a5f661 100644 --- a/doc/src/fix_saed_vtk.txt +++ b/doc/src/fix_saed_vtk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index f5be0f93a54c459ead80c691dd4905df678760c4..14fceb7b49e87a01596f1e8f131c4aecd84d26de 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,12 +65,12 @@ to it. :line -Styles with a r {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The region keyword is also supported by Kokkos, but a Kokkos-enabled region must be used. See the region "region"_region.html command for @@ -85,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -103,10 +103,10 @@ so that setforce values are not counted multiple times. Default is to to override forces at the outermost level. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms before the forces on individual atoms are +changed by the fix. The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 46452a1f7e932eaf2531525f7ee6d557fceffb37..ea38de41cd1ba8b0ad9f2c759db429666798f524 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -145,12 +145,12 @@ info of atoms in the molecule. :line -Styles with a suffix are functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, -depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -162,8 +162,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -195,10 +195,9 @@ No information about these fixes is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various "output -commands"_Section_howto.html#howto_15. No parameter of these fixes -can be used with the {start/stop} keywords of the "run"_run.html -command. These fixes are not invoked during "energy -minimization"_minimize.html. +commands"_Howto_output.html. No parameter of these fixes can be used +with the {start/stop} keywords of the "run"_run.html command. These +fixes are not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 24726d8610abf0a79db6e14b163731d61ff46404..33db2bf7cc9e25d81e6b842e6b8282d6ed5feb07 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -56,10 +56,9 @@ examples/USER/dpd directory. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -71,8 +70,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index cb4a40f0fd0a3cbea0f95de29562e5e4faea110b..2f083dafc337f887ab75da54c4859dd901701844 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,12 +111,12 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a vector list of 7 quantities, which can be accessed -by various "output commands"_Section_howto.html#howto_15. The -quantities in the vector are in this order: the x-, y-, and -z-component of the pulling force, the total force in direction of the -pull, the equilibrium distance of the spring, the distance between the -two reference points, and finally the accumulated PMF (the sum of -pulling forces times displacement). +by various "output commands"_Howto_output.html. The quantities in the +vector are in this order: the x-, y-, and z-component of the pulling +force, the total force in direction of the pull, the equilibrium +distance of the spring, the distance between the two reference points, +and finally the accumulated PMF (the sum of pulling forces times +displacement). The force is the total force on the group of atoms by the spring. In the case of the {couple} style, it is the force on the fix group diff --git a/doc/src/fix_smd_adjust_dt.txt b/doc/src/fix_smd_adjust_dt.txt index 86b7363300929bada7f049fae3f3c13cf3cec11f..740b10559d8aced34b4c1428bb355b20c144f325 100644 --- a/doc/src/fix_smd_adjust_dt.txt +++ b/doc/src/fix_smd_adjust_dt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_integrate_tlsph.txt b/doc/src/fix_smd_integrate_tlsph.txt index 17c9c0f400f4cdf5dfc67966d5b1f51d4d0f4672..cd676a51ce3cdc3eb1978e8d8d29ff7f3acc7832 100644 --- a/doc/src/fix_smd_integrate_tlsph.txt +++ b/doc/src/fix_smd_integrate_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_integrate_ulsph.txt b/doc/src/fix_smd_integrate_ulsph.txt index 28e38c7f970a9d99a07294bd77f4fb66a54ced00..7f16b4b7ceabf7288252e5be36e84bda4c949465 100644 --- a/doc/src/fix_smd_integrate_ulsph.txt +++ b/doc/src/fix_smd_integrate_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_move_triangulated_surface.txt b/doc/src/fix_smd_move_triangulated_surface.txt index 2cba001267433e921d908bd9d344cb1152886fde..aeabf187686e105a9af292b6e5fd93ab01216095 100644 --- a/doc/src/fix_smd_move_triangulated_surface.txt +++ b/doc/src/fix_smd_move_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_smd_setvel.txt b/doc/src/fix_smd_setvel.txt index f93a7d0965b3eecb29dd130db7bbfbe0ae64bd63..6634751d6ad9e1ef17333982a7826b1c1e7d724b 100644 --- a/doc/src/fix_smd_setvel.txt +++ b/doc/src/fix_smd_setvel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -66,9 +66,9 @@ None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global 3-vector of forces, which can be accessed -by various "output commands"_Section_howto.html#howto_15. This is the -total force on the group of atoms. The vector values calculated by this -fix are "extensive". +by various "output commands"_Howto_output.html. This is the total +force on the group of atoms. The vector values calculated by this fix +are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_smd_wall_surface.txt b/doc/src/fix_smd_wall_surface.txt index feb65b2312823ece1b261e5349750500018b6ed7..a19b2c4cfb7eb2478ca21f684589491127b71eab 100644 --- a/doc/src/fix_smd_wall_surface.txt +++ b/doc/src/fix_smd_wall_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 014a43aacc706e03b37ceb37ca906a1fb248f275..690fc3e67c381a9cddd7469e22d9a925f75e4c14 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -105,19 +105,19 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -spring energy = 0.5 * K * r^2. +"output commands"_Howto_output.html. The scalar is the spring energy += 0.5 * K * r^2. This fix also computes global 4-vector which can be accessed by -various "output commands"_Section_howto.html#howto_15. The first 3 -quantities in the vector are xyz components of the total force added -to the group of atoms by the spring. In the case of the {couple} -style, it is the force on the fix group (group-ID) or the negative of -the force on the 2nd group (group-ID2). The 4th quantity in the -vector is the magnitude of the force added by the spring, as a -positive value if (r-R0) > 0 and a negative value if (r-R0) < 0. This -sign convention can be useful when using the spring force to compute a -potential of mean force (PMF). +various "output commands"_Howto_output.html. The first 3 quantities +in the vector are xyz components of the total force added to the group +of atoms by the spring. In the case of the {couple} style, it is the +force on the fix group (group-ID) or the negative of the force on the +2nd group (group-ID2). The 4th quantity in the vector is the +magnitude of the force added by the spring, as a positive value if +(r-R0) > 0 and a negative value if (r-R0) < 0. This sign convention +can be useful when using the spring force to compute a potential of +mean force (PMF). The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt index 7630a009dd3bbfd9d087f5b57060f8f56c216227..9d4e8afd090e3a0ea9bc12af04cf1db4b53b6945 100644 --- a/doc/src/fix_spring_chunk.txt +++ b/doc/src/fix_spring_chunk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,8 +60,8 @@ fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -energy of all the springs, i.e. 0.5 * K * r^2 per-spring. +"output commands"_Howto_output.html. The scalar is the energy of all +the springs, i.e. 0.5 * K * r^2 per-spring. The scalar value calculated by this fix is "extensive". diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt index bff6b38e7e94c44477c07e94efb0b72f909dfc43..b252163958fe5b983faeb2fc25e976bcf602f211 100644 --- a/doc/src/fix_spring_rg.txt +++ b/doc/src/fix_spring_rg.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,10 +51,10 @@ the time the fix is specified, and that value is used as the target. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index 68961a1512d1ba80ddd72da8024333cc51180103..0ac1d5eecb627a363b900d5af01ebef318e200b0 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,10 +57,10 @@ this fix. This allows to set at which level of the "r-RESPA"_run_style.html integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is an -energy which is the sum of the spring energy for each atom, where the -per-atom energy is 0.5 * K * r^2. The scalar value calculated by this -fix is "extensive". +"output commands"_Howto_output.html. The scalar is an energy which is +the sum of the spring energy for each atom, where the per-atom energy +is 0.5 * K * r^2. The scalar value calculated by this fix is +"extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 4e190234fd2b873cb5592c9c335304b53245d5c1..893557b9acad71bd2f1be0690a3b0694b68022f6 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -341,11 +341,11 @@ are relevant to this fix. This fix tabulates several SRD statistics which are stored in a vector of length 12, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The vector values calculated -by this fix are "intensive", meaning they do not scale with the size -of the simulation. Technically, the first 8 do scale with the size of -the simulation, but treating them as intensive means they are not -scaled when printed as part of thermodynamic output. +commands"_Howto_output.html. The vector values calculated by this fix +are "intensive", meaning they do not scale with the size of the +simulation. Technically, the first 8 do scale with the size of the +simulation, but treating them as intensive means they are not scaled +when printed as part of thermodynamic output. These are the 12 quantities. All are values for the current timestep, except for quantity 5 and the last three, each of which are diff --git a/doc/src/fix_store_force.txt b/doc/src/fix_store_force.txt index c988431f9de8dc47b85bfbce1d9cc82de1228270..33ebc962d5da9def4a817dbf6a1e9cdb78c5e4ad 100644 --- a/doc/src/fix_store_force.txt +++ b/doc/src/fix_store_force.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -26,7 +26,7 @@ timestep when the fix is invoked, as described below. This is useful for storing forces before constraints or other boundary conditions are computed which modify the forces, so that unmodified forces can be "written to a dump file"_dump.html or accessed by other "output -commands"_Section_howto.html#howto_15 that use per-atom quantities. +commands"_Howto_output.html that use per-atom quantities. This fix is invoked at the point in the velocity-Verlet timestepping immediately after "pair"_pair_style.html, "bond"_bond_style.html, @@ -54,9 +54,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a per-atom array which can be accessed by various -"output commands"_Section_howto.html#howto_15. The number of columns -for each atom is 3, and the columns store the x,y,z forces on each -atom. The per-atom values be accessed on any timestep. +"output commands"_Howto_output.html. The number of columns for each +atom is 3, and the columns store the x,y,z forces on each atom. The +per-atom values be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_store_state.txt b/doc/src/fix_store_state.txt index df694fb97b4e2dd037d41a21b1200b89d3c3594a..df05adc5b9ceb274061dab5bc7a0dbfc5cc395dd 100644 --- a/doc/src/fix_store_state.txt +++ b/doc/src/fix_store_state.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,8 +68,7 @@ Define a fix that stores attributes for each atom in the group at the time the fix is defined. If {N} is 0, then the values are never updated, so this is a way of archiving an atom attribute at a given time for future use in a calculation or output. See the discussion of -"output commands"_Section_howto.html#howto_15 that take fixes as -inputs. +"output commands"_Howto_output.html that take fixes as inputs. If {N} is not zero, then the attributes will be updated every {N} steps. @@ -108,9 +107,8 @@ fix. If a single input is specified, this fix produces a per-atom vector. If multiple inputs are specified, a per-atom array is produced where the number of columns for each atom is the number of inputs. These -can be accessed by various "output -commands"_Section_howto.html#howto_15. The per-atom values be -accessed on any timestep. +can be accessed by various "output commands"_Howto_output.html. The +per-atom values be accessed on any timestep. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_surface_global.txt b/doc/src/fix_surface_global.txt index b470babab72a14f2761805d4719d8bfc92165546..ade64d2056e0e23e58e3e762620077d6ada3f1f1 100644 --- a/doc/src/fix_surface_global.txt +++ b/doc/src/fix_surface_global.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_temp_berendsen.txt b/doc/src/fix_temp_berendsen.txt index 6944860e140d8ef9c5772a340007905086b86434..c1f1626782abffb6d380b0faae983b6642d67db0 100644 --- a/doc/src/fix_temp_berendsen.txt +++ b/doc/src/fix_temp_berendsen.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -68,8 +68,8 @@ be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. This fix computes a temperature each timestep. To do this, the fix @@ -126,9 +126,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_temp_csvr.txt b/doc/src/fix_temp_csvr.txt index 4129ad73c8fdbe514592b1a33d38e509c74f6f93..e50f821bfe9d55339164064ea18a515d4ac58967 100644 --- a/doc/src/fix_temp_csvr.txt +++ b/doc/src/fix_temp_csvr.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,8 +76,8 @@ normally be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. These fixes compute a temperature each timestep. To do this, the fix @@ -135,9 +135,9 @@ the {start} and {stop} keywords of the "run"_run.html command. See the These fixes are not invoked during "energy minimization"_minimize.html. These fixes compute a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to the fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to the fix. The scalar value calculated by this fix +is "extensive". [Restrictions:] diff --git a/doc/src/fix_temp_rescale.txt b/doc/src/fix_temp_rescale.txt index eff25297c1e295f6bcb775d65147dfac932ea956..5640317f1cf68ae357480d2b641441af9acf752a 100644 --- a/doc/src/fix_temp_rescale.txt +++ b/doc/src/fix_temp_rescale.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -75,8 +75,8 @@ be used on atoms that also have their temperature controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix langevin"_fix_langevin.html commands. -See "this howto section"_Section_howto.html#howto_16 of the manual for -a discussion of different ways to compute temperature and perform +See the "Howto thermostat"_Howto_thermostat.html doc page for a +discussion of different ways to compute temperature and perform thermostatting. This fix computes a temperature each timestep. To do this, the fix @@ -133,9 +133,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_temp_rescale_eff.txt b/doc/src/fix_temp_rescale_eff.txt index f87c1a219249438c0864dba1f2880b0f1bfae9d8..0e08e4f1e81c9451e7c50742263f0b0b7b6988b9 100644 --- a/doc/src/fix_temp_rescale_eff.txt +++ b/doc/src/fix_temp_rescale_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,9 +51,9 @@ system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative energy change due to this fix. The scalar value -calculated by this fix is "extensive". +"output commands"_Howto_output.html. The scalar is the cumulative +energy change due to this fix. The scalar value calculated by this +fix is "extensive". This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index 3c81d62ee0aa7c136765e59267b0a9d85f1a8333..ddfa46261929de1fc4e1ab0c411537e6df97744d 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 0353c095b29d60e4be37a581968a70d06f778492..86fc6f2c72feba87286126f2b48dacf0983bce69 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,9 +108,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative kinetic energy transferred between the bottom and middle -of the simulation box (in the {edim} direction) is stored as a scalar +"output commands"_Howto_output.html. The scalar is the cumulative +kinetic energy transferred between the bottom and middle of the +simulation box (in the {edim} direction) is stored as a scalar quantity by this fix. This quantity is zeroed when the fix is defined and accumulates thereafter, once every N steps. The units of the quantity are energy; see the "units"_units.html command for details. diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 191f9e7c6b8d8667b5baef112f20d16fb435a382..afe5373220095b949e9429f41e800f4e2fa6ad79 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -121,13 +121,12 @@ fix to add the energy stored in the per-atom springs to the system's potential energy as part of "thermodynamic output"_thermo_style.html. This fix computes a global scalar and a global vector quantities which -can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar is an energy which -is the sum of the spring energy for each atom, where the per-atom -energy is 0.5 * k * r^2. The vector has 2 positions, the first one is -the coupling parameter lambda and the second one is the time -derivative of lambda. The scalar and vector values calculated by this -fix are "extensive". +can be accessed by various "output commands"_Howto_output.html. The +scalar is an energy which is the sum of the spring energy for each +atom, where the per-atom energy is 0.5 * k * r^2. The vector has 2 +positions, the first one is the coupling parameter lambda and the +second one is the time derivative of lambda. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_tmd.txt b/doc/src/fix_tmd.txt index 71d8d2c7670a2956a091ed68d293064de4ffcb59..c2541692f5f4cb2667084e11c5f375132e99abf3 100644 --- a/doc/src/fix_tmd.txt +++ b/doc/src/fix_tmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,8 +90,7 @@ For more information about TMD, see "(Schlitter1)"_#Schlitter1 and No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. +by this fix for access by various "output commands"_Howto_output.html. This fix can ramp its rho parameter over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_ttm.txt b/doc/src/fix_ttm.txt index 48dfd254a00de377ddb027c8d8e1c77d54e209a3..6001def5817736192fd0f7ac357a63ce148ca3c1 100644 --- a/doc/src/fix_ttm.txt +++ b/doc/src/fix_ttm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -272,18 +272,17 @@ None of the "fix_modify"_fix_modify.html options are relevant to these fixes. Both fixes compute 2 output quantities stored in a vector of length 2, -which can be accessed by various "output -commands"_Section_howto.html#howto_15. The first quantity is the -total energy of the electronic subsystem. The second quantity is the -energy transferred from the electronic to the atomic subsystem on that -timestep. Note that the velocity verlet integrator applies the fix ttm -forces to the atomic subsystem as two half-step velocity updates: one -on the current timestep and one on the subsequent timestep. -Consequently, the change in the atomic subsystem energy is lagged by -half a timestep relative to the change in the electronic subsystem -energy. As a result of this, users may notice slight fluctuations in -the sum of the atomic and electronic subsystem energies reported at -the end of the timestep. +which can be accessed by various "output commands"_Howto_output.html. +The first quantity is the total energy of the electronic +subsystem. The second quantity is the energy transferred from the +electronic to the atomic subsystem on that timestep. Note that the +velocity verlet integrator applies the fix ttm forces to the atomic +subsystem as two half-step velocity updates: one on the current +timestep and one on the subsequent timestep. Consequently, the change +in the atomic subsystem energy is lagged by half a timestep relative +to the change in the electronic subsystem energy. As a result of this, +users may notice slight fluctuations in the sum of the atomic and +electronic subsystem energies reported at the end of the timestep. The vector values calculated are "extensive". diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 60a34a26c9c671c291ff9ee77946e43e8c0a7c62..b4e8472591dee2164ddb4ef2550431ce0b575e4e 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_vector.txt b/doc/src/fix_vector.txt index 47b3cfc67a2dbe667ce2af1799368b50dc741f50..e1bfbe5738073e466f78f2742ed154e13884dc81 100644 --- a/doc/src/fix_vector.txt +++ b/doc/src/fix_vector.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -37,7 +37,7 @@ simply store them. For a single specified value, the values are stored as a global vector of growing length. For multiple specified values, they are stored as rows in a global array, whose number of rows is growing. The resulting vector or array can be used by other -"output commands"_Section_howto.html#howto_15. +"output commands"_Howto_output.html. One way to to use this command is to accumulate a vector that is time-integrated using the "variable trap()"_variable.html function. @@ -94,7 +94,7 @@ output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for these commands which give the IDs of these computes. Users can also write code for their own compute styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. If no bracketed term is @@ -105,7 +105,7 @@ calculated by the fix is used. Note that some fixes only produce their values on certain timesteps, which must be compatible with {Nevery}, else an error will result. Users can also write code for their own fix styles and "add them to -LAMMPS"_Section_modify.html. +LAMMPS"_Modify.html. If a value begins with "v_", a variable name must follow which has been previously defined in the input script. An equal-style or @@ -127,9 +127,8 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix produces a global vector or global array which can be -accessed by various "output commands"_Section_howto.html#howto_15. -The values can only be accessed on timesteps that are multiples of -{Nevery}. +accessed by various "output commands"_Howto_output.html. The values +can only be accessed on timesteps that are multiples of {Nevery}. A vector is produced if only a single input value is specified. An array is produced if multiple input values are specified. diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index f6603be624da84ba7efa8de3c62a3ff9d5074e65..934da3efdd7820fff834d01e1daf8354e14c39c2 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -100,13 +100,12 @@ accurately infer a viscosity and should try increasing the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in "Section -6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations -deform the simulation box via the "fix deform"_fix_deform.html -command. Thus they cannot be run on a charged system using a "PPPM -solver"_kspace_style.html since PPPM does not currently support -non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; -thus it does not suffer from this limitation. +simulation, as described on the "Howto nemd"_Howto_nemd.html doc page. +NEMD simulations deform the simulation box via the "fix +deform"_fix_deform.html command. Thus they cannot be run on a charged +system using a "PPPM solver"_kspace_style.html since PPPM does not +currently support non-orthogonal boxes. Using fix viscosity keeps the +box orthogonal; thus it does not suffer from this limitation. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -115,13 +114,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which can be accessed by various -"output commands"_Section_howto.html#howto_15. The scalar is the -cumulative momentum transferred between the bottom and middle of the -simulation box (in the {pdim} direction) is stored as a scalar -quantity by this fix. This quantity is zeroed when the fix is defined -and accumulates thereafter, once every N steps. The units of the -quantity are momentum = mass*velocity. The scalar value calculated by -this fix is "intensive". +"output commands"_Howto_output.html. The scalar is the cumulative +momentum transferred between the bottom and middle of the simulation +box (in the {pdim} direction) is stored as a scalar quantity by this +fix. This quantity is zeroed when the fix is defined and accumulates +thereafter, once every N steps. The units of the quantity are +momentum = mass*velocity. The scalar value calculated by this fix is +"intensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt index 9c30e40249a4b4febdef4e17c508766ea8a619d7..c5a3ede0b24a908ffb9ed5652af2d179400a0dd0 100644 --- a/doc/src/fix_viscous.txt +++ b/doc/src/fix_viscous.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,9 +82,9 @@ easily be used as a thermostat. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. The "fix_modify"_fix_modify.html {respa} option is supported by this fix. This allows to set at which level of the "r-RESPA"_run_style.html diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index e814c89a0743af6b7d744ac71d62d71df5c3053d..2ac59d9588155915370d834c1eb2b0e7727602ca 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -263,14 +263,14 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global vector of forces, which can be accessed by various "output -commands"_Section_howto.html#howto_15. Note that the scalar energy is -the sum of interactions with all defined walls. If you want the -energy on a per-wall basis, you need to use multiple fix wall -commands. The length of the vector is equal to the number of walls -defined by the fix. Each vector value is the normal force on a -specific wall. Note that an outward force on a wall will be a -negative value for {lo} walls and a positive value for {hi} walls. -The scalar and vector values calculated by this fix are "extensive". +commands"_Howto_output.html. Note that the scalar energy is the sum +of interactions with all defined walls. If you want the energy on a +per-wall basis, you need to use multiple fix wall commands. The +length of the vector is equal to the number of walls defined by the +fix. Each vector value is the normal force on a specific wall. Note +that an outward force on a wall will be a negative value for {lo} +walls and a positive value for {hi} walls. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. @@ -288,10 +288,9 @@ option for this fix. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -303,8 +302,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/fix_wall_body_polygon.txt b/doc/src/fix_wall_body_polygon.txt new file mode 100644 index 0000000000000000000000000000000000000000..0946a85131ae6c003daa63e7af939f9adf442227 --- /dev/null +++ b/doc/src/fix_wall_body_polygon.txt @@ -0,0 +1,104 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix wall/body/polygon command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polygon = style name of this fix command :l +k_n = normal repulsion strength (force/distance or pressure units) :l +c_n = normal damping coefficient (force/distance or pressure units) :l +c_t = tangential damping coefficient (force/distance or pressure units) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 2d models of body particles of style +{rounded/polygon}. It bounds the simulation domain with wall(s). All +particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +the "Howto body"_Howto_body.html doc page for more details on using +body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html command. + +The {wallstyle} can be planar or cylindrical. The 2 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is +appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if LAMMPS +was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Any dimension (xy) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polygon"_pair_body_rounded_polygon.html + +[Default:] none diff --git a/doc/src/fix_wall_body_polyhedron.txt b/doc/src/fix_wall_body_polyhedron.txt new file mode 100644 index 0000000000000000000000000000000000000000..407cf9fb339047e9b881c0e4df9b950280d5cbed --- /dev/null +++ b/doc/src/fix_wall_body_polyhedron.txt @@ -0,0 +1,103 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix wall/body/polyhedron command :h3 + +[Syntax:] + +fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +wall/body/polyhedron = style name of this fix command :l +k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) :l +c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) :l +c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) :l +wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l +args = list of arguments for a particular style :l + {xplane} or {yplane} args = lo hi + lo,hi = position of lower and upper plane (distance units), either can be NULL) + {zcylinder} args = radius + radius = cylinder radius (distance units) :pre +zero or more keyword/value pairs may be appended to args :l +keyword = {wiggle} :l + {wiggle} values = dim amplitude period + dim = {x} or {y} or {z} + amplitude = size of oscillation (distance units) + period = time of oscillation (time units) :pre +:ule + +[Examples:] + +fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0 + +[Description:] + +This fix is for use with 3d models of body particles of style +{rounded/polyhedron}. It bounds the simulation domain with wall(s). +All particles in the group interact with the wall when they are close +enough to touch it. The nature of the interaction between the wall +and the polygon particles is the same as that between the polygon +particles themselves, which is similar to a Hookean potential. See +the "Howto body"_Howto_body.html doc page for more details on using +body particles. + +The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as +those specified with the "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html command. + +The {wallstyle} can be planar or cylindrical. The 3 planar options +specify a pair of walls in a dimension. Wall positions are given by +{lo} and {hi}. Either of the values can be specified as NULL if a +single wall is desired. For a {zcylinder} wallstyle, the cylinder's +axis is at x = y = 0.0, and the radius of the cylinder is specified. + +Optionally, the wall can be moving, if the {wiggle} keyword is appended. + +For the {wiggle} keyword, the wall oscillates sinusoidally, similar to +the oscillations of particles which can be specified by the "fix +move"_fix_move.html command. This is useful in packing simulations of +particles. The arguments to the {wiggle} keyword specify a dimension +for the motion, as well as it's {amplitude} and {period}. Note that +if the dimension is in the plane of the wall, this is effectively a +shearing motion. If the dimension is perpendicular to the wall, it is +more of a shaking motion. A {zcylinder} wall can only be wiggled in +the z dimension. + +Each timestep, the position of a wiggled wall in the appropriate {dim} +is set according to this equation: + +position = coord + A - A cos (omega * delta) :pre + +where {coord} is the specified initial position of the wall, {A} is +the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. The velocity of the wall is set +to the derivative of this expression. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. No global or per-atom quantities are stored by this fix for +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the BODY package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +Any dimension (xyz) that has a wall must be non-periodic. + +[Related commands:] + +"atom_style body"_atom_style.html, "pair_style +body/rounded/polyhedron"_pair_body_rounded_polyhedron.html + +[Default:] none diff --git a/doc/src/fix_wall_ees.txt b/doc/src/fix_wall_ees.txt index f141a194057f30fbb940922bf04d18044c4937b4..ae16ca40d2ab731af1a4b77ac474d3dd8b00f841 100644 --- a/doc/src/fix_wall_ees.txt +++ b/doc/src/fix_wall_ees.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/fix_wall_gran.txt b/doc/src/fix_wall_gran.txt index 5f1679604e365ae0c3c2b59db43331c4b4925b02..6c2769fc12840c85fdd60248009a45a851d8174a 100644 --- a/doc/src/fix_wall_gran.txt +++ b/doc/src/fix_wall_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -148,9 +148,9 @@ uninterrupted fashion. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index 92fb042194db78bbf7d38794a4c49ee65dcbfa09..187214c1a36ca27c304d291150d16f56d440d204 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -180,9 +180,9 @@ region with a different region ID. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for -access by various "output commands"_Section_howto.html#howto_15. No -parameter of this fix can be used with the {start/stop} keywords of -the "run"_run.html command. This fix is not invoked during "energy +access by various "output commands"_Howto_output.html. No parameter +of this fix can be used with the {start/stop} keywords of the +"run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index 4d7756c237d708840fc085a27b0540bdbe35c45d..eecf69ebf2b80164672bb2b21cdb48f3ce855a0d 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -91,10 +91,10 @@ define the lattice spacings. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index 954ec65bf6a1c059226c1beac58bea86fab0fb84..78be84eb638224ec631841fabc022bf0700a5162 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -130,10 +130,9 @@ position = c0 + A (1 - cos(omega*delta)) :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line @@ -155,10 +154,10 @@ more instructions on how to use the accelerated styles effectively. No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various "output -commands"_Section_howto.html#howto_15. No parameter of this fix can -be used with the {start/stop} keywords of the "run"_run.html command. -This fix is not invoked during "energy minimization"_minimize.html. +by this fix for access by various "output commands"_Howto_output.html. +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. [Restrictions:] diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index 9700545dc909c92f4327db4a155f0da789703b8a..559a2f0d89c0cd8c00cc49be87daf53f793cf6f9 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -156,12 +156,11 @@ integrator the fix is adding its forces. Default is the outermost level. This fix computes a global scalar energy and a global 3-length vector of forces, which can be accessed by various "output -commands"_Section_howto.html#howto_15. The scalar energy is the sum -of energy interactions for all particles interacting with the wall -represented by the region surface. The 3 vector quantities are the -x,y,z components of the total force acting on the wall due to the -particles. The scalar and vector values calculated by this fix are -"extensive". +commands"_Howto_output.html. The scalar energy is the sum of energy +interactions for all particles interacting with the wall represented +by the region surface. The 3 vector quantities are the x,y,z +components of the total force acting on the wall due to the particles. +The scalar and vector values calculated by this fix are "extensive". No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. diff --git a/doc/src/fix_wall_srd.txt b/doc/src/fix_wall_srd.txt index c465896d37578969cad9b33143d24260b097f525..3a50c45ab7592d0c7d3d16dc969423218eaee8b6 100644 --- a/doc/src/fix_wall_srd.txt +++ b/doc/src/fix_wall_srd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -166,9 +166,9 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global array of values which can be accessed by -various "output commands"_Section_howto.html#howto_15. The number of -rows in the array is equal to the number of walls defined by the fix. -The number of columns is 3, for the x,y,z components of force on each +various "output commands"_Howto_output.html. The number of rows in +the array is equal to the number of walls defined by the fix. The +number of columns is 3, for the x,y,z components of force on each wall. Note that an outward normal force on a wall will be a negative value diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 79c2f75b8ba46f2924c2e34ed98c81edd6fe71b8..7a45ed8086a14cdc201eea9cce5f28f80b4df00e 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -61,6 +61,7 @@ Fixes :h1 fix_langevin fix_langevin_drude fix_langevin_eff + fix_langevin_spin fix_latte fix_lb_fluid fix_lb_momentum @@ -99,6 +100,7 @@ Fixes :h1 fix_nve_manifold_rattle fix_nve_noforce fix_nve_sphere + fix_nve_spin fix_nve_tri fix_nvk fix_nvt_asphere @@ -114,6 +116,7 @@ Fixes :h1 fix_planeforce fix_poems fix_pour + fix_precession_spin fix_press_berendsen fix_print fix_property_atom @@ -165,6 +168,8 @@ Fixes :h1 fix_viscosity fix_viscous fix_wall + fix_wall_body_polygon + fix_wall_body_polyhedron fix_wall_ees fix_wall_gran fix_wall_gran_region diff --git a/doc/src/group.txt b/doc/src/group.txt index dddb0459e3711e526e6077318aa6ae51922b0196..847267737286c79b0d99315d20b995907082cf81 100644 --- a/doc/src/group.txt +++ b/doc/src/group.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/group2ndx.txt b/doc/src/group2ndx.txt index 94d188399ba6937874f1d579eb4bdf66c840ea2d..242d6a69a4092798fb073f2f89a4c44957b46061 100644 --- a/doc/src/group2ndx.txt +++ b/doc/src/group2ndx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/if.txt b/doc/src/if.txt index 52fad5aea756031760c56e6e7ec4183266f9212c..513e451034da5f2752b96c4cdd81b3ec26ac58c4 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -65,9 +65,9 @@ above. NOTE: If a command itself requires a quoted argument (e.g. a "print"_print.html command), then double and single quotes can be used and nested in the usual manner, as in the examples above and below. -See "Section 3.2"_Section_commands.html#cmd_2 of the manual for -more details on using quotes in arguments. Only one of level of -nesting is allowed, but that should be sufficient for most use cases. +The "Commands parse"_Commands_parse.html doc page has more details on +using quotes in arguments. Only one of level of nesting is allowed, +but that should be sufficient for most use cases. Note that by using the line continuation character "&", the if command can be spread across many lines, though it is still a single command: diff --git a/doc/src/improper_class2.txt b/doc/src/improper_class2.txt index 14ec6258de654a466ec429328014f420e81cb999..c38f73c64dc017d58ce25e86cb431d5c068e9b1e 100644 --- a/doc/src/improper_class2.txt +++ b/doc/src/improper_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -87,10 +87,9 @@ radians internally; hence the units of M are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -102,8 +101,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt index 5c01a23ae9cda2b729894bb87a8b4108ff4a11b7..8ed65f95350a3a56eb776b5fe5ad67c3257d939d 100644 --- a/doc/src/improper_coeff.txt +++ b/doc/src/improper_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -67,9 +67,9 @@ the style to display the formula it computes and coefficients specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul diff --git a/doc/src/improper_cossq.txt b/doc/src/improper_cossq.txt index 138a6a16503b125003b15ec1ceb394f18963e1eb..04aa45255cb2faf860dcd0493b53e301c6a65bde 100644 --- a/doc/src/improper_cossq.txt +++ b/doc/src/improper_cossq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,10 +53,9 @@ X0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_cvff.txt b/doc/src/improper_cvff.txt index 5f69eccc60a1d060b894c89f487d591fa1a8b0b8..d01faf288554e0281f1841e45c9f0c415083c547 100644 --- a/doc/src/improper_cvff.txt +++ b/doc/src/improper_cvff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,10 +54,9 @@ n (0,1,2,3,4,6) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -69,8 +68,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_distance.txt b/doc/src/improper_distance.txt index 7d49d17c976f262d39ff642380f23aadb0701595..93235fe60197f01fc50297ec4f8d0504c16c6b9a 100644 --- a/doc/src/improper_distance.txt +++ b/doc/src/improper_distance.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_fourier.txt b/doc/src/improper_fourier.txt index f9062da207b329cb7616ca38420e8878675252b4..78cc1b3f760fe81de8682983f11bc0f90615f9d4 100644 --- a/doc/src/improper_fourier.txt +++ b/doc/src/improper_fourier.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -48,10 +48,9 @@ all (integer >= 0) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -63,8 +62,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_harmonic.txt b/doc/src/improper_harmonic.txt index bb17e5a641e8da1b4b92f3e1b5ecfe8245fddf1a..f398dc425f935f605c3446075783df2b91d49c00 100644 --- a/doc/src/improper_harmonic.txt +++ b/doc/src/improper_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,10 +58,9 @@ internally; hence the units of K are in energy/radian^2. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -73,8 +72,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_hybrid.txt b/doc/src/improper_hybrid.txt index 0c2beaef18c07dc3cfcc8ad136a8940486bdeef8..42afbe8577dc30163dcc8e5053de9cc05022b6a2 100644 --- a/doc/src/improper_hybrid.txt +++ b/doc/src/improper_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt index 34683ca2bb0000db8f32f9e93838f344e0287b4c..2c0f2f0af84e1275c8511fc3d65f2508163a89cd 100644 --- a/doc/src/improper_inversion_harmonic.txt +++ b/doc/src/improper_inversion_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt index af9964c7437af081e5a50ba8daf4359c94882593..f97af101fcffaf64ce4dacc34bc7824e4312d185 100644 --- a/doc/src/improper_none.txt +++ b/doc/src/improper_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/improper_ring.txt b/doc/src/improper_ring.txt index c02d39247403622fe51e1ffbc4e47df43e11db77..60bbca170a9a3d06cc3d819d847fdf37370691d9 100644 --- a/doc/src/improper_ring.txt +++ b/doc/src/improper_ring.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -57,10 +57,9 @@ theta0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -72,8 +71,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index 861701590fedcfce745e2542fd7c69c943e4e5a3..3d29b28ec4a69b2200db24e2fb742fdf1c7fabd4 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -60,9 +60,9 @@ specified by the associated "improper_coeff"_improper_coeff.html command. Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The list of these with -links to the individual styles are given in the improper section of -"this page"_Section_commands.html#cmd_5. +which are included in the LAMMPS distribution. The full list of all +improper styles is on the "Commands bond"_Commands_bond.html#improper +doc page. "improper_style none"_improper_none.html - turn off improper interactions "improper_style zero"_improper_zero.html - topology but no interactions diff --git a/doc/src/improper_umbrella.txt b/doc/src/improper_umbrella.txt index d6df9ee6cccc8ec2f391a2583ac495caa0ad07e9..b05cf4b181bfceaed1160cebb650d99922af039a 100644 --- a/doc/src/improper_umbrella.txt +++ b/doc/src/improper_umbrella.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -22,7 +22,7 @@ improper_coeff 1 100.0 180.0 :pre The {umbrella} improper style uses the following potential, which is commonly referred to as a classic inversion and used in the -"DREIDING"_Section_howto.html#howto_4 force field: +"DREIDING"_Howto_bioFF.html force field: :c,image(Eqs/improper_umbrella.jpg) @@ -51,10 +51,9 @@ omega0 (degrees) :ul Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/improper_zero.txt b/doc/src/improper_zero.txt index 2a298573d5e359ef1676519ef494526fa14a2bc7..f3f3485b57cf0c6daf81233f1432e9b43f2aeb42 100644 --- a/doc/src/improper_zero.txt +++ b/doc/src/improper_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/include.txt b/doc/src/include.txt index 95d08db3522d8d291512e477801860f41f78004a..c11405631365e173f57589d3a11825884a4b0157 100644 --- a/doc/src/include.txt +++ b/doc/src/include.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/info.txt b/doc/src/info.txt index d5b5bd97b942842c03a26011d66ce7049b1c3a27..99211de4fb5745edccf401a78f2045c756dee695 100644 --- a/doc/src/info.txt +++ b/doc/src/info.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/jump.txt b/doc/src/jump.txt index 4e3799f7b1c48fafa179454b458c2eff588c4453..b5afeb6559f4c80629947cf9376ae455fdde1a63 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 6d27bb7076344adfd81ba2a0b7242c985a3eff02..dd7b1e8deadfdd3e6defeddaa0cc85d3e4467370 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -285,15 +285,15 @@ performance and accuracy in the results is obtained when these values are different. The {disp/auto} option controls whether the pppm/disp is allowed to -generate PPPM parameters automatically. If set to {no}, parameters have -to be specified using the {gewald/disp}, {mesh/disp}, -{force/disp/real} or {force/disp/kspace} keywords, or -the code will stop with an error message. When this option is set to -{yes}, the error message will not appear and the simulation will start. -For a typical application, using the automatic parameter generation -will provide simulations that are either inaccurate or slow. Using this -option is thus not recommended. For guidelines on how to obtain good -parameters, see the "How-To"_Section_howto.html#howto_24 discussion. +generate PPPM parameters automatically. If set to {no}, parameters +have to be specified using the {gewald/disp}, {mesh/disp}, +{force/disp/real} or {force/disp/kspace} keywords, or the code will +stop with an error message. When this option is set to {yes}, the +error message will not appear and the simulation will start. For a +typical application, using the automatic parameter generation will +provide simulations that are either inaccurate or slow. Using this +option is thus not recommended. For guidelines on how to obtain good +parameters, see the "Howto dispersion"_Howto_dispersion.html doc page. [Restrictions:] none diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 4f27c9aa78e95cb2819b65d44be17acfb53e4a6f..55ad4ab6107b828fd74e5daa91025063d29c5115 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -145,8 +145,8 @@ speedup in the KSpace time (8x less mesh points, 2x more expensive). However, for low relative accuracy, the staggered PPPM mesh size may be essentially the same as for regular PPPM, which means the method will be up to 2x slower in the KSpace time (simply 2x more expensive). -For more details and timings, see -"Section 5"_Section_accelerate.html. +For more details and timings, see the "Speed tips"_Speed_tips.html doc +page. NOTE: Using {pppm/stagger} may not give the same increase in the accuracy of energy and pressure as it does in forces, so some caution @@ -161,15 +161,16 @@ similar to the {ewald/disp} style. The 1/r^6 capability means that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. -For these styles, you will possibly want to adjust the default choice of -parameters by using the "kspace_modify"_kspace_modify.html command. +For these styles, you will possibly want to adjust the default choice +of parameters by using the "kspace_modify"_kspace_modify.html command. This can be done by either choosing the Ewald and grid parameters, or by specifying separate accuracies for the real and kspace -calculations. When not making any settings, the simulation will stop with -an error message. Further information on the influence of the parameters -and how to choose them is described in "(Isele-Holder)"_#Isele-Holder2012, -"(Isele-Holder2)"_#Isele-Holder2013 and the -"How-To"_Section_howto.html#howto_24 discussion. +calculations. When not making any settings, the simulation will stop +with an error message. Further information on the influence of the +parameters and how to choose them is described in +"(Isele-Holder)"_#Isele-Holder2012, +"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto +dispersion"_Howto_dispersion.html doc page. :line @@ -267,10 +268,9 @@ relative RMS error. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. More specifically, the {pppm/gpu} style performs charge assignment and force interpolation calculations on the GPU. These processes are @@ -291,8 +291,8 @@ KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if LAMMPS was built with those packages. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/label.txt b/doc/src/label.txt index c6a573141b205b7dea517f3d24881f84f06e3414..adab44188c8cc3a45cc49139e935c2e7c37a9606 100644 --- a/doc/src/label.txt +++ b/doc/src/label.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 0764c593f7e56cc251588d800a53d06a11e232b4..c0ca357f211aa973f0c80f28155b2cc9b6e0ebcd 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -1,34 +1,111 @@ #HTMLDOC 1.8.28 -t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow Manual.html -Section_intro.html +Intro.html +Intro_overview.html +Intro_features.html +Intro_nonfeatures.html +Intro_opensource.html +Intro_authors.html +Intro_website.html Section_start.html -Section_commands.html -Section_packages.html -Section_accelerate.html -accelerate_gpu.html -accelerate_intel.html -accelerate_kokkos.html -accelerate_omp.html -accelerate_opt.html -Section_howto.html -Section_example.html -Section_perf.html -Section_tools.html -Section_modify.html -Section_python.html -Section_errors.html -Section_history.html - -lammps_tutorials.html -tutorial_bash_on_windows.html -tutorial_drude.html -tutorial_github.html -tutorial_pylammps.html - -lammps_support.html -body.html -manifolds.html +Commands.html +Commands_input.html +Commands_parse.html +Commands_structure.html +Commands_category.html +Commands_all.html +Commands_fix.html +Commands_compute.html +Commands_pair.html +Commands_bond.html +Commands_kspace.html +Packages.html +Packages_standard.html +Packages_user.html +Packages_details.html +Speed.html +Speed_bench.html +Speed_measure.html +Speed_tips.html +Speed_packages.html +Speed_gpu.html +Speed_intel.html +Speed_kokkos.html +Speed_omp.html +Speed_opt.html +Speed_compare.html +Howto.html +Howto_github.html +Howto_pylammps.html +Howto_bash.html +Howto_restart.html +Howto_viz.html +Howto_multiple.html +Howto_replica.html +Howto_library.html +Howto_couple.html +Howto_output.html +Howto_chunk.html +Howto_2d.html +Howto_triclinic.html +Howto_walls.html +Howto_nemd.html +Howto_granular.html +Howto_spherical.html +Howto_dispersion.html +Howto_temperature.html +Howto_thermostat.html +Howto_barostat.html +Howto_elastic.html +Howto_kappa.html +Howto_viscosity.html +Howto_diffusion.html +Howto_bioFF.html +Howto_tip3p.html +Howto_tip4p.html +Howto_spc.html +Howto_body.html +Howto_polarizable.html +Howto_coreshell.html +Howto_drude.html +Howto_drude2.html +Howto_manifold.html +Howto_spins.html +Examples.html +Tools.html +Modify.html +Modify_overview.html +Modify_contribute.html +Modify_atom.html +Modify_pair.html +Modify_bond.html +Modify_compute.html +Modify_fix.html +Modify_command.html +Modify_dump.html +Modify_kspace.html +Modify_min.html +Modify_region.html +Modify_body.html +Modify_thermo.html +Modify_variable.html +Python.html +Python_overview.html +Python_run.html +Python_shlib.html +Python_install.html +Python_mpi.html +Python_test.html +Python_library.html +Python_pylammps.html +Python_examples.html +Python_call.html +Errors.html +Errors_common.html +Errors_bugs.html +Errors_messages.html +Errors_warnings.html lammps_commands.html atom_modify.html @@ -176,6 +253,7 @@ fix_ipi.html fix_langevin.html fix_langevin_drude.html fix_langevin_eff.html +fix_langevin_spin.html fix_latte.html fix_lb_fluid.html fix_lb_momentum.html @@ -213,6 +291,7 @@ fix_nve_line.html fix_nve_manifold_rattle.html fix_nve_noforce.html fix_nve_sphere.html +fix_nve_spin.html fix_nve_tri.html fix_nvk.html fix_nvt_asphere.html @@ -229,6 +308,7 @@ fix_pimd.html fix_planeforce.html fix_poems.html fix_pour.html +fix_precession_spin.html fix_press_berendsen.html fix_print.html fix_property_atom.html @@ -280,6 +360,8 @@ fix_vector.html fix_viscosity.html fix_viscous.html fix_wall.html +fix_wall_body_polygon.html +fix_wall_body_polyhedron.html fix_wall_ees.html fix_wall_gran.html fix_wall_gran_region.html @@ -317,6 +399,7 @@ compute_displace_atom.html compute_dpd.html compute_dpd_atom.html compute_edpd_temp_atom.html +compute_entropy_atom.html compute_erotate_asphere.html compute_erotate_rigid.html compute_erotate_sphere.html @@ -381,6 +464,7 @@ compute_smd_ulsph_strain_rate.html compute_smd_ulsph_stress.html compute_smd_vol.html compute_sna_atom.html +compute_spin.html compute_stress_atom.html compute_tally.html compute_tdpd_cc_atom.html @@ -419,8 +503,9 @@ pair_agni.html pair_airebo.html pair_awpmd.html pair_beck.html -pair_body.html +pair_body_nparticle.html pair_body_rounded_polygon.html +pair_body_rounded_polyhedron.html pair_bop.html pair_born.html pair_brownian.html @@ -506,6 +591,10 @@ pair_sph_lj.html pair_sph_rhosum.html pair_sph_taitwater.html pair_sph_taitwater_morris.html +pair_spin_dmi.html +pair_spin_exchange.html +pair_spin_magelec.html +pair_spin_neel.html pair_srp.html pair_sw.html pair_table.html diff --git a/doc/src/lammps_support.txt b/doc/src/lammps_support.txt deleted file mode 100644 index fa460ce6c23054e8409ad9b6e5392173c0972995..0000000000000000000000000000000000000000 --- a/doc/src/lammps_support.txt +++ /dev/null @@ -1,7 +0,0 @@ - -Supporting Information :h1 - -This section of the manual contains supporting information that -is not documenting individual commands but general concepts and -supporting information about entities like body particles or -manifolds. diff --git a/doc/src/lammps_tutorials.txt b/doc/src/lammps_tutorials.txt deleted file mode 100644 index 5ceda65b600744e9133168348bcc55ea78629bfc..0000000000000000000000000000000000000000 --- a/doc/src/lammps_tutorials.txt +++ /dev/null @@ -1,6 +0,0 @@ - -Tutorials :h2 - -The following pages contain some in-depth tutorials for -selected topics, that did not fit into any other place -in the manual. diff --git a/doc/src/lattice.txt b/doc/src/lattice.txt index 7a90df1f5d553697e7433d4b41cc4a2b241a4531..6f16dc54323ae72ec99eed888f2c1a953e124647 100644 --- a/doc/src/lattice.txt +++ b/doc/src/lattice.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/log.txt b/doc/src/log.txt index 92bb12e6dbccf42c9c8d1b80d587088e91bf88c7..76037685194b5ba9b324b02d35ffd0ed34ea26d3 100644 --- a/doc/src/log.txt +++ b/doc/src/log.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/mass.txt b/doc/src/mass.txt index 4b75132ccfb63a763cb6f238201e19216b736d0a..c6939630441165e80bd0bacb0007e56fedbec7af 100644 --- a/doc/src/mass.txt +++ b/doc/src/mass.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt index 73d142f5fabe4556a91064f674e62a37bed26773..9408eea167bbc49274a203b0fe4586f724e8659a 100644 --- a/doc/src/min_modify.txt +++ b/doc/src/min_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt index 245ac5864c1d41bdbce4a42568e5ee555a25bb3d..4948a34864a4424a031e86ab4ace7937c1fd09fe 100644 --- a/doc/src/min_style.txt +++ b/doc/src/min_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line min_style command :h3 diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index a3f2c5d0bf5aaa430740076b09ea39fad0b35baa..910fc7f821051bee5f28753442d479e85f7f27e7 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index ecec62256a82a3b2e67f9fe64a2af6f796f0c66e..88c6292d8b6d3bc63f075917f38df9f9482fcbae 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -98,19 +98,20 @@ molecule (header keyword = inertia). NOTE: The molecule command can be used to define molecules with bonds, angles, dihedrals, imporopers, or special bond lists of neighbors within a molecular topology, so that you can later add the molecules -to your simulation, via one or more of the commands listed above. If -such molecules do not already exist when LAMMPS creates the simulation -box, via the "create_box"_create_box.html or -"read_data"_read_data.html command, when you later add them you may -overflow the pre-allocated data structures which store molecular -topology information with each atom, and an error will be generated. -Both the "create_box"_create_box.html command and the data files read -by the "read_data"_read_data.html command have "extra" options which +to your simulation, via one or more of the commands listed above. +Since this topology-related information requires that suitable storage +is reserved when LAMMPS creates the simulation box (e.g. when using +the "create_box"_create_box.html command or the +"read_data"_read_data.html command) suitable space has to be reserved +so you do not overflow those pre-allocated data structures when adding +molecules later. Both the "create_box"_create_box.html command and +the "read_data"_read_data.html command have "extra" options which insure space is allocated for storing topology info for molecules that are added later. -The format of an individual molecule file is similar to the data file -read by the "read_data"_read_data.html commands, and is as follows. +The format of an individual molecule file is similar but +(not identical) to the data file read by the "read_data"_read_data.html +commands, and is as follows. A molecule file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains @@ -175,9 +176,8 @@ LAMMPS uses this info to properly exclude or weight bonded pairwise interactions between bonded atoms. See the "special_bonds"_special_bonds.html command for more details. One reason to list the special bond info explicitly is for the -"thermalized Drude oscillator model"_tutorial_drude.html which treats -the bonds between nuclear cores and Drude electrons in a different -manner. +"thermalized Drude oscillator model"_Howto_drude.html which treats the +bonds between nuclear cores and Drude electrons in a different manner. NOTE: Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to add a @@ -455,7 +455,11 @@ of SHAKE clusters. :line -[Restrictions:] none +[Restrictions:] + +This command must come after the simulation box is define by a +"read_data"_read_data.html, "read_restart"_read_restart.html, or +"create_box"_create_box.html command. [Related commands:] diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 56f075c301046d40a0e940045225d5c3019458e9..fbd77ee32903f1d99f4f63232538e0fd88cdde7d 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -56,9 +56,8 @@ Note that if you have MPI installed, you can run a multi-replica simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on just one or two processors. You will simply not get the performance speed-up you -would see with one or more physical processors per replica. See -"Section 6.5"_Section_howto.html#howto_5 of the manual for further -discussion. +would see with one or more physical processors per replica. See the +"Howto replica"_Howto_replica.html doc page for further discussion. NOTE: As explained below, a NEB calculation perfoms a damped dynamics minimization across all the replicas. The minimizer uses whatever diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index c4544cb29bde3ccf25b708e7d2ad552fc97e7eea..6c4218cff56589fca8b41d6c8c8ab2fa96ee2c5b 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/neighbor.txt b/doc/src/neighbor.txt index 062f79a5bbba0bc7e9042145dd03cebbf1ceebe3..7c7e7b05e5229b3d1144f251543d5b8ded341c60 100644 --- a/doc/src/neighbor.txt +++ b/doc/src/neighbor.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/newton.txt b/doc/src/newton.txt index a3e7f4fa91eec43b623a57f58be483f35ba982e1..fd7b5369203f25c957f62e34d9d68960fee87495 100644 --- a/doc/src/newton.txt +++ b/doc/src/newton.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/next.txt b/doc/src/next.txt index 08f73b896cb7ef13f74c5dd982f07d021fe44eea..5a0b30b2a7fe6ff0d824a066376404808702958f 100644 --- a/doc/src/next.txt +++ b/doc/src/next.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/package.txt b/doc/src/package.txt index 5c698934e857bfa31bdceac69bb3296ff76961c3..c2e7345bb74c4e25a5dc4861194c704d3017232d 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,8 +33,10 @@ args = arguments specific to the style :l last = ID of last GPU to be used on each node {tpa} value = Nthreads Nthreads = # of GPU threads used per atom - {device} value = device_type - device_type = {kepler} or {fermi} or {cypress} or {generic} + {device} value = device_type or platform_id:device_type or platform_id:custom,val1,val2,val3,..,val13 + platform_id = numerical OpenCL platform id (default: -1) + device_type = {kepler} or {fermi} or {cypress} or {intel} or {phi} or {generic} or {custom} + val1,val2,... = custom OpenCL tune parameters (see below for details) {blocksize} value = size size = thread block size for pair force computation {intel} args = NPhi keyword value ... @@ -96,6 +98,9 @@ args = arguments specific to the style :l package gpu 1 package gpu 1 split 0.75 package gpu 2 split -1.0 +package gpu 1 device kepler +package gpu 1 device 2:generic +package gpu 1 device custom,32,4,8,256,11,128,256,128,32,64,8,128,128 package kokkos neigh half comm device package omp 0 neigh no package omp 4 @@ -144,9 +149,9 @@ the style options are set, either to default values or to specified settings. I.e. settings from previous invocations do not persist across multiple invocations. -See the "Section 5.3"_Section_accelerate.html#acc_3 section of the -manual for more details about using the various accelerator packages -for speeding up LAMMPS simulations. +See the "Speed packages"_Speed_packages.html doc page for more details +about using the various accelerator packages for speeding up LAMMPS +simulations. :line @@ -244,12 +249,40 @@ the value can improve performance. The number of threads per atom must be a power of 2 and currently cannot be greater than 32. The {device} keyword can be used to tune parameters optimized for a -specific accelerator, when using OpenCL. For CUDA, the {device} -keyword is ignored. Currently, the device type is limited to NVIDIA -Kepler, NVIDIA Fermi, AMD Cypress, or a generic device. More devices -may be added later. The default device type can be specified when -building LAMMPS with the GPU library, via settings in the -lib/gpu/Makefile that is used. +specific accelerator and platform when using OpenCL. OpenCL supports +the concept of a [platform], which represents one or more devices that +share the same driver (e.g. there would be a different platform for +GPUs from different vendors or for CPU based accelerator support). +In LAMMPS only one platform can be active at a time and by default +the first platform with an accelerator is selected. This is equivalent +to using a platform ID of -1. The platform ID is a number corresponding +to the output of the ocl_get_devices tool. The platform ID is passed +to the GPU library, by prefixing the {device} keyword with that number +separated by a colon. For CUDA, the {device} keyword is ignored. +Currently, the device tuning support is limited to NVIDIA Kepler, NVIDIA +Fermi, AMD Cypress, Intel x86_64 CPU, Intel Xeon Phi, or a generic device. +More devices may be added later. The default device type can be +specified when building LAMMPS with the GPU library, via setting a +variable in the lib/gpu/Makefile that is used. + +In addition, a device type {custom} is available, which is followed by +13 comma separated numbers, which allows to set those tweakable parameters +from the package command. It can be combined with the (colon separated) +platform id. The individual settings are: + +MEM_THREADS +THREADS_PER_ATOM +THREADS_PER_CHARGE +BLOCK_PAIR +MAX_SHARED_TYPES +BLOCK_NBOR_BUILD +BLOCK_BIO_PAIR +BLOCK_ELLIPSE +WARP_SIZE +PPPM_BLOCK_1D +BLOCK_CELL_2D +BLOCK_CELL_ID +MAX_BIO_SHARED_TYPES :ul The {blocksize} keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) diff --git a/doc/src/pair_adp.txt b/doc/src/pair_adp.txt index 9d2a48dcbca399bc00f09458c56941cf3f622b5e..382a97eceaf93bf844915871d3210a4bca0e7666 100644 --- a/doc/src/pair_adp.txt +++ b/doc/src/pair_adp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -125,10 +125,9 @@ array tabulated with a scaling by r. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -140,8 +139,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 402e537dadf39bc5728d6001d32a0709d17e54c0..34f99001390ca24026f0ea3218316ab465d68ac0 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -58,11 +58,11 @@ and input files are provided in the examples/USER/misc/agni directory. :line Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, depending -on your available hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated style takes the same arguments and -should produce the same results, except for round-off and precision -issues. +style without the suffix. They have been optimized to run faster, +depending on your available hardware, as discussed on the "Speed +packages"_Speed_packages.html doc page. The accelerated style takes +the same arguments and should produce the same results, except for +round-off and precision issues. The accelerated style is part of the USER-OMP. They are only enabled if LAMMPS was built with those packages. See the "Making @@ -73,8 +73,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index 1aa017f2786ac95e60556d84b5a900fcab5a1704..94a692226d608687a094d48455070c1084eed3f4 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -176,10 +176,9 @@ thermo_style custom step temp epair v_REBO v_LJ v_TORSION :pre Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -191,8 +190,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt index fe0e3c952a759234f79234c60d825524b8984023..ec87101d0dc2fa89ed9089e13b37ca061ed3a9d9 100644 --- a/doc/src/pair_awpmd.txt +++ b/doc/src/pair_awpmd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_beck.txt b/doc/src/pair_beck.txt index e160f09b3d6fc5764c24bdd367d284e93db55622..ca4186e27b102d8199327d87a3ca0cd9da09f92f 100644 --- a/doc/src/pair_beck.txt +++ b/doc/src/pair_beck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -51,10 +51,9 @@ Rc is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -66,8 +65,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_body.txt b/doc/src/pair_body_nparticle.txt similarity index 87% rename from doc/src/pair_body.txt rename to doc/src/pair_body_nparticle.txt index 7899da832bdbf722bb1c5403dd547890bae5cdb1..9fb88102eb0aece7ace62e32360614fa3bdef106 100644 --- a/doc/src/pair_body.txt +++ b/doc/src/pair_body_nparticle.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -10,29 +10,28 @@ pair_style body command :h3 [Syntax:] -pair_style body cutoff :pre +pair_style body/nparticle cutoff :pre cutoff = global cutoff for interactions (distance units) [Examples:] -pair_style body 3.0 +pair_style body/nparticle 3.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.5 2.5 :pre [Description:] -Style {body} is for use with body particles and calculates pairwise -body/body interactions as well as interactions between body and -point-particles. See "Section 6.14"_Section_howto.html#howto_14 -of the manual and the "body"_body.html doc page for more details on -using body particles. +Style {body/nparticle} is for use with body particles and calculates +pairwise body/body interactions as well as interactions between body +and point-particles. See the "Howto body"_Howto_body.html doc page +for more details on using body particles. This pair style is designed for use with the "nparticle" body style, which is specified as an argument to the "atom-style body" command. -See the "body"_body.html doc page for more details about the body -styles LAMMPS supports. The "nparticle" style treats a body particle -as a rigid body composed of N sub-particles. +See the "Howto body"_Howto_body.html doc page for more details about +the body styles LAMMPS supports. The "nparticle" style treats a body +particle as a rigid body composed of N sub-particles. The coordinates of a body particle are its center-of-mass (COM). If the COMs of a pair of body particles are within the cutoff (global or diff --git a/doc/src/pair_body_rounded_polygon.txt b/doc/src/pair_body_rounded_polygon.txt index b6dc2e37b5a80fce04b7b753ffb7e007c4703ae6..e724874032afffe0d59f1f6fe2622a1669797b35 100644 --- a/doc/src/pair_body_rounded_polygon.txt +++ b/doc/src/pair_body_rounded_polygon.txt @@ -2,18 +2,132 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line pair_style body/rounded/polygon command :h3 +[Syntax:] + +pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + [Description:] -Note: This feature is not yet implemented. +Style {body/rounded/polygon} is for use with 2d models of body +particles of style {rounded/polygon}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex circular disks with a specified diameter. See the "Howto +body"_Howto_body.html doc page for more details on using body +rounded/polygon particles. + +This pairwise interaction between rounded polygons is described in +"Fraige"_#pair-Fraige, where a polygon does not have sharp corners, +but is rounded at its vertices by circles centered on each vertex with +a specified diameter. The edges of the polygon are defined between +pairs of adjacent vertices. The circle diameter for each polygon is +specified in the data file read by the "read data"_read_data.html +command. This is a 2d discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polygon particle is displaced outward from each of its vertices and +edges by half its circle diameter (as in the diagram below of a gray +and yellow square particle). The interaction forces and energies +between two particles are defined with respect to the separation of +their respective rounded surfaces, not by the separation of the +vertices and edges themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, and edge-edge overlaps +are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +Note that F_n and F_t are functions of the surface separation \delta_n += d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j) ++ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two +surfaces overlap and the two surfaces are attractive to each other. + +In "Fraige"_#pair-Fraige, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. [Related commands:] -"pair_style body"_pair_body.html +"pair_coeff"_pair_coeff.html [Default:] none + +:link(pair-Fraige) +[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, +Particuology, 6, 455 (2008). diff --git a/doc/src/pair_body_rounded_polyhedron.txt b/doc/src/pair_body_rounded_polyhedron.txt new file mode 100644 index 0000000000000000000000000000000000000000..0f8548d98eab86a6d5e3647f46119162764409cb --- /dev/null +++ b/doc/src/pair_body_rounded_polyhedron.txt @@ -0,0 +1,129 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style body/rounded/polyhedron command :h3 + +[Syntax:] + +pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre + +c_n = normal damping coefficient +c_t = tangential damping coefficient +mu = normal friction coefficient during gross sliding +delta_ua = multiple contact scaling factor +cutoff = global separation cutoff for interactions (distance units), see below for definition :pre + +[Examples:] + +pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5 +pair_coeff * * 100.0 1.0 +pair_coeff 1 1 100.0 1.0 :pre + +[Description:] + +Style {body/rounded/polygon} is for use with 3d models of body +particles of style {rounded/polyhedron}. It calculates pairwise +body/body interactions which can include body particles modeled as +1-vertex spheres with a specified diameter. See the "Howto +body"_Howto_body.html doc page for more details on using body +rounded/polyhedron particles. + +This pairwise interaction between the rounded polyhedra is described +in "Wang"_#pair-Wang, where a polyhedron does not have sharp corners +and edges, but is rounded at its vertices and edges by spheres +centered on each vertex with a specified diameter. The edges if the +polyhedron are defined between pairs of adjacent vertices. Its faces +are defined by a loop of edges. The sphere diameter for each polygon +is specified in the data file read by the "read data"_read_data.html +command. This is a discrete element model (DEM) which allows for +multiple contact points. + +Note that when two particles interact, the effective surface of each +polyhedron particle is displaced outward from each of its vertices, +edges, and faces by half its sphere diameter. The interaction forces +and energies between two particles are defined with respect to the +separation of their respective rounded surfaces, not by the separation +of the vertices, edges, and faces themselves. + +This means that the specified cutoff in the pair_style command is the +cutoff distance, r_c, for the surface separation, \delta_n (see figure +below). This is the distance at which two particles no longer +interact. If r_c is specified as 0.0, then it is a contact-only +interaction. I.e. the two particles must overlap in order to exert a +repulsive force on each other. If r_c > 0.0, then the force between +two particles will be attractive for surface separations from 0 to +r_c, and repulsive once the particles overlap. + +Note that unlike for other pair styles, the specified cutoff is not +the distance between the centers of two particles at which they stop +interacting. This center-to-center distance depends on the shape and +size of the two particles and their relative orientation. LAMMPS +takes that into account when computing the surface separation distance +and applying the r_c cutoff. + +The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge, +and edge-face overlaps are given by: + +:c,image(Eqs/pair_body_rounded.jpg) + +:c,image(JPG/pair_body_rounded.jpg) + +In "Wang"_#pair-Wang, the tangential friction force between two +particles that are in contact is modeled differently prior to gross +sliding (i.e. static friction) and during gross-sliding (kinetic +friction). The latter takes place when the tangential deformation +exceeds the Coulomb frictional limit. In the current implementation, +however, we do not take into account frictional history, i.e. we do +not keep track of how many time steps the two particles have been in +contact nor calculate the tangential deformation. Instead, we assume +that gross sliding takes place as soon as two particles are in +contact. + +The following coefficients must be defined for each pair of atom types +via the "pair_coeff"_pair_coeff.html command as in the examples above, +or in the data file read by the "read_data"_read_data.html command: + +k_n (energy/distance^2 units) +k_na (energy/distance^2 units) :ul + +Effectively, k_n and k_na are the slopes of the red lines in the plot +above for force versus surface separation, for \delta_n < 0 and 0 < +\delta_n < r_c respectively. + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This pair style does not support the "pair_modify"_pair_modify.html +mix, shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +[Restrictions:] + +These pair styles are part of the BODY package. They are only enabled +if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:link(pair-Wang) +[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular +Matter, 13, 1 (2011). + diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index 2a611e4bd038a50685897244936677ba09311cb9..654a7eb0b332dd5efdd4a9ca41410fbf6bd131df 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_born.txt b/doc/src/pair_born.txt index a016f77fa3ba6c96ef18fbb7d1094e79a0475aab..c408de6db6f23b579f2800d7865fdcd35649f9e6 100644 --- a/doc/src/pair_born.txt +++ b/doc/src/pair_born.txt @@ -3,7 +3,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -12,12 +12,14 @@ pair_style born/omp command :h3 pair_style born/gpu command :h3 pair_style born/coul/long command :h3 pair_style born/coul/long/cs command :h3 +pair_style born/coul/long/cs/gpu command :h3 pair_style born/coul/long/gpu command :h3 pair_style born/coul/long/omp command :h3 pair_style born/coul/msm command :h3 pair_style born/coul/msm/omp command :h3 pair_style born/coul/wolf command :h3 pair_style born/coul/wolf/cs command :h3 +pair_style born/coul/wolf/cs/gpu command :h3 pair_style born/coul/wolf/gpu command :h3 pair_style born/coul/wolf/omp command :h3 pair_style born/coul/dsf command :h3 @@ -106,10 +108,10 @@ The {born/coul/dsf} style computes the Coulomb contribution with the damped shifted force model as in the "coul/dsf"_pair_coul.html style. Style {born/coul/long/cs} is identical to {born/coul/long} except that -a term is added for the "core/shell model"_Section_howto.html#howto_25 -to allow charges on core and shell particles to be separated by r = -0.0. The same correction is introduced for the {born/coul/dsf/cs} -style which is identical to {born/coul/dsf}. And likewise for +a term is added for the "core/shell model"_Howto_coreshell.html to +allow charges on core and shell particles to be separated by r = 0.0. +The same correction is introduced for the {born/coul/dsf/cs} style +which is identical to {born/coul/dsf}. And likewise for {born/coul/wolf/cs} style which is identical to {born/coul/wolf}. Note that these potentials are related to the "Buckingham @@ -143,10 +145,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -158,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_brownian.txt b/doc/src/pair_brownian.txt index 79b71e91c73e3d6a99b129472cea4831e6905324..eaff85cbbca374db982add0557f03b57dedceaaf 100644 --- a/doc/src/pair_brownian.txt +++ b/doc/src/pair_brownian.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -74,7 +74,7 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -88,7 +88,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index d18b39d5d92b0bf7882f51a3a32149ed5d9e56d6..cc782c11cf3f551930264316b838c488de4ddb6e 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -93,9 +93,8 @@ used as the cutoff for the A,C terms, and the second is the cutoff for the Coulombic term. Style {buck/coul/long/cs} is identical to {buck/coul/long} except that -a term is added for the "core/shell model"_Section_howto.html#howto_25 -to allow charges on core and shell particles to be separated by r = -0.0. +a term is added for the "core/shell model"_Howto_coreshell.html to +allow charges on core and shell particles to be separated by r = 0.0. Note that these potentials are related to the "Born-Mayer-Huggins potential"_pair_born.html. @@ -140,10 +139,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -155,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 879972772ba1aceed1ebe3992725373955840ef1..485c35c6b2fffb04c14fa04469bd33a6400c65d5 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 05e760e1b22b44c5901f9160b9fa4f3eaaa44c5c..551204f1a7fe97ea559e98c7cfd1ddd92370d328 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,10 +102,9 @@ global Coulombic cutoff is allowed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 75a8e4bff944f8b6786f61bb50aa7eefe1e082c7..39c6f29b047fdbf02017352a1e787cc60c79cb78 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -184,10 +184,9 @@ the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -199,8 +198,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index 36fae5068b6e055adac9b7a2fb475e0df513968c..104c51474c25764c20a7b064dad9722e548e0809 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -102,10 +102,9 @@ cutoff distance. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -117,8 +116,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index fe9238f423d22af362c51940a639fbc32312fb7e..63f85f23d5e480a77ccc5f0c673cdde81d5a2d16 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -111,9 +111,8 @@ Windows: :line The alphabetic list of pair styles defined in LAMMPS is given on the -"pair_style"_pair_style.html doc page. They are also given in more -compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +"pair_style"_pair_style.html doc page. They are also listed in more +compact form on the "Commands pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the @@ -121,15 +120,15 @@ associated "pair_coeff"_pair_coeff.html command. Note that there are also additional pair styles (not listed on the "pair_style"_pair_style.html doc page) submitted by users which are -included in the LAMMPS distribution. The list of these with links to -the individual styles are given in the pair section of "this -page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution. The full list of all pair styles +is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed on the "pair_style"_pair_style.html doc page) included in the LAMMPS -distribution for faster performance on CPUs and GPUs. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +distribution for faster performance on CPUs, GPUs, and KNLs. The +individual style names on the "Commands pair"_Commands_pair.html doc +page are followed by one or more of (g,i,k,o,t) to indicate which +accerlerated styles exist. :line diff --git a/doc/src/pair_colloid.txt b/doc/src/pair_colloid.txt index 83b15b358bf532f6725853f8fc7e7b2329419ac5..08540cfee082c761259d3d8e3772015557c21210 100644 --- a/doc/src/pair_colloid.txt +++ b/doc/src/pair_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -127,10 +127,9 @@ commands for efficiency: "neighbor multi"_neighbor.html and Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -142,8 +141,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_comb.txt b/doc/src/pair_comb.txt index f5461b1cbc208ca0c5cd01583416f1821b0a6ec8..fc4cddbbae1fefa91ce37e930e2a589279f42566 100644 --- a/doc/src/pair_comb.txt +++ b/doc/src/pair_comb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -112,10 +112,9 @@ nor file {ffield.comb3} with style {comb}. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -127,8 +126,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index 4cca5ee0d78a529162e782121855150daa162e06..2fd9445785e26a44a3b1f7b070caa7531e61003d 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -20,6 +20,7 @@ pair_style coul/dsf/kk command :h3 pair_style coul/dsf/omp command :h3 pair_style coul/long command :h3 pair_style coul/long/cs command :h3 +pair_style coul/long/cs/gpu command :h3 pair_style coul/long/omp command :h3 pair_style coul/long/gpu command :h3 pair_style coul/long/kk command :h3 @@ -204,9 +205,9 @@ pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. Style {coul/long/cs} is identical to {coul/long} except that a term is -added for the "core/shell model"_Section_howto.html#howto_25 to allow -charges on core and shell particles to be separated by r = 0.0. The -same correction is introduced for the {coul/wolf/cs} style which is +added for the "core/shell model"_Howto_coreshell.html to allow charges +on core and shell particles to be separated by r = 0.0. The same +correction is introduced for the {coul/wolf/cs} style which is identical to {coul/wolf}. Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of @@ -225,16 +226,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighbor list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. +See the "Howto tip4p"_Howto_tip4p.html doc page for more information +on how to use the TIP4P pair styles and lists of parameters to set. +Note that the neighbor list cutoff for Coulomb interactions is +effectively extended by a distance 2*qdist when using the TIP4P pair +style, to account for the offset distance of the fictitious charges on +O atoms in water molecules. Thus it is typically best in an +efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +shrink the size of the neighbor list. This leads to slightly larger +cost for the long-range calculation, so you can test the trade-off for +your model. :line @@ -267,10 +268,9 @@ command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -282,8 +282,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_coul_diel.txt b/doc/src/pair_coul_diel.txt index f651cb4b5e4e927d6d9d230bcfe5e37d9260885f..14932c4835043aa7e93cf7b900672def64f10323 100644 --- a/doc/src/pair_coul_diel.txt +++ b/doc/src/pair_coul_diel.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_coul_shield.txt b/doc/src/pair_coul_shield.txt index 19f69688d5b6b1d3da1af094a81340cf8cab1b5d..029e6e5b3b3458ce3fdbab9daaecdad467061dce 100644 --- a/doc/src/pair_coul_shield.txt +++ b/doc/src/pair_coul_shield.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index c1084c608797863a3ecc7528cdb457298d8c3512..6540c4b8f0d4dd72b704854146d50b4f74815720 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -54,8 +54,8 @@ pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre These pair styles are designed to be used with the adiabatic core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2. See -"Section 6.25"_Section_howto.html#howto_25 of the manual for an -overview of the model as implemented in LAMMPS. +the "Howto coreshell"_Howto_coreshell.html doc page for an overview of +the model as implemented in LAMMPS. The styles with a {coul/long} term are identical to the "pair_style born/coul/long"_pair_born.html and "pair_style diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index 2516e5eae4d00113892dd8e97558b59ca13b97e3..1d8abc4521d2b26d2152d2157081a9d718bc3b47 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,10 +186,9 @@ type pair. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -201,8 +200,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 9e29e93430602fd485bef467602d7001c8534fab..1b636795d962254fed114fd7cad91b2b53fb8bac 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -110,10 +110,9 @@ random force. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -125,8 +124,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 867f3f2315dcb9d908438f91710016abe4ccf9d8..0d180ba068ffdec47eb78bc7fc7fcdb458aab766 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -129,10 +129,9 @@ significantly larger timesteps to be taken. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -144,8 +143,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_dsmc.txt b/doc/src/pair_dsmc.txt index 9e24100ab7cf4ce5d6676060370e75e3ef172aa1..2478a96d5ff183f52d21f817a1205eee6ce99855 100644 --- a/doc/src/pair_dsmc.txt +++ b/doc/src/pair_dsmc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_eam.txt b/doc/src/pair_eam.txt index 03e77f53ab0f291be3054b1464d1936b057e95e6..361dacb703d41a95c365abd2ce5101e915fe11d3 100644 --- a/doc/src/pair_eam.txt +++ b/doc/src/pair_eam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -371,10 +371,9 @@ are listed. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -386,7 +385,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for more +See the "Speed packages"_Speed_packages.html doc page for more instructions on how to use the accelerated styles effectively. :line @@ -414,15 +413,10 @@ The eam pair styles can only be used via the {pair} keyword of the [Restrictions:] -All of these styles except the {eam/cd} style are part of the MANYBODY -package. They are only enabled if LAMMPS was built with that package. +All of these styles are part of the MANYBODY package. They are only +enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. -The {eam/cd} style is part of the USER-MISC package and also requires -the MANYBODY package. It is only enabled if LAMMPS was built with -those packages. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. - [Related commands:] "pair_coeff"_pair_coeff.html diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index e5b1420b5938eed1008b780fc226e1258d0c3fa5..cce564856e6c2c420771e4c070b23605e0cdafe8 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -109,10 +109,9 @@ the EDIP package. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -124,8 +123,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index ee7dc9993296b92e353961284670052624ce11b6..a55860297e609eb106b63cda6655babf3f696966 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_eim.txt b/doc/src/pair_eim.txt index 75ad2d4683ee64716ebc003ca5267d5733302760..6490a859c16b361e217faaa3eb04e52386b87143 100644 --- a/doc/src/pair_eim.txt +++ b/doc/src/pair_eim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -136,10 +136,9 @@ needs. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -151,8 +150,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 7eafa235434386bcfe3438367cee1cec1852e74b..08ab1cf3c9b64a40fe70b251500fcecfcd2994f6 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -153,10 +153,9 @@ pair interaction. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -168,8 +167,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt index 9a784e2501638ecda41031366b0777346115c94f..3acad1132d108f61a70bd4c336b63ee14a919601 100644 --- a/doc/src/pair_extep.txt +++ b/doc/src/pair_extep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index f6f46a2de8ace2a7f982d305728b77f42f350ded..9662a4f29c743fefb3bddc480b6f70f75045ff88 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -84,10 +84,9 @@ is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -99,8 +98,8 @@ by including their suffix, or you can use the "-suffix command-line switch7_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gayberne.txt b/doc/src/pair_gayberne.txt index c9235785866f6856ad438fb934afdcc64d4ba781..af41f6879e80ed299050eb6822553e819e22607f 100644 --- a/doc/src/pair_gayberne.txt +++ b/doc/src/pair_gayberne.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,10 +133,9 @@ pair_coeff sigma to 1.0 as well. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index d7e87af013f002a6e6472a4ae45e3f5c27fd3de5..55b00a172f56c4063a20298509cc54856d9b276a 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,10 +179,9 @@ potential. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gromacs.txt b/doc/src/pair_gromacs.txt index ec84a2d57a13d7066fb49624cba932a425447656..9f34ac8c43da024cd0123454dfdc2666116379f3 100644 --- a/doc/src/pair_gromacs.txt +++ b/doc/src/pair_gromacs.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -91,10 +91,9 @@ cutoff(s) specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -106,8 +105,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt index 8f1251cf1f3a96aa50e8f9339a69f20b893336bb..809ff008bc86dbaa33e6f899c354957e09a65fef 100644 --- a/doc/src/pair_gw.txt +++ b/doc/src/pair_gw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d3cf90ec14c2172faf4eec91a5247724acc3428a..60b0b021743374cc08cfdd5cdc58a8605f02c9b0 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -33,8 +33,8 @@ pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 :pre [Description:] The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD) -3-body hydrogen bond interaction for the -"DREIDING"_Section_howto.html#howto_4 force field, given by: +3-body hydrogen bond interaction for the "DREIDING"_Howto_bioFF.html +force field, given by: :c,image(Eqs/pair_hbond_dreiding.jpg) @@ -65,8 +65,8 @@ potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed that the Morse form gives improved results for Dendrimer simulations, when n = 2. -See this "howto section"_Section_howto.html#howto_4 of the manual for -more information on the DREIDING forcefield. +See the "Howto bioFF"_Howto_bioFF.html doc page for more information +on the DREIDING forcefield. NOTE: Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise @@ -166,10 +166,9 @@ optional parameters. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -181,8 +180,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index d37dedc709b82c43e6c49701f3b7916db93ef6d8..9b36109c279e7381ba5a73aea7adad55dee2f3c7 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -315,8 +315,8 @@ off C/C interaction, i.e. by setting the appropriate coefficients to Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. Since the {hybrid} and {hybrid/overlay} styles delegate computation to the individual sub-styles, the suffix versions of the {hybrid} and @@ -334,8 +334,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index 32fe002a306d508de4f3ad7b048df32218e7d856..9c9304c4a73ba02e35d575331f135ad32187a81e 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -23,15 +23,15 @@ pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 pair_coeff * * rebo CH.airebo NULL NULL C pair_coeff * * tersoff BNC.tersoff B N NULL -pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre +pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.69498201415576216335 -pair_coeff 2 2 coul/shield 0.69 +pair_coeff 2 2 coul/shield 0.69 :pre [Description:] The {ilp/graphene/hbn} style computes the registry-dependent interlayer -potential (RDILP) potential as described in "(Leven)"_#Leven and +potential (ILP) potential as described in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2. The normals are calculated in the way as described in "(Kolmogorov)"_#Kolmogorov2. @@ -61,13 +61,13 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are fitted with taper function by setting the cutoff equal to 16.0 Angstrom. Using different cutoff or taper function should be careful. -NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented, -BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and -"(Maaravi)"_#Maaravi2, which is only suitable for long-range -interaction. The parameters in BNCH.ILP provides a good description both -for short- and long-range interaction. This is useful for simulations in -the high pressure (small interlayer distances) regime. The comparison of -two sets of parameters can be found in "(Ouyang)"_#Ouyang. +NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials +are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description +in both short- and long-range interaction regime, while the old ILP parameters +published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for +long-range interaction regime. This feature is essential for simulations in +high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance). +The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1. This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -101,12 +101,12 @@ units, if your simulation does not use {metal} units. [Related commands:] -"pair_coeff"_pair_coeff.html -"pair_none"_pair_none.html -"pair_style hybrid/overlay"_pair_hybrid.html -"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html -"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html -"pair_style pair_coul_shield"_pair_coul_shield.html +"pair_coeff"_pair_coeff.html, +"pair_none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html, +"pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html, +"pair_style pair_coul_shield"_pair_coul_shield.html. [Default:] tap_flag = 1 @@ -121,5 +121,5 @@ units, if your simulation does not use {metal} units. :link(Kolmogorov2) [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) -:link(Ouyang) -[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation. +:link(Ouyang1) +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index c5d910e27c841f9d71e5e6dfd160bfce0a949b46..889c1e892fe69202a92ca98b02650b982c68c849 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -46,8 +46,8 @@ are included in the KIM library by default, in the "What is in the KIM API source package?" section. To use this pair style, you must first download and install the KIM -API library from the "OpenKIM website"_https://openkim.org. The "KIM -section of Section packages"_Section_packages.html#KIM has +API library from the "OpenKIM website"_https://openkim.org. The KIM +section of the "Packages details"_Packages_details.html doc page has instructions on how to do this with a simple make command, when building LAMMPS. diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index 7df1b4d02d364eeadfdb1eefc2d32ae2aac45c9c..8fc6bbff4996ecaefa81e0257048a14c702a7e5d 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -27,7 +27,7 @@ pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre [Description:] -The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi +The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi (KC) interaction potential as described in "(Kolmogorov)"_#Kolmogorov1. No simplification is made, @@ -51,6 +51,15 @@ and {rcut} are included in the parameter file. {S} is designed to facilitate scaling of energies. {rcut} is designed to build the neighbor list for calculating the normals for each atom pair. +NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC) +is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides +a good description in both short- and long-range interaction regime, +while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 +are only suitable for long-range interaction regime. +This feature is essential for simulations in high-pressure regime +(i.e., the interlayer distance smaller than the equilibrium distance). +The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2. + This potential must be used in combination with hybrid/overlay. Other interactions can be set to zero using pair_style {none}. @@ -83,11 +92,11 @@ units. [Related commands:] -"pair_coeff"_pair_coeff.html -"pair_none"_pair_none.html -"pair_style hybrid/overlay"_pair_hybrid.html -"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html -"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html +"pair_coeff"_pair_coeff.html, +"pair_none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. [Default:] tap_flag = 0 @@ -95,3 +104,6 @@ units. :link(Kolmogorov1) [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) + +:link(Ouyang2) +[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh, O. Hod, arXiv:1806.09555 (2018). diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 97f132eacd41e00cd4318cfde24b09e29b4a6ae1..7dad2e3701b852d41a2856e785d80be041f2f5c6 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lcbop.txt b/doc/src/pair_lcbop.txt index 148a1d47a067c014d193b14eb3647bbe9c2cd3be..ddf8551d560ff042b8c3d64331db263e5c3d5289 100644 --- a/doc/src/pair_lcbop.txt +++ b/doc/src/pair_lcbop.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_line_lj.txt b/doc/src/pair_line_lj.txt index 44cfeb48e96ca4043c8e811d2950ae1243dc126a..c2c6beb97f5490ce4cc11ab6cb3c0634375afc0f 100644 --- a/doc/src/pair_line_lj.txt +++ b/doc/src/pair_line_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_list.txt b/doc/src/pair_list.txt index 653e8b0c2d1635c4d10a43889af4b5bd5e99767d..023cc0be4f1c52404fe1f875bdfd86cf03b68e7d 100644 --- a/doc/src/pair_list.txt +++ b/doc/src/pair_list.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index e297d479bc3ae16d3054130ba67d9bb7fe3a0a97..a55cb348d7568f14dd25c715adf8a7fe382f3a23 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -185,9 +185,9 @@ distance are computed directly; interactions outside that distance are computed in reciprocal space. Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except -that a term is added for the "core/shell -model"_Section_howto.html#howto_25 to allow charges on core and shell -particles to be separated by r = 0.0. +that a term is added for the "core/shell model"_Howto_coreshell.html +to allow charges on core and shell particles to be separated by r = +0.0. Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf summation method, described in "Wolf"_#Wolf1, given by: @@ -223,16 +223,16 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more -information on how to use the TIP4P pair styles and lists of -parameters to set. Note that the neighbor list cutoff for Coulomb -interactions is effectively extended by a distance 2*qdist when using -the TIP4P pair style, to account for the offset distance of the -fictitious charges on O atoms in water molecules. Thus it is -typically best in an efficiency sense to use a LJ cutoff >= Coulomb -cutoff + 2*qdist, to shrink the size of the neighbor list. This leads -to slightly larger cost for the long-range calculation, so you can -test the trade-off for your model. +See the "Howto tip4p"_Howto_tip4p.html doc page for more information +on how to use the TIP4P pair styles and lists of parameters to set. +Note that the neighbor list cutoff for Coulomb interactions is +effectively extended by a distance 2*qdist when using the TIP4P pair +style, to account for the offset distance of the fictitious charges on +O atoms in water molecules. Thus it is typically best in an +efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +shrink the size of the neighbor list. This leads to slightly larger +cost for the long-range calculation, so you can test the trade-off for +your model. For all of the {lj/cut} pair styles, the following coefficients must be defined for each pair of atoms types via the @@ -269,10 +269,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -284,8 +283,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj96.txt b/doc/src/pair_lj96.txt index 83f6ec063d4dd6476555a068a7eac6374544a3be..7c68e26acef1c9cf8d21b47fc70ba1109296e502 100644 --- a/doc/src/pair_lj96.txt +++ b/doc/src/pair_lj96.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,10 +49,9 @@ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_cubic.txt b/doc/src/pair_lj_cubic.txt index 4ca8c3c141c39c9c874902f96f5178a1b1941d7a..d04a3d8b9d1b6e021ea2df92d2ee16a74ba5e45d 100644 --- a/doc/src/pair_lj_cubic.txt +++ b/doc/src/pair_lj_cubic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -63,10 +63,9 @@ located at rmin = 2^(1/6)*sigma. In the above example, sigma = Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -78,8 +77,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_expand.txt b/doc/src/pair_lj_expand.txt index e0838426f637da3e3669fc4c35a17afaa6d6083b..3e9996da4d5507158a37cca38cf1db68597dcfdb 100644 --- a/doc/src/pair_lj_expand.txt +++ b/doc/src/pair_lj_expand.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -53,10 +53,9 @@ optional. If not specified, the global LJ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -68,8 +67,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 6be4562d18849130536383878ac5acc084b20f20..1ba3610f8621801864930acf73a20b4d16bd5a04 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -90,7 +90,7 @@ is to enable LAMMPS to "find" the 2 H atoms associated with each O atom. For example, if the atom ID of an O atom in a TIP4P water molecule is 500, then its 2 H atoms must have IDs 501 and 502. -See the "howto section"_Section_howto.html#howto_8 for more +See the the "Howto tip4p"_Howto_tip4p.html doc page for more information on how to use the TIP4P pair style. Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for @@ -156,10 +156,9 @@ specified in the pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -171,8 +170,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index b1678cad5862cf4670a80a68e7c2074337250ba9..575c023579b4cf5b91927dd241c65d3ee9365c83 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -62,10 +62,9 @@ specified, the global values for Rin and Rc are used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -77,8 +76,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 5f7c226cee3ccc7b83c6139bf2a6c25dd2c13468..0fab768b8fbd9eecc9c80d0760262f9d9ea6111b 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,10 +49,9 @@ LJ cutoff specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_lj_soft.txt index 2ef133da554adf3d141e337e3c1b9f4139f72f35..d10fcd0472d24ebd91510e0c4793597292e31127 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_lj_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -207,10 +207,9 @@ directory tree, under examples/USER/fep. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -222,8 +221,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lubricate.txt b/doc/src/pair_lubricate.txt index b39c7545c7e2bdbc90f72631eaadeca06cfe40c5..e9a0a0d2910e5a6036f4993c23e59b0849b88d78 100644 --- a/doc/src/pair_lubricate.txt +++ b/doc/src/pair_lubricate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -143,7 +143,7 @@ must be specified. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "this section"_Section_accelerate.html of +hardware, as discussed in "this section"_Speed.html of the manual. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues. @@ -157,7 +157,7 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "this section"_Section_accelerate.html of the manual for more +See "this section"_Speed.html of the manual for more instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_lubricateU.txt b/doc/src/pair_lubricateU.txt index 720a8539b890c917ab41aa1f0db151c0520a8280..6b74c208bf2c211ec71b9efff608c2345626505e 100644 --- a/doc/src/pair_lubricateU.txt +++ b/doc/src/pair_lubricateU.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mdf.txt b/doc/src/pair_mdf.txt index ca06f1bf8eb12ad7b4050aaa79359f09a100e6fc..e5a8cac845effe56f019729b2660ad001226923d 100644 --- a/doc/src/pair_mdf.txt +++ b/doc/src/pair_mdf.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index c7449428bd05aa010182dc17cb2f9206b69e5303..45f88f0bbec33570565284ab50945076acb85906 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 6653b397a0cd04e7dfb56aa1f4c8df9159a9e4a9..96155120419297e54de85192f772f8fcb05216d5 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -106,10 +106,9 @@ MEAM files. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -121,8 +120,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index fa731799ddd450445ee07d19f4b45c7cc44cc866..ba0953a17c3957825fac150f3b373c92a5df44b9 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt index bcdf717d68cb6d06e84422abffe278f6c382eb94..ad3880e642411c30179bb8a1e9d3b8451cc9c227 100644 --- a/doc/src/pair_meso.txt +++ b/doc/src/pair_meso.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mgpt.txt b/doc/src/pair_mgpt.txt index f8b0c9f0713c99856cbce64bb199ee55068bebbf..09fe61168698455d05fef6b67ed6a80b1b43a962 100644 --- a/doc/src/pair_mgpt.txt +++ b/doc/src/pair_mgpt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_mie.txt b/doc/src/pair_mie.txt index ad602db9f1e02cb1792acb2d1711ad0e189eacdc..818e37272bdd28f962195de66868aee119637d79 100644 --- a/doc/src/pair_mie.txt +++ b/doc/src/pair_mie.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index 34dbb5bc3de7acc4f89588d730dc76b407c07d8e..c043fde5a77f7bb68ed0b74dc52d516589ee88f8 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_momb.txt b/doc/src/pair_momb.txt index 77c4f184d9380f11848bb7e0deedc719802d130d..545b650f75176e7a32d83ce85312e29720731f0c 100644 --- a/doc/src/pair_momb.txt +++ b/doc/src/pair_momb.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 3eb5ac5afe5b8cb089d5dea24ed02cdea1ec0eec..85a42986ec87ed45e30fe3fc3120587b4d345492 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -101,10 +101,9 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -116,8 +115,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_multi_lucy.txt b/doc/src/pair_multi_lucy.txt index 38fd1ede4aa2201cb8e2cb2733877272f4b91e5c..31d52a58c89386b5cca80afcd4b585c4e314fc15 100644 --- a/doc/src/pair_multi_lucy.txt +++ b/doc/src/pair_multi_lucy.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index 57abcf4a4c30c904b55cd07464ca60118ca13d3c..e09dde3f8051128f22a0817f847b3238061f9ad6 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -204,10 +204,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -219,8 +218,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 2395707fb45b63425456a1ca612895b90bc289c8..720b9ea2a1f903f42b54525f4481e63f071aa389 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -92,10 +92,9 @@ a particular simulation; LAMMPS ignores those entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -107,8 +106,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_nm.txt b/doc/src/pair_nm.txt index 81cea1a38d4a255b6fdd01d080cecc67602c3a89..355bfd5573e951c2f28effcc2e4e0aee5c351917 100644 --- a/doc/src/pair_nm.txt +++ b/doc/src/pair_nm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -133,10 +133,9 @@ the "run_style respa"_run_style.html command. They do not support the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -148,8 +147,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Restrictions:] diff --git a/doc/src/pair_none.txt b/doc/src/pair_none.txt index f4e9525198413d49fe26c94ce2795ea12d826d9f..960dc05d97be7d7dda8889bb129d348c9578f374 100644 --- a/doc/src/pair_none.txt +++ b/doc/src/pair_none.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index f272d15a8680d6499df5f7164186789426589413..5ec99152978f42f5f603a1c87329ad005093583f 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 1b55031b2c97dc8c935c0ddb83a567f24d64ab6f..a1d2cfdb7c862f96affbd60ec4d216baef0795bc 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index deca093e3bb1cebb7183f9bb7b8b0df866c09df8..14abd4541e4b3f33d1dac80119d894f8b758608e 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,10 +139,9 @@ details please see the description in "(Mtchell2011a)". Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -154,8 +153,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index c088e8bb2242918fe221ab1241cba70129d6c5f7..eb0c30f249cff1b58a11e21dcb2ff5df14a599fb 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt index 2f8ed7a27c6702b9e80a82d0a14201f714430bd7..1433557e0388e581c94b2668ecc2721fdeea1928 100644 --- a/doc/src/pair_python.txt +++ b/doc/src/pair_python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index 9436b0c4ed1f71b78d18880d411e64855e727aca..3570a52801852be5207d72ef27a45438518ef6bb 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt index 1d13f937061c95963165efc936a680ca14415147..a3b84955cd058937fd28cb84732656e2f3f055ef 100644 --- a/doc/src/pair_reax.txt +++ b/doc/src/pair_reax.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index 39759b3111825077e3ee0e4dffe54b2eeecd4915..ec575486404904c6b92dd165e4d6ae490e8a7303 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -50,11 +50,11 @@ as a package. The {reax/c/kk} style is a Kokkos version of the ReaxFF potential that is derived from the {reax/c} style. The Kokkos version can run on GPUs and can also use OpenMP multithreading. For more information about the -Kokkos package, see "Section 4"_Section_packages.html#kokkos and -"Section 5.3.3"_accelerate_kokkos.html. One important consideration -when using the {reax/c/kk} style is the choice of either half or full -neighbor lists. This setting can be changed using the Kokkos -"package"_package.html command. +Kokkos package, see "Packages details"_Packages_details.html and +"Speed kokkos"_Speed_kokkos.html doc pages. One important +consideration when using the {reax/c/kk} style is the choice of either +half or full neighbor lists. This setting can be changed using the +Kokkos "package"_package.html command. The {reax/c} style differs from the "pair_style reax"_pair_reax.html command in the lo-level implementation details. The {reax} style is a @@ -303,10 +303,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -318,8 +317,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_resquared.txt b/doc/src/pair_resquared.txt index 9ad95eb5fc4e9ddc0bb3f9eda4a1751b0afba726..6e72408ebc1a7243f3d01aadaa79dd02afd66553 100644 --- a/doc/src/pair_resquared.txt +++ b/doc/src/pair_resquared.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -145,10 +145,9 @@ specified in the pair_style command is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -160,8 +159,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 360136a4eaef3df735b65cfc0f8e7ce5ca78dc16..ccf704b6f7f85b163fdcdd375b8821146ee37c37 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -85,10 +85,9 @@ pair_style command. Styles with a {gpu}, {intel}, {kk}, {omp} or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP, and OPT packages respectively. They are only enabled if @@ -100,8 +99,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_smd_hertz.txt b/doc/src/pair_smd_hertz.txt index eeaa3387a44a834cfe4361a75e40d2610d29bdb6..f2d633903ab99a90ac5485e1f871c994b872f69a 100644 --- a/doc/src/pair_smd_hertz.txt +++ b/doc/src/pair_smd_hertz.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt index f73acf74ee5b1a842d2b8cd1a7ed7c632885dd75..3aeaa3155382ee4b0b0b34c0bc8beaa381c68bac 100644 --- a/doc/src/pair_smd_tlsph.txt +++ b/doc/src/pair_smd_tlsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_triangulated_surface.txt b/doc/src/pair_smd_triangulated_surface.txt index c32bf3a22ea89c35efd3231b0ffbfdd72590a810..65526cfba8cc15a6be2d8dd22510106b5d6a40cf 100644 --- a/doc/src/pair_smd_triangulated_surface.txt +++ b/doc/src/pair_smd_triangulated_surface.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index 268fe78d02294eca17134ff7fcffb276512db2be..a5bda54d5f0c46d792fc23bdbdba13f6168bbeee 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index c8d6b21b3f1f024421dc56426aa32da817d887f7..c70202c2e13f536307ad84c1f50133490e8bff72 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index 27dcf6082b892b5a5df64442f2045215c8d5dbd8..f9bd8910e49ddfe37a044cf9e801f937a1b0cd7e 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -175,10 +175,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -190,8 +189,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_soft.txt b/doc/src/pair_soft.txt index 08fa88c477961677b4aafd786e13ad1b89befed9..374711825b5d4bbf656d15fab9a3753c6f2239ce 100644 --- a/doc/src/pair_soft.txt +++ b/doc/src/pair_soft.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -82,10 +82,9 @@ variables. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -97,8 +96,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_sph_heatconduction.txt b/doc/src/pair_sph_heatconduction.txt index 2387056a1b7b4b06235c3d8d88ad5edec4bccbdf..d19c28a3cb5a0fec2f893d69fc23715abed8ae64 100644 --- a/doc/src/pair_sph_heatconduction.txt +++ b/doc/src/pair_sph_heatconduction.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_idealgas.txt b/doc/src/pair_sph_idealgas.txt index 957f901425993d91b248c9a7172a45b0753abd44..a670949a892025d8d30ca9a5d63134020483ddc3 100644 --- a/doc/src/pair_sph_idealgas.txt +++ b/doc/src/pair_sph_idealgas.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_lj.txt b/doc/src/pair_sph_lj.txt index ef89c4ad3eaf351d07dad07e953b6dc4ea3eb139..152e6cf8a292cd5b03f895ff84282b9ac6652d63 100644 --- a/doc/src/pair_sph_lj.txt +++ b/doc/src/pair_sph_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_rhosum.txt b/doc/src/pair_sph_rhosum.txt index 352e717f76484a2b3c2c993560646fd110869b60..3cd1c5abb2577e0d7c155d7d5cedd9ae1b768307 100644 --- a/doc/src/pair_sph_rhosum.txt +++ b/doc/src/pair_sph_rhosum.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_taitwater.txt b/doc/src/pair_sph_taitwater.txt index 9177ca80b868e417e3bf8a23d30f267fd882f3ff..7b9a8188f28b36d30e7a71d64d8b49024ffadd1e 100644 --- a/doc/src/pair_sph_taitwater.txt +++ b/doc/src/pair_sph_taitwater.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_sph_taitwater_morris.txt b/doc/src/pair_sph_taitwater_morris.txt index e6c5a6bb20dc302fa3105af4c3c224d9e2411b98..02f16d8982f5af327d25e4ce43fbeb9fa877015b 100644 --- a/doc/src/pair_sph_taitwater_morris.txt +++ b/doc/src/pair_sph_taitwater_morris.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt new file mode 100644 index 0000000000000000000000000000000000000000..375e59fe89486ebec90679a9a4c08b20f9655bb4 --- /dev/null +++ b/doc/src/pair_spin_dmi.txt @@ -0,0 +1,91 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/dmi command :h3 + +[Syntax:] + +pair_style spin/dmi cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/dmi 4.0 +pair_coeff * * dmi 2.6 0.001 1.0 0.0 0.0 +pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction +between pairs of magnetic spins. +According to the expression reported in "(Rohart)"_#Rohart, one has +the following DM energy: + +:c,image(Eqs/pair_spin_dmi_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j, +and D is the DM vector defining the intensity (in eV) and the direction +of the interaction. + +In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented +from the high spin-orbit layer to the magnetic ultrathin film. + +The application of a spin-lattice Poisson bracket to this energy (as described +in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a +mechanical force F (for spin-lattice calculations only) for each magnetic +particle i: + +:c,image(Eqs/pair_spin_dmi_forces.jpg) + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida5. + +For the {spin/dmi} pair style, the following coefficients must be defined for +each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +|D| (energy units) +Dx, Dy, Dz (direction of D) :ul + +Note that rc is the radius cutoff of the considered DM interaction, |D| is +the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. + +None of those coefficients is optional. If not specified, the {spin/dmi} +pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Rohart) +[(Rohart)] Rohart and Thiaville, +Physical Review B, 88(18), 184422. (2013). +:link(Tranchida5) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt new file mode 100644 index 0000000000000000000000000000000000000000..24eb635b819cd1982c5bc4a37d3e48950e13c28c --- /dev/null +++ b/doc/src/pair_spin_exchange.txt @@ -0,0 +1,98 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/exchange command :h3 + +[Syntax:] + +pair_style spin/exchange cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.0446928 0.003496 1.4885 +pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre + +[Description:] + +Style {spin/exchange} computes the exchange interaction between +pairs of magnetic spins: + +:c,image(Eqs/pair_spin_exchange_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +and J(rij) is a function defining the intensity and the sign of the exchange +interaction for different neighboring shells. This function is defined as: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command (see below for more explanations). + +The coefficients a, b, and d need to be fitted so that the function above matches with +the value of the exchange interaction for the N neighbor shells taken into account. +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida3. + +From this exchange interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_exchange_forces.jpg) + +with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit +vector between sites i and j. + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida3. + +For the {spin/exchange} pair style, the following coefficients must be defined +for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: + +rc (distance units) +a (energy units) +b (adim parameter) +d (distance units) :ul + +Note that rc is the radius cutoff of the considered exchange interaction, +and a, b and d are the three coefficients performing the parametrization +of the function J(rij) defined above. + +None of those coefficients is optional. If not specified, the +{spin/exchange} pair style cannot be used. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida3) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt new file mode 100644 index 0000000000000000000000000000000000000000..b338fae5dcdc3597e16dda8df691a012025114c1 --- /dev/null +++ b/doc/src/pair_spin_magelec.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/me command :h3 + +[Syntax:] + +pair_style spin/me cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/me 4.5 +pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre + +[Description:] + +Style {spin/me} computes a magneto-electric interaction between +pairs of magnetic spins. According to the derivation reported in +"(Katsura)"_#Katsura1, this interaction is defined as: + +:c,image(Eqs/pair_spin_me_interaction.jpg) + +where si and sj are neighboring magnetic spins of two particles, +eij = (ri - rj)/|ri-rj| is the normalized separation vector between the +two particles, and E is an electric polarization vector. +The norm and direction of E are giving the intensity and the +direction of a screened dielectric atomic polarization (in eV). + +From this magneto-electric interaction, each spin i will be submitted +to a magnetic torque omega, and its associated atom can be submitted to a +force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), +such as: + +:c,image(Eqs/pair_spin_me_forces.jpg) + +with h the Planck constant (in metal units). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida4. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_spin_exchange"_pair_spin_exchange.html, "pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Katsura1) +[(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) + +:link(Tranchida4) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt new file mode 100644 index 0000000000000000000000000000000000000000..0967632ed2037ccac12228f089b56c31c8272ad1 --- /dev/null +++ b/doc/src/pair_spin_neel.txt @@ -0,0 +1,81 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style spin/neel command :h3 + +[Syntax:] + +pair_style spin/neel cutoff :pre + +cutoff = global cutoff pair (distance in metal units) :ulb,l + +:ule + +[Examples:] + +pair_style spin/neel 4.0 +pair_coeff * * neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 +pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre + +[Description:] + +Style {spin/neel} computes the Neel pair anisotropy model +between pairs of magnetic spins: + +:c,image(Eqs/pair_spin_neel_interaction.jpg) + +where si and sj are two neighboring magnetic spins of two particles, +rij = ri - rj is the inter-atomic distance between the two particles, +eij = (ri - rj)/|ri-rj| is their normalized separation vector +and g1, q1 and q2 are three functions defining the intensity of the +dipolar and quadrupolar contributions, with: + +:c,image(Eqs/pair_spin_neel_functions.jpg) + +With the functions g(rij) and q(rij) defined and fitted according to the same +Bethe-Slater function used to fit the exchange interaction: + +:c,image(Eqs/pair_spin_exchange_function.jpg) + +where a, b and d are the three constant coefficients defined in the associated +"pair_coeff" command. + +The coefficients a, b, and d need to be fitted so that the function above matches with +the values of the magneto-elastic constant of the materials at stake. + +Examples and more explanations about this function and its parametrization are reported +in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in +future work. + +From this DM interaction, each spin i will be submitted to a magnetic torque +omega and its associated atom to a force F (for spin-lattice calculations only). + +More details about the derivation of these torques/forces are reported in +"(Tranchida)"_#Tranchida6. + +:line + +[Restrictions:] + +All the {pair/spin} styles are part of the SPIN package. +These styles are only enabled if LAMMPS was built with this package, and +if the atom_style "spin" was declared. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"pair_eam"_pair_eam.html, + +[Default:] none + +:line + +:link(Tranchida6) +[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, +Journal of Computational Physics, (2018). diff --git a/doc/src/pair_srp.txt b/doc/src/pair_srp.txt index e7f1e00d1028635db3c8cce28097cf62d54fa7d3..e784ac3d17d5f8fc0415003a6a084560d3a6a3c3 100644 --- a/doc/src/pair_srp.txt +++ b/doc/src/pair_srp.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 475761add76d11df7035cab25631028270e5ba63..cd395133293545306ceb7824e6158b47b5a211fb 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -78,22 +78,22 @@ previously specified pair_coeff values. :line Here is an alphabetic list of pair styles defined in LAMMPS. They are -also given in more compact form in the pair section of "this -page"_Section_commands.html#cmd_5. +also listed in more compact form on the "Commands +pair"_Commands_pair.html doc page. Click on the style to display the formula it computes, arguments specified in the pair_style command, and coefficients specified by the associated "pair_coeff"_pair_coeff.html command. There are also additional pair styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The list of -these with links to the individual styles are given in the pair -section of "this page"_Section_commands.html#cmd_5. +users which are included in the LAMMPS distribution. The full list of +all pair styles is on the "Commands pair"_Commands_pair.html doc page. There are also additional accelerated pair styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs and -GPUs. The list of these with links to the individual styles are given -in the pair section of "this page"_Section_commands.html#cmd_5. +included in the LAMMPS distribution for faster performance on CPUs, +GPUs, and KNLs. The individual style names on the "Commands +pair"_Commands_pair.html doc page are followed by one or more of +(g,i,k,o,t) to indicate which accerlerated styles exist. "pair_style none"_pair_none.html - turn off pairwise interactions "pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions @@ -104,7 +104,7 @@ in the pair section of "this page"_Section_commands.html#cmd_5. "pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart "pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ "pair_style beck"_pair_beck.html - Beck potential -"pair_style body"_pair_body.html - interactions between body particles +"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles "pair_style bop"_pair_bop.html - BOP potential of Pettifor "pair_style born"_pair_born.html - Born-Mayer-Huggins potential "pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index 4932fe55d335bb101db35e478f0681ffe416a69d..e6741791dfe8d103ded1dbcfc27a9bcaf70e9527 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -144,10 +144,9 @@ taken from the ij and ik pairs (sigma, a, gamma) Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -164,8 +163,8 @@ additional 5 to 10 percent performance improvement when the Stillinger-Weber parameters p and q are set to 4 and 0 respectively. These parameters are common for modeling silicon and water. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_table.txt b/doc/src/pair_table.txt index b99491b477224e621da4429d10c0b20b84c66c0d..5e3c1f5ff6f2e1bf58c27589afc653c71c569d18 100644 --- a/doc/src/pair_table.txt +++ b/doc/src/pair_table.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -217,10 +217,9 @@ one that matches the specified keyword. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -232,8 +231,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index cd3a7ef31b87d15268cfe93050889b4699a4adc7..41be067bacfcc6eb60286b7f259926c2729e832b 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -227,10 +227,9 @@ This pair style can only be used via the {pair} keyword of the Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -242,8 +241,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index 918e88992440045bda099cb2ad9849ab4faeff14..821c38f3e4174310f43c6ee504ede9b194ebdab8 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -179,10 +179,9 @@ defined in various papers. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -194,8 +193,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_mod.txt b/doc/src/pair_tersoff_mod.txt index e0c2b5a5cbb07b7c525d58d48eab97cb763971ca..ac1f79a80b772f602f951ed34e373eb3b8bb0f0b 100644 --- a/doc/src/pair_tersoff_mod.txt +++ b/doc/src/pair_tersoff_mod.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -131,10 +131,9 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -146,8 +145,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index 21d57e4e8841570f44f114961af653ad9dde93b4..a89d4e3ea1fbce4376fa787123d1a98bf25dbbb2 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -189,10 +189,9 @@ providing the base ZBL implementation. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -204,8 +203,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_thole.txt b/doc/src/pair_thole.txt index 41a4059cee8d4de828d136343a282310f493403d..7ce8b7cf4bed33dc699d8c08197b01392d1d6ac3 100644 --- a/doc/src/pair_thole.txt +++ b/doc/src/pair_thole.txt @@ -9,7 +9,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -45,8 +45,8 @@ pair_style lj/cut/thole/long 2.6 12.0 :pre The {thole} pair styles are meant to be used with force fields that include explicit polarization through Drude dipoles. This link describes how to use the "thermalized Drude oscillator -model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS -are discussed in "this Section"_Section_howto.html#howto_25. +model"_Howto_drude.html in LAMMPS and polarizable models in LAMMPS are +discussed on the "Howto polarizable"_Howto_polarizable.html doc page. The {thole} pair style should be used as a sub-style within in the "pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a @@ -130,10 +130,9 @@ the {pair_style} command line. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -145,8 +144,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. [Mixing]: diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index 42a5bbdfe2285c61c67ad980eecca779666f553b..3915ffc2383c79220f2b403f7e2d43dc0041ab1e 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 88a22864ccaf960472dbe5ea3f985ea2d375ab23..dbc6fd0664b99572fd39dcab68c60003ceef722f 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,10 +69,9 @@ NOTE: The thermodynamic integration procedure can be performed with this potenti Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -84,8 +83,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index d9c66d45c0cae201fa12b3799bdf562dc9f55a91..2e404e8befcba50b462a0efbb61b48f0ba8cc82e 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -171,10 +171,9 @@ two-body parameters from the CCC and CSiSi entries. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -186,8 +185,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_write.txt b/doc/src/pair_write.txt index 9f5970fcbc6c8c406746d752ac281e2eec3ebc9e..48ad76e76eabf624459cb37139e77ef4a09385f0 100644 --- a/doc/src/pair_write.txt +++ b/doc/src/pair_write.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pair_yukawa.txt b/doc/src/pair_yukawa.txt index e7c063ded9f41227210e17970dc9fb7cc59ed757..5a8363260a5e31f507d279500ea9eb2c78199758 100644 --- a/doc/src/pair_yukawa.txt +++ b/doc/src/pair_yukawa.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -49,10 +49,9 @@ cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -64,8 +63,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index 2037a9451f9e77079971382afde16709657c88e7..515062d9eb679cefc969f91e41c376b265541bd4 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -80,10 +80,9 @@ yukawa/colloid cutoff is used. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -95,8 +94,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_zbl.txt b/doc/src/pair_zbl.txt index 1984cd831f6bf2fef81c9f2ef39c16b04284e309..1472c7b6726d970179eeacd97915edabdfcdd55c 100644 --- a/doc/src/pair_zbl.txt +++ b/doc/src/pair_zbl.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -71,10 +71,9 @@ copper. Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if @@ -86,8 +85,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index e58b33c75f4d0261d43a6eafee975c470e79c627..b324003bd1ca252e6ecaa8a341219dfb11d521cd 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 202aaa9c0f8354ebadf7a2f24156e3fb19b02fd2..4c3eef2cd11c32ea4801ebb830a6a985cc5a734b 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -10,8 +10,9 @@ Pair Styles :h1 pair_airebo pair_awpmd pair_beck - pair_body + pair_body_nparticle pair_body_rounded_polygon + pair_body_rounded_polyhedron pair_bop pair_born pair_brownian @@ -97,6 +98,10 @@ Pair Styles :h1 pair_sph_rhosum pair_sph_taitwater pair_sph_taitwater_morris + pair_spin_dmi + pair_spin_exchange + pair_spin_magelec + pair_spin_neel pair_srp pair_sw pair_table diff --git a/doc/src/partition.txt b/doc/src/partition.txt index 610eee99b300bd96486991c1841cfde1a2b1d8e5..d4fe06c098fd2de94520c38b96346407a0cbf3b9 100644 --- a/doc/src/partition.txt +++ b/doc/src/partition.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/prd.txt b/doc/src/prd.txt index 3c0305e316d4e5c8a321e27ad4662a5dc1807d40..b2145ebad1a43ac0037f484f030a945479dd0ecb 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -69,8 +69,8 @@ simulation with more replicas (partitions) than you have physical processors, e.g you can run a 10-replica simulation on one or two processors. However for PRD, this makes little sense, since running a replica on virtual instead of physical processors,offers no effective -parallel speed-up in searching for infrequent events. See "Section -6.5"_Section_howto.html#howto_5 of the manual for further discussion. +parallel speed-up in searching for infrequent events. See the "Howto +replica"_Howto_replica.html doc page for further discussion. When a PRD simulation is performed, it is assumed that each replica is running the same model, though LAMMPS does not check for this. diff --git a/doc/src/print.txt b/doc/src/print.txt index 77e0c7cfd3d64ed7a6bfeb6dcd17b716f0b1e1f3..476d4104fab9bfcf41aa9ef7b7216523e6faf0d4 100644 --- a/doc/src/print.txt +++ b/doc/src/print.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/processors.txt b/doc/src/processors.txt index e54b2cede3b94e8bb13324c22f3352601b8b79d8..df13ae1f617fd9507bdbf7192b52d668c3ca44df 100644 --- a/doc/src/processors.txt +++ b/doc/src/processors.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/python.txt b/doc/src/python.txt index 1ac2b48528c073a1b40ea4fd210dfb5dfb91a1ae..4f4faca8f43c5fc6ca5db28f748238798405b862 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -99,10 +99,9 @@ They can be substituted for directly in an input script. Or they can be passed to various commands as arguments, so that the variable is evaluated during a simulation run. -A broader overview of how Python can be used with LAMMPS is -given in "Section 11"_Section_python.html. There is an -examples/python directory which illustrates use of the python -command. +A broader overview of how Python can be used with LAMMPS is given on +the "Python"_Python.html doc page. There is an examples/python +directory which illustrates use of the python command. :line @@ -200,9 +199,9 @@ The {here} keyword does the same thing, except that the Python code follows as a single argument to the {here} keyword. This can be done using triple quotes as delimiters, as in the examples above. This allows Python code to be listed verbatim in your input script, with -proper indentation, blank lines, and comments, as desired. See -"Section 3.2"_Section_commands.html#cmd_2, for an explanation of how -triple quotes can be used as part of input script syntax. +proper indentation, blank lines, and comments, as desired. See the +"Commands parse"_Commands_parse.html doc page, for an explanation of +how triple quotes can be used as part of input script syntax. The {exists} keyword takes no argument. It means that Python code containing the required Python function defined by the {func} setting, @@ -331,9 +330,9 @@ to the screen and log file. Note that since the LAMMPS print command itself takes a string in quotes as its argument, the Python string must be delimited with a different style of quotes. -"Section 11.7"_Section_python.html#py_7 describes the syntax for how -Python wraps the various functions included in the LAMMPS library -interface. +The "Pytnon library"_Python_library.html doc page describes the syntax +for how Python wraps the various functions included in the LAMMPS +library interface. A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py: @@ -484,15 +483,16 @@ building LAMMPS. LAMMPS must also be built as a shared library and your Python function must be able to to load the Python module in python/lammps.py that wraps the LAMMPS library interface. These are the same steps required to use Python by itself to wrap LAMMPS. -Details on these steps are explained in "Section -python"_Section_python.html. Note that it is important that the -stand-alone LAMMPS executable and the LAMMPS shared library be -consistent (built from the same source code files) in order for this -to work. If the two have been built at different times using -different source files, problems may occur. +Details on these steps are explained on the "Python"_Python.html doc +page. Note that it is important that the stand-alone LAMMPS +executable and the LAMMPS shared library be consistent (built from the +same source code files) in order for this to work. If the two have +been built at different times using different source files, problems +may occur. [Related commands:] -"shell"_shell.html, "variable"_variable.html, "fix python/invoke"_fix_python_invoke.html +"shell"_shell.html, "variable"_variable.html, "fix +python/invoke"_fix_python_invoke.html [Default:] none diff --git a/doc/src/quit.txt b/doc/src/quit.txt index 843d3de7f3545dfd330f7e7624fe21a3c3c6e430..802df97711e5c4b38e816f12f18043440cb669f3 100644 --- a/doc/src/quit.txt +++ b/doc/src/quit.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index fd297e36c121e1efb8f631c95c182a51587a60c0..ded51a4d99855abfd9abc4361c1f0f2b052729dd 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -322,9 +322,9 @@ with tilt factors that exceed these limits, you can use the "box tilt"_box.html command, with a setting of {large}; a setting of {small} is the default. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto triclinic"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. When a triclinic system is used, the simulation domain should normally @@ -772,9 +772,9 @@ the "bodies" keyword. Each body can have a variable number of integer and/or floating-point values. The number and meaning of the values is defined by the body -style, as described in the "body"_body.html doc page. The body style -is given as an argument to the "atom_style body"_atom_style.html -command. +style, as described in the "Howto body"_Howto_body.html doc page. The +body style is given as an argument to the "atom_style +body"_atom_style.html command. The Ninteger and Ndouble values determine how many integer and floating-point values are specified for this particle. Ninteger and diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index 23f6274582ee9d1ef579ce96ce9692a892866f29..a3c0733e07369da85b63f222069ce12b224a3f13 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -282,11 +282,11 @@ conditions are applied to remap an atom back into the simulation box. NOTE: If you get a warning about inconsistent image flags after reading in a dump snapshot, it means one or more pairs of bonded atoms -now have inconsistent image flags. As discussed in "Section -errors"_Section_errors.html this may or may not cause problems for -subsequent simulations, One way this can happen is if you read image -flag fields from the dump file but do not also use the dump file box -parameters. +now have inconsistent image flags. As discussed on the "Errors +common"_Errors_common.html doc page this may or may not cause problems +for subsequent simulations. One way this can happen is if you read +image flag fields from the dump file but do not also use the dump file +box parameters. LAMMPS knows how to compute unscaled and remapped coordinates for the snapshot column labels discussed above, e.g. {x}, {xs}, {xu}, {xsu}. diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt index a5a2bfcc9743d7402eeb57bfa3dcda678f357829..488c36f02081d5be3c3a9a9067ed2638e4738c63 100644 --- a/doc/src/read_restart.txt +++ b/doc/src/read_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -76,8 +76,7 @@ different than if the run had continued. These pair styles include If a restarted run is immediately different than the run which produced the restart file, it could be a LAMMPS bug, so consider -"reporting it"_Section_errors.html#err_2 if you think the behavior is -wrong. +"reporting it"_Errors_bugs.html if you think the behavior is a bug. Because restart files are binary, they may not be portable to other machines. In this case, you can use the "-restart command-line diff --git a/doc/src/region.txt b/doc/src/region.txt index 5039e4a51615164a410bd85ff6572ac41d3a8bf6..21396ae1fd2b6652fc6928d24f685cfc39bc7031 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -186,9 +186,9 @@ functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent radius. -See "Section 6.12"_Section_howto.html#howto_12 of the doc pages -for a geometric description of triclinic boxes, as defined by LAMMPS, -and how to transform these parameters to and from other commonly used +See the "Howto tricilinc"_Howto_triclinic.html doc page for a +geometric description of triclinic boxes, as defined by LAMMPS, and +how to transform these parameters to and from other commonly used triclinic representations. The {union} style creates a region consisting of the volume of all the @@ -358,12 +358,12 @@ sub-regions can be defined with the {open} keyword. :line -Styles with a {kk} suffix are functionally the same as the -corresponding style without the suffix. They have been optimized to -run faster, depending on your available hardware, as discussed in -"Section 5"_Section_accelerate.html of the manual. The -accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are +functionally the same as the corresponding style without the suffix. +They have been optimized to run faster, depending on your available +hardware, as discussed on the "Speed packages"_Speed_packages.html doc +page. The accelerated styles take the same arguments and should +produce the same results, except for round-off and precision issues. The code using the region (such as a fix or compute) must also be supported by Kokkos or no acceleration will occur. Currently, only {block} style @@ -378,8 +378,8 @@ by including their suffix, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line diff --git a/doc/src/replicate.txt b/doc/src/replicate.txt index 08523ecdd848a58ff04b8b63747fcd6c5c388914..0195dce9114f4a3d0bf30a805a1c0f0e31a70be7 100644 --- a/doc/src/replicate.txt +++ b/doc/src/replicate.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index edf94cc711c2e5a1ff7b34efed059b7e77327981..8eb3ebd5a19458aec21e3c799ef80cacf936e998 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/reset_ids.txt b/doc/src/reset_ids.txt index 8655a9d54f3c5b0f7e97512f6553dd6246bfa321..391b51fde99e167d813bef98b3a62f96786ed1de 100644 --- a/doc/src/reset_ids.txt +++ b/doc/src/reset_ids.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/reset_timestep.txt b/doc/src/reset_timestep.txt index 79a5812ca1f2a569c23d71e48a6dc8ffcc89d002..0d518655fb774108eb95da66297d854300d945b5 100644 --- a/doc/src/reset_timestep.txt +++ b/doc/src/reset_timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/restart.txt b/doc/src/restart.txt index 7c39ae1404eebb9c70d1c7a99730d00200a25af2..6f2dc5ca467c354a9c576d467af4c5d49c1e9301 100644 --- a/doc/src/restart.txt +++ b/doc/src/restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/run.txt b/doc/src/run.txt index 311560d66b57585c0dfb9e0fae8c64d8f39ea236..c7c73463d92d49bb8e72ca9b549e38d50960f67a 100644 --- a/doc/src/run.txt +++ b/doc/src/run.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -126,11 +126,10 @@ and interleaving commands in your input script. For example, a be redefined, e.g. to reset a thermostat temperature. Or this could be useful for invoking a command you have added to LAMMPS that wraps some other code (e.g. as a library) to perform a computation -periodically during a long LAMMPS run. See "this -section"_Section_modify.html of the documentation for info about how -to add new commands to LAMMPS. See "this -section"_Section_howto.html#howto_10 of the documentation for ideas -about how to couple LAMMPS to other codes. +periodically during a long LAMMPS run. See the "Modify"_Modify.html +doc page for info about how to add new commands to LAMMPS. See the +"Howto couple"_Howto_couple.html doc page for ideas about how to +couple LAMMPS to other codes. With the {every} option, N total steps are simulated, in shorter runs of M steps each. After each M-length run, the specified commands are diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index ba836a07dd1510b48e48ad5c8f2714bd5c6252b9..deee51cfd3d6fc0857ea99b5b169d323cbc323c7 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -119,13 +119,13 @@ switches"_Section_start.html#start_6 to change this. The log and screen file for the 2nd partition will not contain thermodynamic output beyond the 1st timestep of the run. -See "Section 5"_Section_accelerate.html of the manual for -performance details of the speed-up offered by the {verlet/split} -style. One important performance consideration is the assignment of -logical processors in the 2 partitions to the physical cores of a -parallel machine. The "processors"_processors.html command has -options to support this, and strategies are discussed in -"Section 5"_Section_accelerate.html of the manual. +See the "Speed packages"_Speed_packages.html doc page for performance +details of the speed-up offered by the {verlet/split} style. One +important performance consideration is the assignment of logical +processors in the 2 partitions to the physical cores of a parallel +machine. The "processors"_processors.html command has options to +support this, and strategies are discussed in "Section +5"_Speed.html of the manual. :line @@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the iterations of level 2 per iteration of level 3, etc. N-1 looping parameters must be specified. -The "timestep"_timestep.html command sets the timestep for the -outermost rRESPA level. Thus if the example command above for a -4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep -would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that -specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html -parameters, "dump"_dump.html every N timesteps, etc) refer to the -outermost timesteps. +Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, +you could choose to have bond interactions computed 8x per large +timestep, angle interactions computed 4x, pair interactions computed +2x, and long-range interactions once per large timestep. + +The "timestep"_timestep.html command sets the large timestep for the +outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for +4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the +inner timestep would be 8x smaller or 0.5 fmsec. All other LAMMPS +commands that specify number of timesteps (e.g. "thermo"_thermo.html +for thermo output every N steps, "neigh_modify +delay/every"_neigh_modify.html parameters, "dump"_dump.html every N +steps, etc) refer to the outermost timesteps. The rRESPA keywords enable you to specify at what level of the hierarchy various forces will be computed. If not specified, the @@ -167,11 +173,17 @@ have their force go ramped to 0.0 so the overlap with the next regime compute forces for all pairs from 5.0 outward, with those from 5.0 to 6.0 having their value ramped in an inverse manner. -Only some pair potentials support the use of the {inner} and {middle} -and {outer} keywords. If not, only the {pair} keyword can be used -with that pair style, meaning all pairwise forces are computed at the -same rRESPA level. See the doc pages for individual pair styles for -details.i +Note that you can use {inner} and {outer} without using {middle} to +split the pairwise computations into two portions instead of three. +Unless you are using a very long pairwise cutoff, a 2-way split is +often faster than a 3-way split, since it avoids too much duplicate +computation of pairwise interactions near the intermediate cutoffs. + +Also note that only a few pair potentials support the use of the +{inner} and {middle} and {outer} keywords. If not, only the {pair} +keyword can be used with that pair style, meaning all pairwise forces +are computed at the same rRESPA level. See the doc pages for +individual pair styles for details. Another option for using pair potentials with rRESPA is with the {hybrid} keyword, which requires the use of the "pair_style hybrid or @@ -238,42 +250,54 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a For non-biomolecular simulations, the {respa} style can be advantageous if there is a clear separation of time scales - fast and -slow modes in the simulation. Even a LJ system can benefit from -rRESPA if the interactions are divided by the inner, middle and outer -keywords. A 2-fold or more speedup can be obtained while maintaining -good energy conservation. In real units, for a pure LJ fluid at -liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1 -Kcal/mol, the following settings seem to work well: +slow modes in the simulation. For example, a system of slowly-moving +charged polymer chains could be setup as follows: + +timestep 4.0 +run_style respa 2 8 :pre + +This is two-level rRESPA with an 8x difference between the short and +long timesteps. The bonds, angles, dihedrals will be computed every +0.5 fs (assuming real units), while the pair and kspace interactions +will be computed once every 4 fs. These are the default settings for +each kind of interaction, so no additional keywords are necessary. + +Even a LJ system can benefit from rRESPA if the interactions are +divided by the inner, middle and outer keywords. A 2-fold or more +speedup can be obtained while maintaining good energy conservation. +In real units, for a pure LJ fluid at liquid density, with a sigma of +3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings +seem to work well: timestep 36.0 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre :line -The {respa/omp} styles is a variant of {respa} adapted for use with +The {respa/omp} style is a variant of {respa} adapted for use with pair, bond, angle, dihedral, improper, or kspace styles with an {omp} -suffix. It is functionally equivalent to {respa} but performs additional -operations required for managing {omp} styles. For more on {omp} styles -see the "Section 5"_Section_accelerate.html of the manual. -Accelerated styles take the same arguments and should produce the same -results, except for round-off and precision issues. +suffix. It is functionally equivalent to {respa} but performs +additional operations required for managing {omp} styles. For more on +{omp} styles see the "Speed omp"_Speed_omp.html doc page. Accelerated +styles take the same arguments and should produce the same results, +except for round-off and precision issues. You can specify {respa/omp} explicitly in your input script, or you can use the "-suffix command-line switch"_Section_start.html#start_6 when you invoke LAMMPS, or you can use the "suffix"_suffix.html command in your input script. -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. +See the "Speed packages"_Speed_packages.html doc page for more +instructions on how to use the accelerated styles effectively. :line [Restrictions:] The {verlet/split} style can only be used if LAMMPS was built with the -REPLICA package. Correspondingly the {respa/omp} style is available only -if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info on packages. +REPLICA package. Correspondingly the {respa/omp} style is available +only if the USER-OMP package was included. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info on packages. Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are @@ -287,6 +311,17 @@ conserving energy to adequate precision. run_style verlet :pre +For run_style respa, the default assignment of interactions +to rRESPA levels is as follows: + +bond forces = level 1 (innermost loop) +angle forces = same level as bond forces +dihedral forces = same level as angle forces +improper forces = same level as dihedral forces +pair forces = leven N (outermost level) +kspace forces = same level as pair forces +inner, middle, outer forces = no default :ul + :line :link(Tuckerman3) diff --git a/doc/src/set.txt b/doc/src/set.txt index 4757d1c5758f9ed027a9932c07452ddcc2567f95..b83ad54f4e5fbef3b26a01372e0f3d959db90c9a 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -17,6 +17,7 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {charge} or {dipole} or {dipole/random} or {quat} or \ + {spin} or {spin/random} or {quat} or \ {quat/random} or {diameter} or {shape} or \ {length} or {tri} or {theta} or {theta/random} or \ {angmom} or {omega} or \ @@ -35,6 +36,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {x},{y},{z} value = atom coordinate (distance units) value can be an atom-style variable (see below) + {vx},{vy},{vz} value = atom velocity (velocity units) + value can be an atom-style variable (see below) {charge} value = atomic charge (charge units) value can be an atom-style variable (see below) {dipole} values = x y z @@ -43,6 +46,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ {dipole/random} value = seed Dlen seed = random # seed (positive integer) for dipole moment orientations Dlen = magnitude of dipole moment (dipole units) + {spin} values = g x y z + g = magnitude of magnetic spin vector (in Bohr magneton's unit) + x,y,z = orientation of magnetic spin vector + any of x,y,z can be an atom-style variable (see below) + {spin/random} value = seed Dlen + seed = random # seed (positive integer) for magnetic spin orientations + Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit) {quat} values = a b c theta a,b,c = unit vector to rotate particle around via right-hand rule theta = rotation angle (degrees) @@ -119,6 +129,7 @@ set type 3 charge 0.5 set type 1*3 charge 0.5 set atom * charge v_atomfile set atom 100*200 x 0.5 y 1.0 +set atom 100 vx 0.0 vy 0.0 vz -1.0 set atom 1492 type 3 :pre [Description:] @@ -217,7 +228,8 @@ IDs. Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of all selected atoms. For {charge}, the "atom style"_atom_style.html -being used must support the use of atomic charge. +being used must support the use of atomic charge. Keywords {vx}, {vy}, +and {vz} set the velocities of all selected atoms. Keyword {dipole} uses the specified x,y,z values as components of a vector to set as the orientation of the dipole moment vectors of the @@ -232,6 +244,15 @@ the orientation of a particular atom is the same, regardless of how many processors are being used. This keyword does not allow use of an atom-style variable. +Keyword {spin} uses the specified g value to set the magnitude of the +magnetic spin vectors, and the x,y,z values as components of a vector +to set as the orientation of the magnetic spin vectors of the selected +atoms. + +Keyword {spin/random} randomizes the orientation of the magnetic spin +vectors for the selected atoms and sets the magnitude of each to the +specified {Dlen} value. + Keyword {quat} uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The particles must define a quaternion for their orientation diff --git a/doc/src/shell.txt b/doc/src/shell.txt index 205164f874173abd4de45b045e91ec741092acb9..d274f498e595c5abcfca59c182bd36c827016c90 100644 --- a/doc/src/shell.txt +++ b/doc/src/shell.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 1021c4856b02cc7cb91901d429eb8c1fc2ca22c4..a57b61664d56e76b28d3aad9f2059bdbb24a9c31 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 74f69b6dfe96296259f536c80e621b23b89edef1..bb0619f1e04af5ab1bafc7772c2e40f09e1f3767 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/tad.txt b/doc/src/tad.txt index f5e7c6d6537cc50d6e3905249b847cca20cc7eed..a26ff79318ceed4f91cd402bb095a08c546baea5 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -92,9 +92,8 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See "Section -6.5"_Section_howto.html#howto_5 of the manual for further discussion of -multi-replica simulations. +partitions remain idle. See the "Howto replica"_Howto_replica.html doc +page for further discussion of multi-replica simulations. A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows: diff --git a/doc/src/temper.txt b/doc/src/temper.txt index b1c47c8076e1affde9b4c4ecc45c89148ddbd412..c7b482acc6467948a15321a363e138f5fb1962ae 100644 --- a/doc/src/temper.txt +++ b/doc/src/temper.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -32,14 +32,13 @@ replicas (ensembles) of a system. Two or more replicas must be used. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line -switch; see "Section 2.6"_Section_start.html#start_6 of the -manual. Note that if you have MPI installed, you can run a -multi-replica simulation with more replicas (partitions) than you have -physical processors, e.g you can run a 10-replica simulation on one or -two processors. You will simply not get the performance speed-up you -would see with one or more physical processors per replica. See "this -section"_Section_howto.html#howto_5 of the manual for further -discussion. +switch; see "Section 2.6"_Section_start.html#start_6 of the manual. +Note that if you have MPI installed, you can run a multi-replica +simulation with more replicas (partitions) than you have physical +processors, e.g you can run a 10-replica simulation on one or two +processors. You will simply not get the performance speed-up you +would see with one or more physical processors per replica. See the +"Howto replica"_Howto_replica.html doc page for further discussion. Each replica's temperature is controlled at a different value by a fix with {fix-ID} that controls temperature. Most thermostat fix styles diff --git a/doc/src/temper_grem.txt b/doc/src/temper_grem.txt index 6145c8704cc131b96d21464031c9697733be02d1..9cb1bab78465c890c0f6377d9c5fb45d0803b145 100644 --- a/doc/src/temper_grem.txt +++ b/doc/src/temper_grem.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index 4ad49f9e3327ded89da41c2fd405929175990a67..4eee225de73cfd0e3ea3b4354a293d902fa8250c 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line temper/npt command :h3 diff --git a/doc/src/thermo.txt b/doc/src/thermo.txt index 1d5d34995cd3cc979f3537b529950032be2ea4ba..5f12f987076bc54f50df9cbd5f37aa9c2be40b7e 100644 --- a/doc/src/thermo.txt +++ b/doc/src/thermo.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_modify.txt b/doc/src/thermo_modify.txt index e9aca0f20a1b2ed5c2d90ec3a70714c2dea25bf4..ca2957de776a5d3054da85a0eddfbcaad25bedf9 100644 --- a/doc/src/thermo_modify.txt +++ b/doc/src/thermo_modify.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/thermo_style.txt b/doc/src/thermo_style.txt index 6102169ee363ca2bdb9dc41d1663f9c1dcb442aa..cbc2612f28c69a49bcd4dcb28b3b1c7a132fd85c 100644 --- a/doc/src/thermo_style.txt +++ b/doc/src/thermo_style.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -108,12 +108,11 @@ Style {custom} is the most general setting and allows you to specify which of the keywords listed above you want printed on each thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are references to "computes"_compute.html, "fixes"_fix.html, and -equal-style "variables"_variable.html that have been defined -elsewhere in the input script or can even be new styles which users -have added to LAMMPS (see the "Section 10"_Section_modify.html -section of the documentation). Thus the {custom} style provides a -flexible means of outputting essentially any desired quantity as a -simulation proceeds. +equal-style "variables"_variable.html that have been defined elsewhere +in the input script or can even be new styles which users have added +to LAMMPS. See the "Modify"_Modify.html doc page for details on the +latter. Thus the {custom} style provides a flexible means of +outputting essentially any desired quantity as a simulation proceeds. All styles except {custom} have {vol} appended to their list of outputs if the simulation box volume changes during the simulation. @@ -287,11 +286,11 @@ takes place. The keywords {cella}, {cellb}, {cellc}, {cellalpha}, {cellbeta}, {cellgamma}, correspond to the usual crystallographic quantities that -define the periodic unit cell of a crystal. See "this -section"_Section_howto.html#howto_12 of the doc pages for a geometric -description of triclinic periodic cells, including a precise definition -of these quantities in terms of the internal LAMMPS cell dimensions -{lx}, {ly}, {lz}, {yz}, {xz}, {xy}. +define the periodic unit cell of a crystal. See the "Howto +triclinic"_Howto_triclinic.html doc page for a geometric description +of triclinic periodic cells, including a precise definition of these +quantities in terms of the internal LAMMPS cell dimensions {lx}, {ly}, +{lz}, {yz}, {xz}, {xy}. :line diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 768c3e1353fb3e6495f63f2d84830c060b4bf74a..10737dbda0cebfea9b99582c28327168aa55faa6 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/timestep.txt b/doc/src/timestep.txt index 639ad6f31136ff9a34f085b8d254b983a9e1ba4d..ee0ace05b9cf7397539cf615e4a87217270f4949 100644 --- a/doc/src/timestep.txt +++ b/doc/src/timestep.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt deleted file mode 100644 index 338439ac8e9387c080e8bfd32bf237e85984ec0e..0000000000000000000000000000000000000000 --- a/doc/src/tutorials.txt +++ /dev/null @@ -1,15 +0,0 @@ -Tutorials :h1 - - diff --git a/doc/src/uncompute.txt b/doc/src/uncompute.txt index 49b46781d7ac363156674ef935881dacab2e048f..4c788d472207b302a51f73abddaf34803cae5062 100644 --- a/doc/src/uncompute.txt +++ b/doc/src/uncompute.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/undump.txt b/doc/src/undump.txt index a2a371aca5187a9248e8e33e33792087040a66e7..cc3d8b9103ffd2d9eff33bf3dbaefda820c29903 100644 --- a/doc/src/undump.txt +++ b/doc/src/undump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/unfix.txt b/doc/src/unfix.txt index dcc4499b20b4b784779f9038b30c541a5585335e..9608b39c7e2c2056023b9da6607b8e280ed52a11 100644 --- a/doc/src/unfix.txt +++ b/doc/src/unfix.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/units.txt b/doc/src/units.txt index 0b856dcc68b67a9f7df9f159e779f8fb5a097379..8df8fe6810ec1163f366a7e53ad4f019418425da 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/variable.txt b/doc/src/variable.txt index c0851464c3f14e11629b8e65ee58a171499a4e45..c6598ccb514d2855259038e99d1560488f7cdff9 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -124,8 +124,8 @@ provide, so that the variable gets its value from the evaluation of the Python code. Variables of style {internal} are used by a few commands which set their value directly. -NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the -manual, an input script can use "immediate" variables, specified as +NOTE: As discussed on the "Commands parse"_Commands_parse.html doc +page, an input script can use "immediate" variables, specified as $(formula) with parenthesis, where the formula has the same syntax as equal-style variables described on this page. This is a convenient way to evaluate a formula immediately without using the variable @@ -198,7 +198,7 @@ the same thing. :line -"This section"_Section_commands.html#cmd_2 of the manual explains how +The "Commands parse"_Commands_parse.html doc page explains how occurrences of a variable name in an input script line are replaced by the variable's string. The variable name can be referenced as $x if the name "x" is a single character, or as $\{LoopVar\} if the name @@ -296,17 +296,24 @@ list of runs (e.g. 1000) without having to list N strings in the input script. For the {string} style, a single string is assigned to the variable. -The only difference between this and using the {index} style with a -single string is that a variable with {string} style can be redefined. -E.g. by another command later in the input script, or if the script is -read again in a loop. +Two differences between this this and using the {index} style exist: +a variable with {string} style can be redefined, e.g. by another command later +in the input script, or if the script is read again in a loop. The other +difference is that {string} performs variable substitution even if the +string parameter is quoted. For the {format} style, an equal-style variable is specified along with a C-style format string, e.g. "%f" or "%.10g", which must be appropriate for formatting a double-precision floating-point value. -This allows an equal-style variable to be formatted specifically for -output as a string, e.g. by the "print"_print.html command, if the -default format "%.15g" has too much precision. +The default format is "%.15g". This variable style allows an +equal-style variable to be formatted precisely when it is evaluated. + +If you simply wish to print a variable value with desired precision to +the screen or logfile via the "print"_print.html or "fix +print"_fix_print.html commands, you can also do this by specifying an +"immediate" variable with a trailing colon and format string, as part +of the string argument of those commands. This is explained on the +"Commands parse"_Commands_parse.html doc page. For the {getenv} style, a single string is assigned to the variable which should be the name of an environment variable. When the @@ -1112,24 +1119,23 @@ Vectors" discussion above. If you want an equal-style variable to be evaluated immediately, it may be the case that you do not need to define a variable at all. See -"Section 3.2"_Section_commands.html#cmd_2 of the manual, which -describes the use of "immediate" variables in an input script, -specified as $(formula) with parenthesis, where the formula has the -same syntax as equal-style variables described on this page. This -effectively evaluates a formula immediately without using the variable -command to define a named variable. +the "Commands parse"_Commands_parse.html doc page for info on how to +use "immediate" variables in an input script, specified as $(formula) +with parenthesis, where the formula has the same syntax as equal-style +variables described on this page. This effectively evaluates a +formula immediately without using the variable command to define a +named variable. More generally, there is a difference between referencing a variable with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_" (e.g. v_x or v_abc). The former can be used in any input script command, including a variable command. The input script parser evaluates the reference variable immediately and substitutes its value -into the command. As explained in "Section -3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use -un-named "immediate" variables for this purpose. For example, a -string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script -command evaluates the string between the parenthesis as an equal-style -variable formula. +into the command. As explained on the "Commands +parse"_Commands_parse.html doc page, you can also use un-named +"immediate" variables for this purpose. For example, a string like +this $((xlo+xhi)/2+sqrt(v_area)) in an input script command evaluates +the string between the parenthesis as an equal-style variable formula. Referencing a variable with a leading "v_" is an optional or required kind of argument for some commands (e.g. the "fix @@ -1173,10 +1179,9 @@ quotes if it contains variables preceded by $ signs. For example, variable vratio equal "$\{vfinal\}/$\{v0\}" :pre -This is because the quotes prevent variable substitution (see "this -section"_Section_commands.html#cmd_2 on parsing input script -commands), and thus an error will occur when the formula for "vratio" -is evaluated later. +This is because the quotes prevent variable substitution (explained on +the "Commands parse"_Commands_parse.html doc page), and thus an error +will occur when the formula for "vratio" is evaluated later. :line diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index b8299a5acfc1576484c8f3683eba5eb9e947e4d0..96d3fa6dc4fa53e1b7d399fc2d774afbff682de5 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line @@ -139,10 +139,9 @@ if rot = yes, the angular momentum is zeroed. If specified, the {temp} keyword is used by {create} and {scale} to specify a "compute"_compute.html that calculates temperature in a desired way, e.g. by first subtracting out a velocity bias, as -discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc -pages. If this keyword is not specified, {create} and {scale} -calculate temperature using a compute that is defined internally as -follows: +discussed on the "Howto thermostat"_Howto_thermostat.html doc page. +If this keyword is not specified, {create} and {scale} calculate +temperature using a compute that is defined internally as follows: compute velocity_temp group-ID temp :pre @@ -161,11 +160,11 @@ The {bias} keyword with a {yes} setting is used by {create} and If the temperature compute also calculates a velocity bias, the the bias is subtracted from atom velocities before the {create} and {scale} operations are performed. After the operations, the bias is -added back to the atom velocities. See "Section -6.16"_Section_howto.html#howto_16 of the doc pages for more discussion -of temperature computes with biases. Note that the velocity bias is -only applied to atoms in the temperature compute specified with the -{temp} keyword. +added back to the atom velocities. See the "Howto +thermostat"_Howto_thermostat.html doc page for more discussion of +temperature computes with biases. Note that the velocity bias is only +applied to atoms in the temperature compute specified with the {temp} +keyword. As an example, assume atoms are currently streaming in a flow direction (which could be separately initialized with the {ramp} diff --git a/doc/src/write_coeff.txt b/doc/src/write_coeff.txt index 764e119a9d1d310ae5f969a9163d1ec5753ebe1d..5dc4b331dedbe2940286af653c81a76654cb1347 100644 --- a/doc/src/write_coeff.txt +++ b/doc/src/write_coeff.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index c76f20319c3182a2d9298d8aada887cb806878f3..d8a33f457f2ab15cb38d6922ec54c5b5b8d5d202 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_dump.txt b/doc/src/write_dump.txt index 840716085feff0aaf6b7790befc98b902be87ea3..e67697900129a153801eb53f454641075955189d 100644 --- a/doc/src/write_dump.txt +++ b/doc/src/write_dump.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt index ff3b652dba75feefdb3841bf764f885cc0b3a9d1..3935a5d5387bfd6118134c605058a146fbc81a43 100644 --- a/doc/src/write_restart.txt +++ b/doc/src/write_restart.txt @@ -2,7 +2,7 @@ :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) -:link(lc,Section_commands.html#comm) +:link(lc,Commands_all.html) :line diff --git a/doc/utils/converters/lammpsdoc/txt2html.py b/doc/utils/converters/lammpsdoc/txt2html.py index 79a75d72f6e4be7796e685e7025adbef0d9eb5ff..ed9f47a4e4ae3cfe4c6363a34ab9b7deb42b8c0c 100755 --- a/doc/utils/converters/lammpsdoc/txt2html.py +++ b/doc/utils/converters/lammpsdoc/txt2html.py @@ -662,14 +662,15 @@ class TxtConverter: parser = self.get_argument_parser() parsed_args = parser.parse_args(args) - write_to_files = len(parsed_args.files) > 1 + write_to_files = parsed_args.output_dir or (len(parsed_args.files) > 1) for filename in parsed_args.files: if parsed_args.skip_files and filename in parsed_args.skip_files: continue with open(filename, 'r') as f: - print("Converting", filename, "...", file=err) + if parsed_args.verbose: + print("Converting", filename, "...", file=err) content = f.read() converter = self.create_converter(parsed_args) @@ -683,7 +684,10 @@ class TxtConverter: result = msg if write_to_files: - output_filename = self.get_output_filename(filename) + if parsed_args.output_dir: + output_filename = os.path.join(parsed_args.output_dir, os.path.basename(self.get_output_filename(filename))) + else: + output_filename = self.get_output_filename(filename) with open(output_filename, "w+t") as outfile: outfile.write(result) else: @@ -698,6 +702,8 @@ class Txt2HtmlConverter(TxtConverter): 'HTML file. useful when set of HTML files' ' will be converted to PDF') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('--generate-title', dest='create_title', action='store_true', help='add HTML head page' 'title based on first ' 'h1,h2,h3,h4... element') diff --git a/doc/utils/converters/lammpsdoc/txt2rst.py b/doc/utils/converters/lammpsdoc/txt2rst.py index 17d0916157a4f2d9b07ec655522ac6999b6978cb..8119ad3a7869c5345ffad166536f98ffa7bd20ba 100755 --- a/doc/utils/converters/lammpsdoc/txt2rst.py +++ b/doc/utils/converters/lammpsdoc/txt2rst.py @@ -395,6 +395,8 @@ class Txt2RstConverter(TxtConverter): parser = argparse.ArgumentParser(description='converts a text file with simple formatting & markup into ' 'Restructured Text for Sphinx.') parser.add_argument('-x', metavar='file-to-skip', dest='skip_files', action='append') + parser.add_argument('--verbose', '-v', dest='verbose', action='store_true') + parser.add_argument('--output-directory', '-o', dest='output_dir') parser.add_argument('files', metavar='file', nargs='+', help='one or more files to convert') return parser diff --git a/doc/utils/requirements.txt b/doc/utils/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..2806c164989aa9137a6c1860716ae9abccef75ad --- /dev/null +++ b/doc/utils/requirements.txt @@ -0,0 +1 @@ +Sphinx diff --git a/doc/utils/txt2html/txt2html b/doc/utils/txt2html/txt2html new file mode 100755 index 0000000000000000000000000000000000000000..023631eac1b472cdcaf4e8c4757c72c386446ecf Binary files /dev/null and b/doc/utils/txt2html/txt2html differ diff --git a/examples/DIFFUSE/README b/examples/DIFFUSE/README index df2a675f73b778dd3d4fda1bafff791f2bebf4a6..e78ca2eacf1a109ec3aeb79b3b13e3444ed7d7a9 100644 --- a/examples/DIFFUSE/README +++ b/examples/DIFFUSE/README @@ -47,7 +47,7 @@ compute the diffusion coefficient. You can see that both measures give roughly the same answer and rapidly become roughly constant for the 100K step simulation. -Dcoeff = 0.36 +Dcoeff = 0.33 (2) in.vacf.2d @@ -58,4 +58,4 @@ that point in time, converted into the diffusion coefficient. You can see the VACF approach gives a more noise, fluctuating value for the diffusion coefficient, compared to the MSD approach. -Dcoeff = 0.25 to 0.45 +Dcoeff = ~0.25 diff --git a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 b/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 deleted file mode 100644 index 473aa565278ec6802b78373adcf4b510722c93da..0000000000000000000000000000000000000000 --- a/examples/DIFFUSE/log.13Oct16.msd.2d.g++.8 +++ /dev/null @@ -1,245 +0,0 @@ -LAMMPS (13 Oct 2016) -# sample LAMMPS input script for diffusion of 2d LJ liquid -# mean-squared displacement via compute msd - -# settings - -variable x equal 40 -variable y equal 40 - -variable rho equal 0.6 -variable t equal 1.0 -variable rc equal 2.5 - -# problem setup - -units lj -dimension 2 -atom_style atomic -neigh_modify delay 0 every 1 - -lattice sq2 ${rho} -lattice sq2 0.6 -Lattice spacing in x,y,z = 1.82574 1.82574 1.82574 -region simbox block 0 $x 0 $y -0.1 0.1 -region simbox block 0 40 0 $y -0.1 0.1 -region simbox block 0 40 0 40 -0.1 0.1 -create_box 1 simbox -Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) - 4 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 3200 atoms - -pair_style lj/cut ${rc} -pair_style lj/cut 2.5 -pair_coeff * * 1 1 - -mass * 1.0 -velocity all create $t 97287 -velocity all create 1 97287 - -fix 1 all nve -fix 2 all langevin $t $t 0.1 498094 -fix 2 all langevin 1 $t 0.1 498094 -fix 2 all langevin 1 1 0.1 498094 -fix 3 all enforce2d - -# equilibration run - -thermo 1000 -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 53 53 1 -Memory usage per processor = 2.478 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1 -1.56492 0 -0.5652325 -1.5346995 - 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 - 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416 - 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 - 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 - 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 -Loop time of 0.554412 on 8 procs for 5000 steps with 3200 atoms - -Performance: 3896017.421 tau/day, 9018.559 timesteps/s -98.9% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.23992 | 0.24608 | 0.25161 | 0.7 | 44.39 -Neigh | 0.063106 | 0.064417 | 0.066279 | 0.4 | 11.62 -Comm | 0.072465 | 0.085066 | 0.094837 | 2.3 | 15.34 -Output | 0.00013208 | 0.00013691 | 0.00014591 | 0.0 | 0.02 -Modify | 0.11441 | 0.11621 | 0.11769 | 0.3 | 20.96 -Other | | 0.04251 | | | 7.67 - -Nlocal: 400 ave 406 max 394 min -Histogram: 1 1 0 1 0 2 1 0 1 1 -Nghost: 202.5 ave 212 max 191 min -Histogram: 1 0 0 0 3 1 0 2 0 1 -Neighs: 2800.88 ave 2903 max 2690 min -Histogram: 1 1 0 0 1 2 1 0 1 1 - -Total # of neighbors = 22407 -Ave neighs/atom = 7.00219 -Neighbor list builds = 599 -Dangerous builds = 0 - -unfix 2 - -# data gathering run - -reset_timestep 0 - -# factor of 4 in 2 variables is for 2d - -compute msd all msd com yes -variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6) -fix 9 all vector 10 c_msd[4] -variable fitslope equal slope(f_9)/4/(10*dt) - -thermo_style custom step temp c_msd[4] v_twopoint v_fitslope - -# only need to run for 10K steps to make a good 100-frame movie - -#dump 1 all custom 1 tmp.dump id type vx vy vz - -#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2 - -thermo 1000 -run 100000 -Memory usage per processor = 2.853 Mbytes -Step Temp c_msd[4] v_twopoint v_fitslope - 0 0.97069905 0 0 5e+20 - 1000 0.98138076 4.0484996 0.20242494 0.18046446 - 2000 0.97606079 9.2121392 0.23030346 0.2091528 - 3000 0.97924866 14.815034 0.24691721 0.22619184 - 4000 0.98568451 20.516817 0.25646019 0.23715506 - 5000 0.97551815 27.33922 0.27339219 0.24709999 - 6000 0.98482252 34.37734 0.28647782 0.25735178 - 7000 0.9672559 41.696689 0.29783348 0.26654059 - 8000 0.9836541 48.340277 0.30212673 0.27440308 - 9000 0.99087147 56.042692 0.31134828 0.28113047 - 10000 0.99663166 63.69663 0.31848314 0.28767921 - 11000 0.97776688 71.144109 0.32338231 0.29344527 - 12000 0.98246011 78.301774 0.32625739 0.29849471 - 13000 0.98788732 85.061923 0.32716124 0.3026655 - 14000 0.96872483 91.1658 0.32559214 0.30601023 - 15000 0.98955796 97.278388 0.32426129 0.3084275 - 16000 0.99855196 104.23997 0.3257499 0.31049883 - 17000 0.98600861 110.66055 0.3254722 0.31220348 - 18000 0.98696963 116.90111 0.32472531 0.31352676 - 19000 0.9881192 124.21305 0.32687644 0.31480062 - 20000 0.98527319 131.09874 0.32774685 0.31596198 - 21000 0.99015191 137.89263 0.32831579 0.31705324 - 22000 0.97972418 146.68982 0.33338595 0.31833889 - 23000 0.98911012 155.1264 0.33723129 0.31979515 - 24000 0.98810498 162.88634 0.33934653 0.32131187 - 25000 0.96961962 170.37907 0.34075814 0.32276215 - 26000 0.99118408 179.26511 0.34474059 0.32427111 - 27000 0.98515159 185.90764 0.3442734 0.32574529 - 28000 0.98951677 192.12183 0.34307469 0.32700292 - 29000 0.9832026 196.99457 0.33964581 0.32799023 - 30000 0.98449493 203.48475 0.33914124 0.3287171 - 31000 0.96585993 210.06193 0.33880956 0.32935775 - 32000 0.98758117 218.94174 0.34209646 0.33001591 - 33000 0.98875584 225.96489 0.34237104 0.33072947 - 34000 0.98007229 233.5792 0.34349882 0.3314385 - 35000 0.98415295 241.98148 0.34568783 0.33216634 - 36000 0.98101154 250.30876 0.34765106 0.33295272 - 37000 0.97606878 258.2127 0.34893608 0.33377673 - 38000 0.97220293 266.40464 0.35053242 0.33459273 - 39000 0.979783 272.8578 0.34981769 0.33539728 - 40000 0.98375673 279.87598 0.34984497 0.33609699 - 41000 0.97506523 288.07676 0.35131312 0.33677708 - 42000 0.97106749 296.11647 0.3525196 0.33751312 - 43000 0.97717259 304.46747 0.35403194 0.33823441 - 44000 0.98541435 312.57228 0.35519578 0.3389771 - 45000 0.97678287 321.82674 0.35758527 0.33973306 - 46000 0.98169719 329.78197 0.35845866 0.34051748 - 47000 0.99471466 337.11283 0.35863066 0.34127239 - 48000 0.98332437 346.0754 0.3604952 0.34202442 - 49000 0.98126947 356.11859 0.36338631 0.34282132 - 50000 0.98809751 365.65248 0.36565248 0.34368171 - 51000 0.95919516 373.91833 0.36658659 0.34454516 - 52000 0.98097913 381.26492 0.36660089 0.34538506 - 53000 0.97774072 388.81031 0.36680218 0.34618232 - 54000 0.99096915 395.56767 0.36626636 0.3469296 - 55000 0.97652739 401.72735 0.36520668 0.34760374 - 56000 0.99185306 407.28834 0.3636503 0.34819906 - 57000 0.96289342 414.75298 0.3638184 0.34871992 - 58000 0.97871716 424.69443 0.36611588 0.34927986 - 59000 0.98637393 433.14205 0.36706953 0.34986296 - 60000 0.98009845 438.14533 0.36512111 0.35040349 - 61000 0.99416712 446.08007 0.3656394 0.35088379 - 62000 0.97612483 450.90846 0.36363585 0.35132647 - 63000 0.97786531 455.36749 0.36140277 0.35167458 - 64000 0.99080668 458.04873 0.35785057 0.3519105 - 65000 0.97952497 461.31241 0.3548557 0.3520506 - 66000 0.98095955 463.91727 0.35145248 0.35207764 - 67000 0.98370788 468.93 0.34994776 0.35204043 - 68000 0.96931818 471.07765 0.34638063 0.35192685 - 69000 0.98512552 474.59146 0.34390685 0.35174053 - 70000 0.98065743 478.66071 0.3419005 0.35149002 - 71000 0.98971283 482.57357 0.33984054 0.35119434 - 72000 0.99890324 485.32018 0.3370279 0.35084345 - 73000 0.98649924 490.19497 0.33574998 0.35043722 - 74000 0.98723422 496.04991 0.33516886 0.35003351 - 75000 1.0025633 501.6313 0.33442087 0.34962094 - 76000 0.97859959 505.97813 0.33288035 0.34921013 - 77000 0.97973006 510.55334 0.33152814 0.3487692 - 78000 0.9903944 515.06966 0.33017286 0.34830833 - 79000 0.96847518 518.76483 0.32833217 0.3478214 - 80000 0.99171112 524.18127 0.32761329 0.34733349 - 81000 0.97202573 529.09959 0.32660468 0.3468315 - 82000 0.99368438 535.80271 0.32670897 0.34633058 - 83000 0.97932483 543.08233 0.32715803 0.34586259 - 84000 0.99078651 547.57861 0.32593965 0.34540839 - 85000 0.98973457 552.24581 0.32485048 0.34493584 - 86000 0.9835873 557.3493 0.32404029 0.34446152 - 87000 0.97180564 564.93434 0.32467491 0.34400358 - 88000 0.99743353 571.39837 0.32465817 0.3435667 - 89000 0.98993437 577.81703 0.32461631 0.3431411 - 90000 0.9926071 583.39378 0.32410765 0.342724 - 91000 0.98800458 591.08741 0.3247733 0.34232767 - 92000 0.98501879 596.10133 0.32396811 0.34193949 - 93000 0.98810082 604.02652 0.32474544 0.3415681 - 94000 0.97563748 609.43676 0.32416849 0.341209 - 95000 0.97283448 615.15754 0.32376713 0.34084828 - 96000 0.9883071 622.30912 0.32411933 0.34049871 - 97000 0.97717678 628.84457 0.32414669 0.34016355 - 98000 0.97190208 634.37377 0.32366009 0.3398341 - 99000 0.98687379 640.66666 0.32356902 0.33950845 - 100000 0.97559757 646.96406 0.32348203 0.33919036 -Loop time of 9.58779 on 8 procs for 100000 steps with 3200 atoms - -Performance: 4505729.040 tau/day, 10429.928 timesteps/s -99.4% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.8572 | 4.9363 | 4.9822 | 1.7 | 51.49 -Neigh | 1.3583 | 1.376 | 1.3991 | 1.2 | 14.35 -Comm | 1.5192 | 1.7079 | 1.8264 | 7.2 | 17.81 -Output | 0.0085125 | 0.0086059 | 0.0089455 | 0.1 | 0.09 -Modify | 0.77663 | 0.7903 | 0.81378 | 1.3 | 8.24 -Other | | 0.7686 | | | 8.02 - -Nlocal: 400 ave 413 max 391 min -Histogram: 2 1 0 2 0 0 1 1 0 1 -Nghost: 204.75 ave 213 max 197 min -Histogram: 1 1 0 1 0 3 0 1 0 1 -Neighs: 2800.62 ave 2959 max 2661 min -Histogram: 1 1 1 2 0 0 0 1 1 1 - -Total # of neighbors = 22405 -Ave neighs/atom = 7.00156 -Neighbor list builds = 12728 -Dangerous builds = 0 -Total wall time: 0:00:10 diff --git a/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 new file mode 100644 index 0000000000000000000000000000000000000000..113da9040d8a8eb37b84a4245ce3d904e219db3c --- /dev/null +++ b/examples/DIFFUSE/log.3Aug18.msd.2d.g++.8 @@ -0,0 +1,251 @@ +LAMMPS (2 Aug 2018) +# sample LAMMPS input script for diffusion of 2d LJ liquid +# mean-squared displacement via compute msd + +# settings + +variable x equal 40 +variable y equal 40 + +variable rho equal 0.6 +variable t equal 1.0 +variable rc equal 2.5 + +# problem setup + +units lj +dimension 2 +atom_style atomic +neigh_modify delay 0 every 1 + +lattice sq2 ${rho} +lattice sq2 0.6 +Lattice spacing in x,y,z = 1.82574 1.82574 1.82574 +region simbox block 0 $x 0 $y -0.1 0.1 +region simbox block 0 40 0 $y -0.1 0.1 +region simbox block 0 40 0 40 -0.1 0.1 +create_box 1 simbox +Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) + 4 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 3200 atoms + Time spent = 0.000706911 secs + +pair_style lj/cut ${rc} +pair_style lj/cut 2.5 +pair_coeff * * 1 1 + +mass * 1.0 +velocity all create $t 97287 +velocity all create 1 97287 + +fix 1 all nve +fix 2 all langevin $t $t 0.1 498094 +fix 2 all langevin 1 $t 0.1 498094 +fix 2 all langevin 1 1 0.1 498094 +fix 3 all enforce2d + +# equilibration run + +thermo 1000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 53 53 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -1.56492 0 -0.5652325 -1.5346995 + 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 + 2000 0.99008371 -1.5748206 0 -0.58504633 1.0809416 + 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 + 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 + 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 +Loop time of 0.667446 on 8 procs for 5000 steps with 3200 atoms + +Performance: 3236214.756 tau/day, 7491.238 timesteps/s +99.9% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.22913 | 0.24877 | 0.28382 | 3.6 | 37.27 +Neigh | 0.064419 | 0.071256 | 0.080013 | 1.7 | 10.68 +Comm | 0.103 | 0.14054 | 0.17204 | 5.5 | 21.06 +Output | 0.00010705 | 0.00013995 | 0.00021911 | 0.0 | 0.02 +Modify | 0.13457 | 0.14973 | 0.16887 | 2.6 | 22.43 +Other | | 0.05701 | | | 8.54 + +Nlocal: 400 ave 406 max 394 min +Histogram: 1 1 0 1 0 2 1 0 1 1 +Nghost: 202.5 ave 212 max 191 min +Histogram: 1 0 0 0 3 1 0 2 0 1 +Neighs: 2800.88 ave 2903 max 2690 min +Histogram: 1 1 0 0 1 2 1 0 1 1 + +Total # of neighbors = 22407 +Ave neighs/atom = 7.00219 +Neighbor list builds = 599 +Dangerous builds = 0 + +unfix 2 + +# data gathering run + +reset_timestep 0 + +# factor of 4 in 2 variables is for 2d + +compute msd all msd com yes +variable twopoint equal c_msd[4]/4/(step*dt+1.0e-6) +fix 9 all vector 10 c_msd[4] +variable fitslope equal slope(f_9)/4/(10*dt) + +thermo_style custom step temp c_msd[4] v_twopoint v_fitslope + +# only need to run for 10K steps to make a good 100-frame movie + +#dump 1 all custom 1 tmp.dump id type vx vy vz + +#dump 2 all image 100 image.*.jpg type type zoom 1.6 adiam 1.2 + +thermo 1000 +run 100000 +Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes +Step Temp c_msd[4] v_twopoint v_fitslope + 0 0.97069905 0 0 5e+20 + 1000 0.98138076 4.0484996 0.20242494 0.20685564 + 2000 0.97606079 9.2121392 0.23030346 0.23687918 + 3000 0.97924866 14.815034 0.24691721 0.25405247 + 4000 0.98568451 20.516817 0.25646019 0.26353644 + 5000 0.97551815 27.33922 0.27339219 0.27544492 + 6000 0.98482252 34.37734 0.28647782 0.28966619 + 7000 0.9672559 41.696689 0.29783348 0.30165524 + 8000 0.9836541 48.340277 0.30212673 0.31085371 + 9000 0.99087147 56.042692 0.31134828 0.31811489 + 10000 0.99663166 63.69663 0.31848314 0.32589374 + 11000 0.97776688 71.144109 0.32338231 0.33219745 + 12000 0.98246011 78.301774 0.32625739 0.33723 + 13000 0.98788732 85.061923 0.32716124 0.34053027 + 14000 0.96872483 91.1658 0.32559214 0.34231162 + 15000 0.98955796 97.278388 0.32426129 0.34229511 + 16000 0.99855196 104.23997 0.3257499 0.34217252 + 17000 0.98600861 110.66055 0.3254722 0.34172446 + 18000 0.98696963 116.90111 0.32472531 0.3408227 + 19000 0.9881192 124.21305 0.32687644 0.34036538 + 20000 0.98527319 131.09874 0.32774685 0.34003478 + 21000 0.99015191 137.89263 0.32831579 0.33987868 + 22000 0.97972418 146.68982 0.33338595 0.34060035 + 23000 0.98911012 155.1264 0.33723129 0.34201036 + 24000 0.98810498 162.88634 0.33934653 0.34371488 + 25000 0.96961962 170.37907 0.34075814 0.34531409 + 26000 0.99118408 179.26511 0.34474059 0.34717195 + 27000 0.98515159 185.90764 0.3442734 0.34898035 + 28000 0.98951677 192.12183 0.34307469 0.35021808 + 29000 0.9832026 196.99457 0.33964581 0.35075459 + 30000 0.98449493 203.48475 0.33914124 0.35066186 + 31000 0.96585993 210.06193 0.33880956 0.35046715 + 32000 0.98758117 218.94174 0.34209646 0.35046623 + 33000 0.98875584 225.96489 0.34237104 0.35073944 + 34000 0.98007229 233.5792 0.34349882 0.35109188 + 35000 0.98415295 241.98148 0.34568783 0.35157879 + 36000 0.98101154 250.30876 0.34765106 0.3523013 + 37000 0.97606878 258.2127 0.34893608 0.35318097 + 38000 0.97220293 266.40464 0.35053242 0.3540743 + 39000 0.979783 272.8578 0.34981769 0.35496561 + 40000 0.98375673 279.87598 0.34984497 0.35558182 + 41000 0.97506523 288.07676 0.35131312 0.35618259 + 42000 0.97106749 296.11647 0.3525196 0.35698571 + 43000 0.97717259 304.46747 0.35403194 0.3577736 + 44000 0.98541435 312.57228 0.35519578 0.35865003 + 45000 0.97678287 321.82674 0.35758527 0.35958623 + 46000 0.98169719 329.78197 0.35845866 0.36062236 + 47000 0.99471466 337.11283 0.35863066 0.36158322 + 48000 0.98332437 346.0754 0.3604952 0.36255042 + 49000 0.98126947 356.11859 0.36338631 0.3636628 + 50000 0.98809751 365.65248 0.36565248 0.36496809 + 51000 0.95919516 373.91833 0.36658659 0.36628073 + 52000 0.98097913 381.26492 0.36660089 0.36752237 + 53000 0.97774072 388.81031 0.36680218 0.36863962 + 54000 0.99096915 395.56767 0.36626636 0.36961521 + 55000 0.97652739 401.72735 0.36520668 0.37038579 + 56000 0.99185306 407.28834 0.3636503 0.37094092 + 57000 0.96289342 414.75298 0.3638184 0.37130039 + 58000 0.97871716 424.69443 0.36611588 0.37180428 + 59000 0.98637393 433.14205 0.36706953 0.37239862 + 60000 0.98009845 438.14533 0.36512111 0.37288487 + 61000 0.99416712 446.08007 0.3656394 0.37321496 + 62000 0.97612483 450.90846 0.36363585 0.37345792 + 63000 0.97786531 455.36749 0.36140277 0.37344803 + 64000 0.99080668 458.04873 0.35785057 0.37313914 + 65000 0.97952497 461.31241 0.3548557 0.3725875 + 66000 0.98095955 463.91727 0.35145248 0.37174735 + 67000 0.98370788 468.93 0.34994776 0.37076942 + 68000 0.96931818 471.07765 0.34638063 0.36961868 + 69000 0.98512552 474.59146 0.34390685 0.36830908 + 70000 0.98065743 478.66071 0.3419005 0.36686789 + 71000 0.98971283 482.57357 0.33984054 0.36535224 + 72000 0.99890324 485.32018 0.3370279 0.36373174 + 73000 0.98649924 490.19497 0.33574998 0.36200692 + 74000 0.98723422 496.04991 0.33516886 0.36034919 + 75000 1.0025633 501.6313 0.33442087 0.35872052 + 76000 0.97859959 505.97813 0.33288035 0.35714939 + 77000 0.97973006 510.55334 0.33152814 0.35553808 + 78000 0.9903944 515.06966 0.33017286 0.35391584 + 79000 0.96847518 518.76483 0.32833217 0.35226287 + 80000 0.99171112 524.18127 0.32761329 0.35065267 + 81000 0.97202573 529.09959 0.32660468 0.34904364 + 82000 0.99368438 535.80271 0.32670897 0.34747913 + 83000 0.97932483 543.08233 0.32715803 0.34605097 + 84000 0.99078651 547.57861 0.32593965 0.34469765 + 85000 0.98973457 552.24581 0.32485048 0.34332115 + 86000 0.9835873 557.3493 0.32404029 0.34197018 + 87000 0.97180564 564.93434 0.32467491 0.34069702 + 88000 0.99743353 571.39837 0.32465817 0.33951258 + 89000 0.98993437 577.81703 0.32461631 0.33838511 + 90000 0.9926071 583.39378 0.32410765 0.33730429 + 91000 0.98800458 591.08741 0.3247733 0.33630505 + 92000 0.98501879 596.10133 0.32396811 0.33534725 + 93000 0.98810082 604.02652 0.32474544 0.33445545 + 94000 0.97563748 609.43676 0.32416849 0.33361404 + 95000 0.97283448 615.15754 0.32376713 0.33278044 + 96000 0.9883071 622.30912 0.32411933 0.33199212 + 97000 0.97717678 628.84457 0.32414669 0.33125729 + 98000 0.97190208 634.37377 0.32366009 0.33054877 + 99000 0.98687379 640.66666 0.32356902 0.32986014 + 100000 0.97559757 646.96406 0.32348203 0.32920186 +Loop time of 7.61838 on 8 procs for 100000 steps with 3200 atoms + +Performance: 5670494.518 tau/day, 13126.145 timesteps/s +100.0% CPU use with 8 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.5458 | 3.6709 | 3.8234 | 4.3 | 48.19 +Neigh | 1.1363 | 1.1513 | 1.1753 | 1.0 | 15.11 +Comm | 1.5901 | 1.7017 | 1.8664 | 6.9 | 22.34 +Output | 0.0041966 | 0.0043583 | 0.0050626 | 0.4 | 0.06 +Modify | 0.63816 | 0.65537 | 0.68918 | 2.0 | 8.60 +Other | | 0.4348 | | | 5.71 + +Nlocal: 400 ave 413 max 391 min +Histogram: 2 1 0 2 0 0 1 1 0 1 +Nghost: 204.75 ave 213 max 197 min +Histogram: 1 1 0 1 0 3 0 1 0 1 +Neighs: 2800.62 ave 2959 max 2661 min +Histogram: 1 1 1 2 0 0 0 1 1 1 + +Total # of neighbors = 22405 +Ave neighs/atom = 7.00156 +Neighbor list builds = 12728 +Dangerous builds = 0 +Total wall time: 0:00:08 diff --git a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 similarity index 84% rename from examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 rename to examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 index 458315bc29de64e5a2102de7e98ed958e591252c..80c57ada9c31b8e299944689fd1cba2f6afb95f4 100644 --- a/examples/DIFFUSE/log.13Oct16.vacf.2d.g++.8 +++ b/examples/DIFFUSE/log.3Aug18.vacf.2d.g++.8 @@ -1,4 +1,4 @@ -LAMMPS (13 Oct 2016) +LAMMPS (2 Aug 2018) # sample LAMMPS input script for diffusion of 2d LJ liquid # mean-squared displacement via compute msd @@ -29,6 +29,7 @@ Created orthogonal box = (0 0 -0.182574) to (73.0297 73.0297 0.182574) 4 by 2 by 1 MPI processor grid create_atoms 1 box Created 3200 atoms + Time spent = 0.000712872 secs pair_style lj/cut ${rc} pair_style lj/cut 2.5 @@ -49,13 +50,18 @@ fix 3 all enforce2d thermo 1000 run 5000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 53 53 1 -Memory usage per processor = 2.478 Mbytes + binsize = 1.4, bins = 53 53 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.052 | 3.052 | 3.052 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -1.56492 0 -0.5652325 -1.5346995 1000 0.97537833 -1.5723957 0 -0.5973222 0.92877783 @@ -63,20 +69,20 @@ Step Temp E_pair E_mol TotEng Press 3000 1.0111412 -1.5848987 0 -0.57407352 1.0174297 4000 1.0055417 -1.5857581 0 -0.58053054 0.95647691 5000 0.97069905 -1.5851114 0 -0.61471567 0.90108287 -Loop time of 0.557588 on 8 procs for 5000 steps with 3200 atoms +Loop time of 0.648098 on 8 procs for 5000 steps with 3200 atoms -Performance: 3873826.669 tau/day, 8967.191 timesteps/s -99.1% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 3332829.949 tau/day, 7714.884 timesteps/s +99.9% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.23784 | 0.24683 | 0.25594 | 1.0 | 44.27 -Neigh | 0.062975 | 0.06439 | 0.0662 | 0.4 | 11.55 -Comm | 0.083826 | 0.092564 | 0.1035 | 2.1 | 16.60 -Output | 0.00011778 | 0.00012615 | 0.00014257 | 0.1 | 0.02 -Modify | 0.11466 | 0.11648 | 0.1187 | 0.4 | 20.89 -Other | | 0.0372 | | | 6.67 +Pair | 0.22614 | 0.24602 | 0.27481 | 2.8 | 37.96 +Neigh | 0.066875 | 0.07135 | 0.077825 | 1.2 | 11.01 +Comm | 0.098293 | 0.12744 | 0.1569 | 5.6 | 19.66 +Output | 0.0001049 | 0.00012228 | 0.00014496 | 0.0 | 0.02 +Modify | 0.13725 | 0.14919 | 0.16903 | 2.4 | 23.02 +Other | | 0.05398 | | | 8.33 Nlocal: 400 ave 406 max 394 min Histogram: 1 1 0 1 0 2 1 0 1 1 @@ -114,7 +120,7 @@ thermo_style custom step temp c_vacf[4] v_vacf thermo 1000 run 100000 -Memory usage per processor = 2.853 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.427 | 3.427 | 3.427 Mbytes Step Temp c_vacf[4] v_vacf 0 0.97069905 1.9407914 0 1000 0.98138076 0.029239763 0.22157396 @@ -217,20 +223,20 @@ Step Temp c_vacf[4] v_vacf 98000 0.97190208 0.015065013 0.20906937 99000 0.98687379 -0.036869401 0.22993959 100000 0.97559757 0.045464091 0.23369283 -Loop time of 10.8346 on 8 procs for 100000 steps with 3200 atoms +Loop time of 8.16691 on 8 procs for 100000 steps with 3200 atoms -Performance: 3987213.825 tau/day, 9229.662 timesteps/s -99.5% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 5289636.190 tau/day, 12244.528 timesteps/s +100.0% CPU use with 8 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.8486 | 4.9469 | 5.0248 | 2.8 | 45.66 -Neigh | 1.3613 | 1.374 | 1.3916 | 0.8 | 12.68 -Comm | 1.8181 | 1.9534 | 2.0665 | 5.7 | 18.03 -Output | 0.016565 | 0.016701 | 0.017039 | 0.1 | 0.15 -Modify | 1.8395 | 1.9053 | 1.9704 | 2.8 | 17.59 -Other | | 0.6383 | | | 5.89 +Pair | 3.5668 | 3.6612 | 3.7867 | 4.0 | 44.83 +Neigh | 1.1409 | 1.1555 | 1.1804 | 1.4 | 14.15 +Comm | 1.581 | 1.711 | 1.8239 | 7.1 | 20.95 +Output | 0.016626 | 0.016831 | 0.017569 | 0.2 | 0.21 +Modify | 1.225 | 1.2594 | 1.3008 | 2.0 | 15.42 +Other | | 0.363 | | | 4.45 Nlocal: 400 ave 413 max 391 min Histogram: 2 1 0 2 0 0 1 1 0 1 @@ -243,4 +249,4 @@ Total # of neighbors = 22405 Ave neighs/atom = 7.00156 Neighbor list builds = 12728 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:08 diff --git a/examples/SPIN/README b/examples/SPIN/README new file mode 100644 index 0000000000000000000000000000000000000000..5ad252e7f2c71ee1d0232ec1f67f4ee39a91f612 --- /dev/null +++ b/examples/SPIN/README @@ -0,0 +1,20 @@ +This directory contains examples and applications of the SPIN package +===================================================================== + +- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide +examples of spin-lattice calculations. + +- the bfo repository provides an example of spin dynamics calculation +performed on a fixed lattice, and applied to the multiferroic +material bismuth-oxide. + +- the read_restart directory provides examples allowing to write or +read data files, and restart magneto-mechanical simulations. + +- vizualization of the dump files can be achieved using Ovito or +VMD. See the vmd repository for help vizualizing results with VMD. + +** Note, the aim of this repository is mainly to provide users with +examples. Better values and tuning of the magnetic and mechanical +interactions can be achieved for more accurate materials +simulations. ** diff --git a/examples/SPIN/bfo/in.spin.bfo b/examples/SPIN/bfo/in.spin.bfo new file mode 100644 index 0000000000000000000000000000000000000000..de23ba87ba2b825c129b88fd55fcfcb33703eb01 --- /dev/null +++ b/examples/SPIN/bfo/in.spin.bfo @@ -0,0 +1,56 @@ +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + +#pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +#thermo_style custom step time v_magnorm v_emag temp etotal +thermo_style custom step time v_magnorm pe ke v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..8e9eb82d1fe23962eb6110ea22c17319f406792e --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.1 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.0013566 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.272 | 7.272 | 7.272 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.0096526211 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342235 -3.8784006 0 -3.8656019 + 200 0.04 0.0092074832 -5.111441 0 -5.0986001 + 250 0.05 0.0089713115 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256081 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715548 -8.7738491 0 -8.7609521 + 400 0.08 0.008211486 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483243 -11.18751 0 -11.174637 + 500 0.1 0.0076849713 -12.386462 0 -12.37362 + 550 0.11 0.007424064 -13.580633 0 -13.567832 + 600 0.12 0.0071680699 -14.770519 0 -14.757759 + 650 0.13 0.0069192726 -15.956579 0 -15.943853 + 700 0.14 0.0066793495 -17.139049 0 -17.126343 + 750 0.15 0.0064488038 -18.317803 0 -18.305099 + 800 0.16 0.0062267571 -19.492336 0 -19.479616 + 850 0.17 0.0060112235 -20.661925 0 -20.649176 + 900 0.18 0.0057995251 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592263 -25.285621 0 -25.272717 + 1100 0.22 0.0049391661 -26.431928 0 -26.419004 + 1150 0.23 0.0047179149 -27.578212 0 -27.565281 + 1200 0.24 0.0044991004 -28.727051 0 -28.714128 + 1250 0.25 0.0042864034 -29.880967 0 -29.868062 + 1300 0.26 0.0040824475 -31.042054 0 -31.029173 + 1350 0.27 0.0038883007 -32.21165 0 -32.198795 + 1400 0.28 0.0037036595 -33.390159 0 -33.377326 + 1450 0.29 0.0035274815 -34.577121 0 -34.564302 + 1500 0.3 0.0033587207 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429081 -38.177601 0 -38.164801 + 1650 0.33 0.0028989804 -39.387757 0 -39.374962 + 1700 0.34 0.0027692024 -40.602665 0 -40.589873 + 1750 0.35 0.0026581403 -41.823341 0 -41.81054 + 1800 0.36 0.0025686991 -43.05145 0 -43.038628 + 1850 0.37 0.002500124 -44.288966 0 -44.276111 + 1900 0.38 0.0024477804 -45.537752 0 -45.52486 + 1950 0.39 0.0024050049 -46.799255 0 -46.786336 + 2000 0.4 0.0023657031 -48.074388 0 -48.061466 + 2050 0.41 0.0023260844 -49.363587 0 -49.350695 + 2100 0.42 0.0022848329 -50.666866 0 -50.654039 + 2150 0.43 0.0022419759 -51.983781 0 -51.971055 + 2200 0.44 0.0021972506 -53.31336 0 -53.300764 + 2250 0.45 0.0021488322 -54.654121 0 -54.641676 + 2300 0.46 0.0020929483 -56.004207 0 -55.991918 + 2350 0.47 0.0020244601 -57.361586 0 -57.349442 + 2400 0.48 0.001938225 -58.72428 0 -58.712247 + 2450 0.49 0.0018309419 -60.09064 0 -60.078671 + 2500 0.5 0.0017030436 -61.459658 0 -61.447705 + 2550 0.51 0.0015599449 -62.831213 0 -62.819237 + 2600 0.52 0.0014117554 -64.206088 0 -64.194074 + 2650 0.53 0.0012709942 -65.585701 0 -65.573657 + 2700 0.54 0.0011490452 -66.971565 0 -66.959515 + 2750 0.55 0.001053009 -68.364663 0 -68.352635 + 2800 0.56 0.00098415327 -69.765002 0 -69.753017 + 2850 0.57 0.00093809306 -71.171532 0 -71.159598 + 2900 0.58 0.00090656933 -72.58234 0 -72.570459 + 2950 0.59 0.00088069677 -73.994931 0 -73.983099 + 3000 0.6 0.00085472643 -75.406507 0 -75.39472 + 3050 0.61 0.00082842902 -76.814319 0 -76.802575 + 3100 0.62 0.00080642618 -78.216074 0 -78.204373 + 3150 0.63 0.00079463972 -79.610246 0 -79.598589 + 3200 0.64 0.0007962304 -80.996103 0 -80.984494 + 3250 0.65 0.00080980411 -82.37346 0 -82.361903 + 3300 0.66 0.00083070982 -83.742356 0 -83.730855 + 3350 0.67 0.00085389185 -85.102808 0 -85.091374 + 3400 0.68 0.00087624091 -86.454619 0 -86.443259 + 3450 0.69 0.00089741986 -87.797089 0 -87.785814 + 3500 0.7 0.00091910796 -89.12875 0 -89.117567 + 3550 0.71 0.00094318459 -90.447312 0 -90.436232 + 3600 0.72 0.00096989367 -91.750008 0 -91.739046 + 3650 0.73 0.00099713096 -93.034224 0 -93.023402 + 3700 0.74 0.0010212995 -94.298186 0 -94.287529 + 3750 0.75 0.0010391164 -95.5414 0 -95.530926 + 3800 0.76 0.0010491462 -96.764626 0 -96.754338 + 3850 0.77 0.0010521238 -97.969346 0 -97.95923 + 3900 0.78 0.0010500324 -99.156875 0 -99.146899 + 3950 0.79 0.0010447043 -100.32743 0 -100.31756 + 4000 0.8 0.0010368986 -101.4796 0 -101.46978 + 4050 0.81 0.0010263632 -102.61044 0 -102.60064 + 4100 0.82 0.0010126933 -103.71619 0 -103.70639 + 4150 0.83 0.00099631895 -104.79338 0 -104.78358 + 4200 0.84 0.0009789075 -105.8398 0 -105.82998 + 4250 0.85 0.00096287608 -106.85496 0 -106.84515 + 4300 0.86 0.00095034023 -107.84011 0 -107.83029 + 4350 0.87 0.00094219078 -108.7976 0 -108.78778 + 4400 0.88 0.00093779428 -109.73016 0 -109.72031 + 4450 0.89 0.0009354459 -110.63996 0 -110.63008 + 4500 0.9 0.00093342614 -111.52805 0 -111.51812 + 4550 0.91 0.0009311077 -112.39417 0 -112.38416 + 4600 0.92 0.00092926689 -113.23706 0 -113.22697 + 4650 0.93 0.00092921566 -114.05512 0 -114.04495 + 4700 0.94 0.00093142598 -114.84701 0 -114.83675 + 4750 0.95 0.00093479851 -115.61197 0 -115.60164 + 4800 0.96 0.0009369799 -116.3499 0 -116.33951 + 4850 0.97 0.00093516768 -117.06128 0 -117.05084 + 4900 0.98 0.00092684411 -117.74695 0 -117.73645 + 4950 0.99 0.00091046222 -118.40798 0 -118.39742 + 5000 1 0.00088619957 -119.04554 0 -119.03492 +Loop time of 128.304 on 1 procs for 5000 steps with 5780 atoms + +Performance: 0.673 ns/day, 35.640 hours/ns, 38.970 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.227 | 24.227 | 24.227 | 0.0 | 18.88 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.081048 | 0.081048 | 0.081048 | 0.0 | 0.06 +Output | 39.796 | 39.796 | 39.796 | 0.0 | 31.02 +Modify | 64.112 | 64.112 | 64.112 | 0.0 | 49.97 +Other | | 0.08788 | | | 0.07 + +Nlocal: 5780 ave 5780 max 5780 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1065 ave 1065 max 1065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 92480 ave 92480 max 92480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:02:08 diff --git a/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..c0f96b81954d032ece3935718bf95099e22c643e --- /dev/null +++ b/examples/SPIN/bfo/log.11May18.spin.bfo.g++.4 @@ -0,0 +1,212 @@ +LAMMPS (11 May 2018) +# layer sc iron atoms (in the [001] plane) in bismuth oxide + +clear +units metal +atom_style spin + +dimension 3 +boundary p p f + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +Lattice spacing in x,y,z = 3.96 3.96 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (134.64 134.64 19.8) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 5780 atoms + Time spent = 0.000355959 secs + +# setting mass, mag. moments, and interactions for bfo + +mass 1 1.0 + +set group all spin/random 11 2.50 + 5780 settings made for spin/random + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.1 21 +fix 3 all nve/spin lattice no + +timestep 0.0002 + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_bfo.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 5000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.1 + ghost atom cutoff = 6.1 + binsize = 3.05, bins = 45 45 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair spin/magelec, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.862 | 6.862 | 6.862 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.010071723 -0.13298298 0 -0.12034311 + 50 0.01 0.0098643821 -1.3898985 0 -1.3772103 + 100 0.02 0.009652621 -2.6381677 0 -2.6254222 + 150 0.03 0.0094342234 -3.8784007 0 -3.8656019 + 200 0.04 0.009207483 -5.1114411 0 -5.0986001 + 250 0.05 0.0089713114 -6.3380611 0 -6.3251904 + 300 0.06 0.0087256079 -7.5587787 0 -7.5458894 + 350 0.07 0.0084715546 -8.7738491 0 -8.7609521 + 400 0.08 0.0082114858 -9.9833855 0 -9.9704932 + 450 0.09 0.0079483242 -11.18751 0 -11.174637 + 500 0.1 0.0076849711 -12.386462 0 -12.37362 + 550 0.11 0.0074240638 -13.580633 0 -13.567832 + 600 0.12 0.0071680697 -14.770519 0 -14.757759 + 650 0.13 0.0069192724 -15.956579 0 -15.943853 + 700 0.14 0.0066793493 -17.139049 0 -17.126343 + 750 0.15 0.0064488035 -18.317803 0 -18.305099 + 800 0.16 0.0062267569 -19.492336 0 -19.479616 + 850 0.17 0.0060112233 -20.661925 0 -20.649176 + 900 0.18 0.005799525 -21.825931 0 -21.813141 + 950 0.19 0.0055886511 -22.98413 0 -22.971297 + 1000 0.2 0.0053757923 -24.136967 0 -24.124095 + 1050 0.21 0.0051592265 -25.285621 0 -25.272717 + 1100 0.22 0.0049391664 -26.431928 0 -26.419004 + 1150 0.23 0.0047179153 -27.578212 0 -27.565281 + 1200 0.24 0.0044991009 -28.727051 0 -28.714128 + 1250 0.25 0.0042864039 -29.880967 0 -29.868062 + 1300 0.26 0.004082448 -31.042054 0 -31.029174 + 1350 0.27 0.0038883012 -32.21165 0 -32.198795 + 1400 0.28 0.0037036599 -33.390159 0 -33.377326 + 1450 0.29 0.0035274817 -34.577121 0 -34.564302 + 1500 0.3 0.0033587208 -35.771483 0 -35.758672 + 1550 0.31 0.0031969501 -36.971996 0 -36.95919 + 1600 0.32 0.0030429079 -38.177601 0 -38.164801 + 1650 0.33 0.0028989801 -39.387757 0 -39.374962 + 1700 0.34 0.0027692022 -40.602666 0 -40.589873 + 1750 0.35 0.0026581401 -41.823341 0 -41.81054 + 1800 0.36 0.002568699 -43.05145 0 -43.038628 + 1850 0.37 0.0025001242 -44.288966 0 -44.276111 + 1900 0.38 0.0024477808 -45.537752 0 -45.52486 + 1950 0.39 0.0024050056 -46.799255 0 -46.786336 + 2000 0.4 0.002365704 -48.074388 0 -48.061466 + 2050 0.41 0.0023260854 -49.363587 0 -49.350695 + 2100 0.42 0.002284834 -50.666866 0 -50.654039 + 2150 0.43 0.0022419771 -51.983781 0 -51.971055 + 2200 0.44 0.0021972518 -53.31336 0 -53.300764 + 2250 0.45 0.0021488333 -54.654121 0 -54.641676 + 2300 0.46 0.0020929494 -56.004207 0 -55.991918 + 2350 0.47 0.0020244612 -57.361586 0 -57.349441 + 2400 0.48 0.0019382262 -58.72428 0 -58.712247 + 2450 0.49 0.001830943 -60.090639 0 -60.078671 + 2500 0.5 0.0017030446 -61.459658 0 -61.447704 + 2550 0.51 0.0015599459 -62.831213 0 -62.819237 + 2600 0.52 0.0014117562 -64.206088 0 -64.194074 + 2650 0.53 0.001270995 -65.5857 0 -65.573657 + 2700 0.54 0.001149046 -66.971565 0 -66.959515 + 2750 0.55 0.0010530098 -68.364663 0 -68.352635 + 2800 0.56 0.00098415418 -69.765002 0 -69.753017 + 2850 0.57 0.00093809402 -71.171532 0 -71.159598 + 2900 0.58 0.00090657031 -72.58234 0 -72.570459 + 2950 0.59 0.00088069773 -73.994931 0 -73.983099 + 3000 0.6 0.00085472731 -75.406507 0 -75.39472 + 3050 0.61 0.00082842975 -76.814319 0 -76.802575 + 3100 0.62 0.00080642669 -78.216074 0 -78.204373 + 3150 0.63 0.00079464 -79.610246 0 -79.59859 + 3200 0.64 0.00079623049 -80.996103 0 -80.984494 + 3250 0.65 0.00080980416 -82.373461 0 -82.361903 + 3300 0.66 0.00083070997 -83.742356 0 -83.730856 + 3350 0.67 0.00085389223 -85.102809 0 -85.091374 + 3400 0.68 0.00087624159 -86.454619 0 -86.44326 + 3450 0.69 0.00089742086 -87.79709 0 -87.785815 + 3500 0.7 0.00091910931 -89.12875 0 -89.117568 + 3550 0.71 0.00094318635 -90.447312 0 -90.436233 + 3600 0.72 0.00096989594 -91.750008 0 -91.739047 + 3650 0.73 0.00099713386 -93.034224 0 -93.023403 + 3700 0.74 0.0010213031 -94.298186 0 -94.287529 + 3750 0.75 0.0010391209 -95.541401 0 -95.530926 + 3800 0.76 0.0010491514 -96.764626 0 -96.754339 + 3850 0.77 0.0010521296 -97.969347 0 -97.959231 + 3900 0.78 0.0010500386 -99.156876 0 -99.146899 + 3950 0.79 0.0010447106 -100.32743 0 -100.31756 + 4000 0.8 0.0010369046 -101.4796 0 -101.46978 + 4050 0.81 0.0010263688 -102.61044 0 -102.60064 + 4100 0.82 0.0010126985 -103.71619 0 -103.70639 + 4150 0.83 0.00099632366 -104.79338 0 -104.78358 + 4200 0.84 0.00097891183 -105.8398 0 -105.82998 + 4250 0.85 0.00096288003 -106.85496 0 -106.84515 + 4300 0.86 0.00095034371 -107.84011 0 -107.83029 + 4350 0.87 0.00094219371 -108.7976 0 -108.78778 + 4400 0.88 0.00093779663 -109.73016 0 -109.72031 + 4450 0.89 0.00093544766 -110.63996 0 -110.63008 + 4500 0.9 0.00093342739 -111.52805 0 -111.51812 + 4550 0.91 0.00093110855 -112.39417 0 -112.38416 + 4600 0.92 0.00092926746 -113.23706 0 -113.22697 + 4650 0.93 0.00092921608 -114.05512 0 -114.04495 + 4700 0.94 0.0009314263 -114.84701 0 -114.83675 + 4750 0.95 0.0009347987 -115.61197 0 -115.60164 + 4800 0.96 0.00093697985 -116.3499 0 -116.33951 + 4850 0.97 0.00093516726 -117.06128 0 -117.05084 + 4900 0.98 0.00092684316 -117.74695 0 -117.73645 + 4950 0.99 0.00091046061 -118.40798 0 -118.39742 + 5000 1 0.00088619727 -119.04554 0 -119.03492 +Loop time of 37.142 on 4 procs for 5000 steps with 5780 atoms + +Performance: 2.326 ns/day, 10.317 hours/ns, 134.619 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.2804 | 6.3487 | 6.4569 | 2.7 | 17.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.15385 | 0.27957 | 0.36215 | 14.6 | 0.75 +Output | 10.573 | 10.784 | 10.994 | 4.8 | 29.03 +Modify | 19.48 | 19.707 | 19.925 | 3.7 | 53.06 +Other | | 0.02255 | | | 0.06 + +Nlocal: 1445 ave 1445 max 1445 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 555 ave 555 max 555 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 23120 ave 23120 max 23120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 92480 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:37 diff --git a/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..3af058baf721c59a57e61971e1211bee9a8e9305 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1,6006 @@ +Cobalt EAM potential: G. P. Purja Pun and Y. Mishin, Phys. Rev. B xx, 004100 (2012) (in press) +Data below r = 1.5 A is extrapolated. F(Rho) data not extrapolated. +Created on Wed Sep 26 17:29:54 2012 +1 Co +10000 4.788742913000000e-04 10000 6.499539000000001e-04 6.499539000000000e+00 +27 5.893320000000000e+01 2.507000000000000e+00 hcp + -1.680303080000000e-02 -1.879913964471138e-02 -2.091739081044659e-02 -2.303564197615629e-02 -2.503175082079116e-02 + -2.681996612041136e-02 -2.846010103933253e-02 -3.003179469400266e-02 -3.154842562124295e-02 -3.300931506782415e-02 + -3.442381570000001e-02 -3.580233366714632e-02 -3.714945763166951e-02 -3.846832763111274e-02 -3.976210669053554e-02 + -4.103374908125148e-02 -4.228535107207521e-02 -4.351872320172212e-02 -4.473539109100971e-02 -4.593674531110434e-02 + -4.712392115246503e-02 -4.829795108118731e-02 -4.945971154662068e-02 -5.061001094949964e-02 -5.174954151284258e-02 + -5.287894548568519e-02 -5.399878139884967e-02 -5.510957102742049e-02 -5.621177284174523e-02 -5.730581735016625e-02 + -5.839208651773948e-02 -5.947094067448531e-02 -6.054270215356945e-02 -6.160767623453070e-02 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2.671593859185241e-07 2.498478511400059e-07 2.333896726605378e-07 2.177564985206194e-07 2.029204500538344e-07 + 1.888541210793108e-07 1.755305458522738e-07 1.629232393506973e-07 1.510062144201093e-07 1.397539174372155e-07 + 1.291412703741045e-07 1.191437050672961e-07 1.097370923617762e-07 1.008977778162274e-07 9.260259669902208e-08 + 8.482883141984319e-08 7.755426670738778e-08 7.075715683240311e-08 6.441620467100832e-08 5.851063608240125e-08 + 5.302013495440350e-08 4.792483459927075e-08 4.320538955913144e-08 3.884291294265582e-08 3.481898425658018e-08 + 3.111569527451850e-08 2.771559342817648e-08 2.460171067137196e-08 2.175758348333717e-08 1.916719757773861e-08 + 1.681503457183268e-08 1.468607978947252e-08 1.276576812429566e-08 1.104003874048358e-08 9.495328649625366e-09 + 8.118528715645258e-09 6.897042498203040e-09 5.818760232281117e-09 4.872032311209139e-09 4.045732447740840e-09 + 3.329210679517489e-09 2.712284881132093e-09 2.185301687016959e-09 1.739076161987666e-09 1.364901589086205e-09 + 1.054599065845252e-09 8.004535320102697e-10 5.952414597054672e-10 4.322622496028902e-10 3.052766304104823e-10 + 2.085502003918036e-10 1.368642901349301e-10 8.546164059834664e-11 5.010215808832263e-11 2.705311520847365e-11 + 1.304599438344934e-11 5.339090781311160e-12 1.692041320615927e-12 3.321208355096226e-13 6.781366937015517e-15 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat new file mode 100644 index 0000000000000000000000000000000000000000..dce45c090dfb92ea3d9dd2c31fe925df9dc1bc01 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fcc_cobalt.dat @@ -0,0 +1,5 @@ +2.503 0.01476 +3.54 0.001497 +4.33 0.001578 +5.01 -0.001224 +5.597 0.000354 diff --git a/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..09be6db3e4de0ed5b564fdcc460c0ba3d9efbdb2 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/exchange_fit_fcc_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_cobalt.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc new file mode 100644 index 0000000000000000000000000000000000000000..fd6833727bebf8b13f795cfdec73100f8fc8a6f2 --- /dev/null +++ b/examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc @@ -0,0 +1,63 @@ +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..d832b0001a894877a2e512db25db55f4676ac61a --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000651121 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94112 95.094679 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94071 81.578321 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93912 62.802727 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93551 43.35108 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92942 27.749821 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92118 19.149389 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91199 18.453387 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.90364 24.249423 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89806 33.548008 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89668 42.973172 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.9 49.902539 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90735 53.166772 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91706 53.153416 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.92692 51.377187 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.9348 49.725449 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.93921 49.663576 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93974 51.681567 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.937 55.166554 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.93239 58.718232 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92755 60.75567 -2372.4636 +Loop time of 4.1303 on 1 procs for 1000 steps with 500 atoms + +Performance: 2.092 ns/day, 11.473 hours/ns, 242.113 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.142 | 2.142 | 2.142 | 0.0 | 51.86 +Neigh | 0.0094573 | 0.0094573 | 0.0094573 | 0.0 | 0.23 +Comm | 0.023293 | 0.023293 | 0.023293 | 0.0 | 0.56 +Output | 0.00031972 | 0.00031972 | 0.00031972 | 0.0 | 0.01 +Modify | 1.9488 | 1.9488 | 1.9488 | 0.0 | 47.18 +Other | | 0.006488 | | | 0.16 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 24065 ave 24065 max 24065 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 48130 ave 48130 max 48130 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48130 +Ave neighs/atom = 96.26 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..358d7cfc7ab3c195d3056dc21fcbc358b18ac48e --- /dev/null +++ b/examples/SPIN/cobalt_fcc/log.11May18.spin.cobalt_fcc.g++.4 @@ -0,0 +1,142 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.54 +Lattice spacing in x,y,z = 3.54 3.54 3.54 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.7 17.7 17.7) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000240088 secs + +# setting mass, mag. moments, and interactions for fcc cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix_modify 1 energy yes + +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +thermo_style custom f_1 + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time f_1 v_magx v_magy v_magnorm v_emag temp etotal +thermo 50 + +#compute outsp all property/atom spx spy spz sp fmx fmy fmz +#dump 100 all custom 1 dump_cobalt_fcc.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.163 | 5.163 | 5.163 Mbytes +Step Time f_1 v_magx v_magy v_magnorm v_emag Temp TotEng + 0 0 0.049785486 0 0 1 -187.94116 100.00543 -2372.4636 + 50 0.005 0.049785486 0 0 1 -187.94101 95.174807 -2372.4636 + 100 0.01 0.049785486 0 0 1 -187.94029 81.854304 -2372.4636 + 150 0.015 0.049785486 0 0 1 -187.93834 63.270938 -2372.4636 + 200 0.02 0.049785486 0 0 1 -187.93446 43.867262 -2372.4636 + 250 0.025 0.049785486 0 0 1 -187.92831 28.075261 -2372.4636 + 300 0.03 0.049785486 0 0 1 -187.92031 19.046222 -2372.4636 + 350 0.035 0.049785486 0 0 1 -187.91161 17.79071 -2372.4636 + 400 0.04 0.049785486 0 0 1 -187.9039 23.079994 -2372.4636 + 450 0.045 0.049785486 0 0 1 -187.89895 32.127316 -2372.4636 + 500 0.05 0.049785486 0 0 1 -187.89801 41.709644 -2372.4636 + 550 0.055 0.049785486 0 0 1 -187.90146 49.246292 -2372.4636 + 600 0.06 0.049785486 0 0 1 -187.90859 53.465535 -2372.4636 + 650 0.065 0.049785486 0 0 1 -187.91778 54.522857 -2372.4636 + 700 0.07 0.049785486 0 0 1 -187.9269 53.635521 -2372.4636 + 750 0.075 0.049785486 0 0 1 -187.93396 52.419678 -2372.4636 + 800 0.08 0.049785486 0 0 1 -187.9376 52.176558 -2372.4636 + 850 0.085 0.049785486 0 0 1 -187.93744 53.380592 -2372.4636 + 900 0.09 0.049785486 0 0 1 -187.93412 55.551378 -2372.4636 + 950 0.095 0.049785486 0 0 1 -187.92902 57.540047 -2372.4636 + 1000 0.1 0.049785486 0 0 1 -187.92378 58.088674 -2372.4636 +Loop time of 1.71411 on 4 procs for 1000 steps with 500 atoms + +Performance: 5.041 ns/day, 4.761 hours/ns, 583.392 timesteps/s +97.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.54717 | 0.57392 | 0.58784 | 2.1 | 33.48 +Neigh | 0.0023484 | 0.0025793 | 0.0026793 | 0.3 | 0.15 +Comm | 0.058548 | 0.073335 | 0.10006 | 5.9 | 4.28 +Output | 0.00042272 | 0.00079203 | 0.0018559 | 0.0 | 0.05 +Modify | 1.0577 | 1.0611 | 1.0625 | 0.2 | 61.90 +Other | | 0.00239 | | | 0.14 + +Nlocal: 125 ave 133 max 116 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 1099 ave 1108 max 1091 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 6032.5 ave 6417 max 5489 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 12065 ave 13062 max 10970 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 48260 +Ave neighs/atom = 96.52 +Neighbor list builds = 6 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000000000000000000000000000000000..6a47c9eebef2dc333daa871fc882f2afc038bd4c --- /dev/null +++ b/examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..fa7dba417e94468ce01ea5225db9a00aed2205dd --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat new file mode 100644 index 0000000000000000000000000000000000000000..0968fa3edb793657830c65c64e99656de20a8274 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/exchange_fit_hcp_co/exchange_hcp_co.dat @@ -0,0 +1,9 @@ +2.25569176882662 73.37931034482759 +2.3817863397548162 47.99999999999999 +2.4518388791593697 34.39080459770115 +2.507880910683012 31.816091954022987 +2.5359019264448337 28.137931034482747 +2.5779334500875657 25.011494252873554 +2.6339754816112086 19.126436781609186 +2.760070052539404 13.241379310344826 +3.5446584938704033 6.068965517241367 diff --git a/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp new file mode 100644 index 0000000000000000000000000000000000000000..35aa1df86c4a2c2bdfff40f3e35f032939311b90 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp @@ -0,0 +1,59 @@ +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 +#set group all spin 1.72 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 20000 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..4bb513de18886c91f1a4ef0fb3909e188d998489 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.1 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000801802 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.401 | 7.401 | 7.401 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29714 99.845593 -2375.8943 + 20 0.002 1 -187.30356 99.367234 -2375.8943 + 30 0.003 1 -187.31419 98.573996 -2375.8943 + 40 0.004 1 -187.32896 97.472027 -2375.8943 + 50 0.005 1 -187.34772 96.069944 -2375.8943 + 60 0.006 1 -187.37032 94.378764 -2375.8943 + 70 0.007 1 -187.39656 92.411827 -2375.8943 + 80 0.008 1 -187.4262 90.184697 -2375.8943 + 90 0.009 1 -187.459 87.715037 -2375.8943 + 100 0.01 1 -187.49466 85.022479 -2375.8943 + 110 0.011 1 -187.53289 82.128462 -2375.8943 + 120 0.012 1 -187.57334 79.05606 -2375.8943 + 130 0.013 1 -187.61568 75.82979 -2375.8943 + 140 0.014 1 -187.65953 72.475403 -2375.8943 + 150 0.015 1 -187.70453 69.019658 -2375.8943 + 160 0.016 1 -187.75028 65.490086 -2375.8943 + 170 0.017 1 -187.79642 61.914735 -2375.8943 + 180 0.018 1 -187.84254 58.321911 -2375.8943 + 190 0.019 1 -187.88828 54.739907 -2375.8943 + 200 0.02 1 -187.93324 51.196728 -2375.8943 + 210 0.021 1 -187.97708 47.719812 -2375.8943 + 220 0.022 1 -188.01947 44.335762 -2375.8943 + 230 0.023 1 -188.06003 41.07007 -2375.8943 + 240 0.024 1 -188.09853 37.946852 -2375.8944 + 250 0.025 1 -188.13457 34.988599 -2375.8944 + 260 0.026 1 -188.16795 32.215943 -2375.8944 + 270 0.027 1 -188.19851 29.647465 -2375.8944 + 280 0.028 1 -188.22593 27.299481 -2375.8944 + 290 0.029 1 -188.25011 25.185896 -2375.8944 + 300 0.03 1 -188.27095 23.318075 -2375.8945 + 310 0.031 1 -188.2883 21.70475 -2375.8945 + 320 0.032 1 -188.30213 20.35194 -2375.8945 + 330 0.033 1 -188.31251 19.262946 -2375.8945 + 340 0.034 1 -188.31928 18.438347 -2375.8945 + 350 0.035 1 -188.32258 17.876036 -2375.8945 + 360 0.036 1 -188.32249 17.571322 -2375.8945 + 370 0.037 1 -188.31913 17.517032 -2375.8945 + 380 0.038 1 -188.31264 17.703653 -2375.8945 + 390 0.039 1 -188.30321 18.119513 -2375.8945 + 400 0.04 1 -188.29102 18.750969 -2375.8945 + 410 0.041 1 -188.2763 19.582631 -2375.8945 + 420 0.042 1 -188.25929 20.597597 -2375.8945 + 430 0.043 1 -188.24025 21.777699 -2375.8945 + 440 0.044 1 -188.21945 23.103765 -2375.8945 + 450 0.045 1 -188.19719 24.555878 -2375.8946 + 460 0.046 1 -188.17368 26.113643 -2375.8946 + 470 0.047 1 -188.1493 27.756439 -2375.8946 + 480 0.048 1 -188.12429 29.463677 -2375.8946 + 490 0.049 1 -188.09895 31.21504 -2375.8946 + 500 0.05 1 -188.07354 32.990713 -2375.8946 + 510 0.051 1 -188.04832 34.771601 -2375.8945 + 520 0.052 1 -188.02358 36.539517 -2375.8945 + 530 0.053 1 -187.99951 38.27736 -2375.8945 + 540 0.054 1 -187.97636 39.969275 -2375.8945 + 550 0.055 1 -187.95437 41.600775 -2375.8945 + 560 0.056 1 -187.93364 43.158863 -2375.8944 + 570 0.057 1 -187.9144 44.632119 -2375.8944 + 580 0.058 1 -187.89669 46.010765 -2375.8944 + 590 0.059 1 -187.88074 47.286714 -2375.8944 + 600 0.06 1 -187.86658 48.453573 -2375.8944 + 610 0.061 1 -187.85422 49.506668 -2375.8943 + 620 0.062 1 -187.84377 50.443021 -2375.8943 + 630 0.063 1 -187.8352 51.261297 -2375.8943 + 640 0.064 1 -187.8285 51.961764 -2375.8943 + 650 0.065 1 -187.8236 52.54622 -2375.8943 + 660 0.066 1 -187.8205 53.017899 -2375.8943 + 670 0.067 1 -187.81909 53.381374 -2375.8943 + 680 0.068 1 -187.81926 53.64244 -2375.8943 + 690 0.069 1 -187.82092 53.807997 -2375.8943 + 700 0.07 1 -187.82391 53.885909 -2375.8943 + 710 0.071 1 -187.82814 53.884865 -2375.8943 + 720 0.072 1 -187.83339 53.814238 -2375.8943 + 730 0.073 1 -187.83952 53.68392 -2375.8943 + 740 0.074 1 -187.84635 53.504185 -2375.8943 + 750 0.075 1 -187.85375 53.285525 -2375.8943 + 760 0.076 1 -187.86153 53.038494 -2375.8943 + 770 0.077 1 -187.86952 52.773567 -2375.8943 + 780 0.078 1 -187.87758 52.500994 -2375.8943 + 790 0.079 1 -187.88549 52.230655 -2375.8943 + 800 0.08 1 -187.89313 51.971933 -2375.8943 + 810 0.081 1 -187.90035 51.733593 -2375.8943 + 820 0.082 1 -187.90702 51.523671 -2375.8943 + 830 0.083 1 -187.91302 51.349376 -2375.8943 + 840 0.084 1 -187.91824 51.217006 -2375.8943 + 850 0.085 1 -187.9226 51.131875 -2375.8943 + 860 0.086 1 -187.92602 51.098259 -2375.8943 + 870 0.087 1 -187.92844 51.119356 -2375.8943 + 880 0.088 1 -187.92979 51.197261 -2375.8943 + 890 0.089 1 -187.93011 51.332955 -2375.8943 + 900 0.09 1 -187.92937 51.526314 -2375.8943 + 910 0.091 1 -187.92757 51.77613 -2375.8943 + 920 0.092 1 -187.92475 52.080145 -2375.8943 + 930 0.093 1 -187.92096 52.435106 -2375.8943 + 940 0.094 1 -187.91624 52.836825 -2375.8943 + 950 0.095 1 -187.91068 53.280251 -2375.8943 + 960 0.096 1 -187.90435 53.759559 -2375.8943 + 970 0.097 1 -187.89734 54.268246 -2375.8943 + 980 0.098 1 -187.88981 54.799223 -2375.8943 + 990 0.099 1 -187.88185 55.344928 -2375.8943 + 1000 0.1 1 -187.87357 55.897438 -2375.8943 + 1010 0.101 1 -187.86511 56.448585 -2375.8943 + 1020 0.102 1 -187.8566 56.990069 -2375.8943 + 1030 0.103 1 -187.84817 57.513575 -2375.8943 + 1040 0.104 1 -187.83995 58.010887 -2375.8943 + 1050 0.105 1 -187.83208 58.474004 -2375.8943 + 1060 0.106 1 -187.8247 58.89524 -2375.8943 + 1070 0.107 1 -187.81789 59.267328 -2375.8943 + 1080 0.108 1 -187.81177 59.583518 -2375.8943 + 1090 0.109 1 -187.80646 59.837665 -2375.8943 + 1100 0.11 1 -187.80204 60.024306 -2375.8943 + 1110 0.111 1 -187.79861 60.138734 -2375.8943 + 1120 0.112 1 -187.79625 60.177056 -2375.8943 + 1130 0.113 1 -187.79497 60.136244 -2375.8943 + 1140 0.114 1 -187.79485 60.014176 -2375.8943 + 1150 0.115 1 -187.7959 59.809665 -2375.8943 + 1160 0.116 1 -187.79811 59.52248 -2375.8943 + 1170 0.117 1 -187.80157 59.153353 -2375.8943 + 1180 0.118 1 -187.80618 58.703971 -2375.8943 + 1190 0.119 1 -187.81193 58.176956 -2375.8943 + 1200 0.12 1 -187.81879 57.575849 -2375.8943 + 1210 0.121 1 -187.82668 56.905072 -2375.8943 + 1220 0.122 1 -187.83554 56.169878 -2375.8943 + 1230 0.123 1 -187.84528 55.376297 -2375.8943 + 1240 0.124 1 -187.85581 54.53107 -2375.8943 + 1250 0.125 1 -187.86702 53.641573 -2375.8943 + 1260 0.126 1 -187.8788 52.715739 -2375.8943 + 1270 0.127 1 -187.89103 51.761969 -2375.8943 + 1280 0.128 1 -187.90358 50.789036 -2375.8943 + 1290 0.129 1 -187.91632 49.805988 -2375.8943 + 1300 0.13 1 -187.92911 48.822045 -2375.8943 + 1310 0.131 1 -187.94182 47.846491 -2375.8943 + 1320 0.132 1 -187.95428 46.888574 -2375.8943 + 1330 0.133 1 -187.96643 45.957394 -2375.8943 + 1340 0.134 1 -187.9781 45.061794 -2375.8943 + 1350 0.135 1 -187.9892 44.210263 -2375.8943 + 1360 0.136 1 -187.99955 43.410832 -2375.8943 + 1370 0.137 1 -188.00907 42.670979 -2375.8943 + 1380 0.138 1 -188.01767 41.997547 -2375.8943 + 1390 0.139 1 -188.02525 41.396655 -2375.8943 + 1400 0.14 1 -188.03177 40.873631 -2375.8944 + 1410 0.141 1 -188.03711 40.432952 -2375.8944 + 1420 0.142 1 -188.04124 40.078172 -2375.8944 + 1430 0.143 1 -188.04413 39.811902 -2375.8944 + 1440 0.144 1 -188.04575 39.635775 -2375.8944 + 1450 0.145 1 -188.04607 39.550435 -2375.8943 + 1460 0.146 1 -188.04515 39.555512 -2375.8943 + 1470 0.147 1 -188.04298 39.649651 -2375.8943 + 1480 0.148 1 -188.03961 39.830523 -2375.8943 + 1490 0.149 1 -188.03508 40.094865 -2375.8943 + 1500 0.15 1 -188.02944 40.438519 -2375.8943 + 1510 0.151 1 -188.02275 40.856491 -2375.8943 + 1520 0.152 1 -188.01515 41.343019 -2375.8943 + 1530 0.153 1 -188.00671 41.891643 -2375.8943 + 1540 0.154 1 -187.99753 42.495295 -2375.8943 + 1550 0.155 1 -187.98772 43.14639 -2375.8943 + 1560 0.156 1 -187.9774 43.836918 -2375.8943 + 1570 0.157 1 -187.9667 44.558553 -2375.8943 + 1580 0.158 1 -187.95576 45.302751 -2375.8943 + 1590 0.159 1 -187.94466 46.060862 -2375.8943 + 1600 0.16 1 -187.93356 46.824226 -2375.8943 + 1610 0.161 1 -187.92257 47.584289 -2375.8943 + 1620 0.162 1 -187.91183 48.332703 -2375.8943 + 1630 0.163 1 -187.90145 49.061422 -2375.8943 + 1640 0.164 1 -187.89155 49.762798 -2375.8943 + 1650 0.165 1 -187.88222 50.429671 -2375.8943 + 1660 0.166 1 -187.87357 51.055445 -2375.8943 + 1670 0.167 1 -187.86569 51.634167 -2375.8943 + 1680 0.168 1 -187.85864 52.160588 -2375.8943 + 1690 0.169 1 -187.85249 52.630219 -2375.8943 + 1700 0.17 1 -187.8473 53.039377 -2375.8943 + 1710 0.171 1 -187.84311 53.385221 -2375.8943 + 1720 0.172 1 -187.83994 53.665778 -2375.8943 + 1730 0.173 1 -187.83781 53.879954 -2375.8943 + 1740 0.174 1 -187.83671 54.027539 -2375.8943 + 1750 0.175 1 -187.83663 54.109201 -2375.8943 + 1760 0.176 1 -187.83753 54.126472 -2375.8943 + 1770 0.177 1 -187.83941 54.081708 -2375.8943 + 1780 0.178 1 -187.8422 53.97806 -2375.8943 + 1790 0.179 1 -187.84584 53.819424 -2375.8943 + 1800 0.18 1 -187.85025 53.610389 -2375.8943 + 1810 0.181 1 -187.85535 53.356163 -2375.8943 + 1820 0.182 1 -187.86105 53.06251 -2375.8943 + 1830 0.183 1 -187.86723 52.735671 -2375.8943 + 1840 0.184 1 -187.87384 52.382262 -2375.8943 + 1850 0.185 1 -187.88075 52.009201 -2375.8943 + 1860 0.186 1 -187.88784 51.623613 -2375.8943 + 1870 0.187 1 -187.89501 51.232726 -2375.8943 + 1880 0.188 1 -187.90214 50.843782 -2375.8943 + 1890 0.189 1 -187.90912 50.463929 -2375.8943 + 1900 0.19 1 -187.91585 50.100133 -2375.8943 + 1910 0.191 1 -187.92222 49.759075 -2375.8943 + 1920 0.192 1 -187.92814 49.447064 -2375.8943 + 1930 0.193 1 -187.93351 49.169949 -2375.8943 + 1940 0.194 1 -187.93826 48.933036 -2375.8943 + 1950 0.195 1 -187.94232 48.741013 -2375.8943 + 1960 0.196 1 -187.94561 48.597888 -2375.8943 + 1970 0.197 1 -187.94809 48.506926 -2375.8943 + 1980 0.198 1 -187.94972 48.470605 -2375.8943 + 1990 0.199 1 -187.95047 48.490576 -2375.8943 + 2000 0.2 1 -187.95033 48.567643 -2375.8943 +Loop time of 10.5391 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.640 ns/day, 14.638 hours/ns, 189.770 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.9958 | 4.9958 | 4.9958 | 0.0 | 47.40 +Neigh | 0.020741 | 0.020741 | 0.020741 | 0.0 | 0.20 +Comm | 0.05899 | 0.05899 | 0.05899 | 0.0 | 0.56 +Output | 1.1598 | 1.1598 | 1.1598 | 0.0 | 11.00 +Modify | 4.2885 | 4.2885 | 4.2885 | 0.0 | 40.69 +Other | | 0.01522 | | | 0.14 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2444 ave 2444 max 2444 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 27041 ave 27041 max 27041 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 54082 ave 54082 max 54082 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 54082 +Ave neighs/atom = 108.164 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..4e7e6b1b976dbccb98b136c39daa3ebc0689e3b6 --- /dev/null +++ b/examples/SPIN/cobalt_hcp/log.11May18.spin.cobalt_hcp.g++.4 @@ -0,0 +1,318 @@ +LAMMPS (11 May 2018) +# hcp cobalt in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000241518 secs + +# setting mass, mag. moments, and interactions for hcp cobalt + +mass 1 58.93 + +#set group all spin/random 31 1.72 +set group all spin 1.72 0.0 0.0 1.0 + 500 settings made for spin +velocity all create 100 4928459 rot yes dist gaussian + +#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0 +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 +#pair_coeff * * spin/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652 + + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 +fix 3 all nve/spin lattice yes + +timestep 0.0001 + + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 10 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.59954 + ghost atom cutoff = 6.59954 + binsize = 3.29977, bins = 4 7 7 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.314 | 7.314 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 1 -187.29499 100.00543 -2375.8943 + 10 0.001 1 -187.29721 99.841045 -2375.8943 + 20 0.002 1 -187.30385 99.349208 -2375.8943 + 30 0.003 1 -187.31485 98.533905 -2375.8943 + 40 0.004 1 -187.33011 97.401749 -2375.8943 + 50 0.005 1 -187.34949 95.961938 -2375.8943 + 60 0.006 1 -187.37283 94.22618 -2375.8943 + 70 0.007 1 -187.39992 92.208606 -2375.8943 + 80 0.008 1 -187.43051 89.92566 -2375.8943 + 90 0.009 1 -187.46434 87.39597 -2375.8943 + 100 0.01 1 -187.5011 84.640195 -2375.8943 + 110 0.011 1 -187.54047 81.680862 -2375.8943 + 120 0.012 1 -187.5821 78.542172 -2375.8943 + 130 0.013 1 -187.62564 75.249797 -2375.8943 + 140 0.014 1 -187.67069 71.830656 -2375.8943 + 150 0.015 1 -187.71686 68.312673 -2375.8943 + 160 0.016 1 -187.76377 64.724523 -2375.8943 + 170 0.017 1 -187.81099 61.095365 -2375.8943 + 180 0.018 1 -187.85814 57.454566 -2375.8943 + 190 0.019 1 -187.90481 53.831412 -2375.8943 + 200 0.02 1 -187.95061 50.254822 -2375.8943 + 210 0.021 1 -187.99517 46.753056 -2375.8943 + 220 0.022 1 -188.03812 43.353428 -2375.8943 + 230 0.023 1 -188.07913 40.082023 -2375.8943 + 240 0.024 1 -188.11787 36.963429 -2375.8943 + 250 0.025 1 -188.15409 34.020481 -2375.8943 + 260 0.026 1 -188.1875 31.27403 -2375.8943 + 270 0.027 1 -188.21782 28.74271 -2375.8943 + 280 0.028 1 -188.2449 26.44276 -2375.8943 + 290 0.029 1 -188.26857 24.387875 -2375.8943 + 300 0.03 1 -188.28877 22.589076 -2375.8944 + 310 0.031 1 -188.30529 21.054615 -2375.8944 + 320 0.032 1 -188.31814 19.789913 -2375.8944 + 330 0.033 1 -188.3273 18.797563 -2375.8944 + 340 0.034 1 -188.33284 18.077336 -2375.8944 + 350 0.035 1 -188.33478 17.626237 -2375.8945 + 360 0.036 1 -188.33319 17.438611 -2375.8945 + 370 0.037 1 -188.32824 17.506247 -2375.8945 + 380 0.038 1 -188.32007 17.818564 -2375.8945 + 390 0.039 1 -188.30888 18.362769 -2375.8945 + 400 0.04 1 -188.2949 19.124086 -2375.8945 + 410 0.041 1 -188.27837 20.085983 -2375.8945 + 420 0.042 1 -188.25957 21.230423 -2375.8945 + 430 0.043 1 -188.23868 22.538112 -2375.8945 + 440 0.044 1 -188.21604 23.988778 -2375.8945 + 450 0.045 1 -188.19195 25.561447 -2375.8945 + 460 0.046 1 -188.16672 27.234703 -2375.8945 + 470 0.047 1 -188.14064 28.986964 -2375.8946 + 480 0.048 1 -188.11402 30.796738 -2375.8946 + 490 0.049 1 -188.08713 32.642869 -2375.8945 + 500 0.05 1 -188.06032 34.504776 -2375.8945 + 510 0.051 1 -188.03383 36.362662 -2375.8945 + 520 0.052 1 -188.00793 38.197721 -2375.8945 + 530 0.053 1 -187.98284 39.992314 -2375.8945 + 540 0.054 1 -187.95884 41.730127 -2375.8945 + 550 0.055 1 -187.93612 43.396298 -2375.8945 + 560 0.056 1 -187.91489 44.97754 -2375.8945 + 570 0.057 1 -187.89524 46.462224 -2375.8945 + 580 0.058 1 -187.87735 47.840443 -2375.8945 + 590 0.059 1 -187.8613 49.104064 -2375.8945 + 600 0.06 1 -187.84719 50.246744 -2375.8945 + 610 0.061 1 -187.83509 51.26393 -2375.8944 + 620 0.062 1 -187.82506 52.152839 -2375.8944 + 630 0.063 1 -187.81706 52.912413 -2375.8944 + 640 0.064 1 -187.81109 53.543272 -2375.8944 + 650 0.065 1 -187.80708 54.047636 -2375.8944 + 660 0.066 1 -187.80499 54.429234 -2375.8944 + 670 0.067 1 -187.8047 54.693202 -2375.8944 + 680 0.068 1 -187.80613 54.845965 -2375.8944 + 690 0.069 1 -187.80914 54.895106 -2375.8944 + 700 0.07 1 -187.81356 54.849238 -2375.8944 + 710 0.071 1 -187.81923 54.71786 -2375.8943 + 720 0.072 1 -187.82608 54.511181 -2375.8943 + 730 0.073 1 -187.83388 54.239987 -2375.8943 + 740 0.074 1 -187.84244 53.91548 -2375.8943 + 750 0.075 1 -187.85158 53.549112 -2375.8943 + 760 0.076 1 -187.86112 53.152433 -2375.8943 + 770 0.077 1 -187.87086 52.736925 -2375.8943 + 780 0.078 1 -187.88063 52.313858 -2375.8943 + 790 0.079 1 -187.89026 51.894138 -2375.8943 + 800 0.08 1 -187.89958 51.488169 -2375.8943 + 810 0.081 1 -187.90842 51.105725 -2375.8943 + 820 0.082 1 -187.91663 50.755829 -2375.8943 + 830 0.083 1 -187.92411 50.446651 -2375.8943 + 840 0.084 1 -187.93071 50.185404 -2375.8943 + 850 0.085 1 -187.93637 49.978262 -2375.8943 + 860 0.086 1 -187.94099 49.830307 -2375.8943 + 870 0.087 1 -187.9445 49.745473 -2375.8943 + 880 0.088 1 -187.94685 49.726517 -2375.8943 + 890 0.089 1 -187.94802 49.774999 -2375.8943 + 900 0.09 1 -187.94799 49.891282 -2375.8943 + 910 0.091 1 -187.94678 50.074549 -2375.8943 + 920 0.092 1 -187.94441 50.322833 -2375.8943 + 930 0.093 1 -187.94093 50.633063 -2375.8943 + 940 0.094 1 -187.93639 51.001126 -2375.8943 + 950 0.095 1 -187.93089 51.421938 -2375.8943 + 960 0.096 1 -187.9245 51.889531 -2375.8943 + 970 0.097 1 -187.91733 52.397148 -2375.8943 + 980 0.098 1 -187.9095 52.937345 -2375.8943 + 990 0.099 1 -187.90113 53.502108 -2375.8943 + 1000 0.1 1 -187.89236 54.082966 -2375.8943 + 1010 0.101 1 -187.88332 54.671115 -2375.8943 + 1020 0.102 1 -187.87415 55.257545 -2375.8943 + 1030 0.103 1 -187.86501 55.833162 -2375.8943 + 1040 0.104 1 -187.85602 56.388915 -2375.8943 + 1050 0.105 1 -187.84734 56.915918 -2375.8943 + 1060 0.106 1 -187.83909 57.405575 -2375.8943 + 1070 0.107 1 -187.83143 57.849686 -2375.8943 + 1080 0.108 1 -187.82446 58.240564 -2375.8943 + 1090 0.109 1 -187.8183 58.571132 -2375.8943 + 1100 0.11 1 -187.81306 58.835016 -2375.8943 + 1110 0.111 1 -187.80883 59.026633 -2375.8943 + 1120 0.112 1 -187.8057 59.141258 -2375.8943 + 1130 0.113 1 -187.80372 59.17509 -2375.8943 + 1140 0.114 1 -187.80295 59.125305 -2375.8943 + 1150 0.115 1 -187.80341 58.990092 -2375.8943 + 1160 0.116 1 -187.80515 58.76868 -2375.8943 + 1170 0.117 1 -187.80814 58.461352 -2375.8943 + 1180 0.118 1 -187.81244 58.069457 -2375.8943 + 1190 0.119 1 -187.81794 57.595377 -2375.8944 + 1200 0.12 1 -187.82458 57.042514 -2375.8944 + 1210 0.121 1 -187.83233 56.415256 -2375.8944 + 1220 0.122 1 -187.84112 55.718931 -2375.8944 + 1230 0.123 1 -187.85086 54.959744 -2375.8944 + 1240 0.124 1 -187.86145 54.144707 -2375.8944 + 1250 0.125 1 -187.87277 53.281562 -2375.8944 + 1260 0.126 1 -187.88471 52.378686 -2375.8944 + 1270 0.127 1 -187.89713 51.445 -2375.8944 + 1280 0.128 1 -187.9099 50.489858 -2375.8944 + 1290 0.129 1 -187.92288 49.522943 -2375.8944 + 1300 0.13 1 -187.93591 48.554147 -2375.8944 + 1310 0.131 1 -187.94886 47.593456 -2375.8944 + 1320 0.132 1 -187.96157 46.650829 -2375.8944 + 1330 0.133 1 -187.97391 45.736073 -2375.8944 + 1340 0.134 1 -187.98573 44.858733 -2375.8944 + 1350 0.135 1 -187.99691 44.027964 -2375.8944 + 1360 0.136 1 -188.00731 43.252426 -2375.8944 + 1370 0.137 1 -188.01678 42.540178 -2375.8943 + 1380 0.138 1 -188.02529 41.898568 -2375.8943 + 1390 0.139 1 -188.0327 41.334152 -2375.8943 + 1400 0.14 1 -188.03894 40.852606 -2375.8943 + 1410 0.141 1 -188.04396 40.45866 -2375.8944 + 1420 0.142 1 -188.04768 40.156041 -2375.8944 + 1430 0.143 1 -188.05007 39.947416 -2375.8944 + 1440 0.144 1 -188.05107 39.834367 -2375.8944 + 1450 0.145 1 -188.0507 39.817378 -2375.8944 + 1460 0.146 1 -188.04898 39.895828 -2375.8944 + 1470 0.147 1 -188.04595 40.068005 -2375.8945 + 1480 0.148 1 -188.04164 40.331129 -2375.8945 + 1490 0.149 1 -188.03603 40.681394 -2375.8945 + 1500 0.15 1 -188.02929 41.114003 -2375.8945 + 1510 0.151 1 -188.02148 41.623259 -2375.8945 + 1520 0.152 1 -188.0127 42.20263 -2375.8945 + 1530 0.153 1 -188.00302 42.844846 -2375.8945 + 1540 0.154 1 -187.99255 43.541977 -2375.8945 + 1550 0.155 1 -187.98148 44.285554 -2375.8945 + 1560 0.156 1 -187.96989 45.066666 -2375.8945 + 1570 0.157 1 -187.95793 45.876084 -2375.8945 + 1580 0.158 1 -187.94574 46.704378 -2375.8945 + 1590 0.159 1 -187.93346 47.542032 -2375.8945 + 1600 0.16 1 -187.92122 48.379564 -2375.8945 + 1610 0.161 1 -187.90916 49.207642 -2375.8945 + 1620 0.162 1 -187.89742 50.0172 -2375.8945 + 1630 0.163 1 -187.88613 50.799541 -2375.8945 + 1640 0.164 1 -187.87536 51.546446 -2375.8944 + 1650 0.165 1 -187.86531 52.250265 -2375.8944 + 1660 0.166 1 -187.85604 52.904001 -2375.8944 + 1670 0.167 1 -187.84765 53.501394 -2375.8944 + 1680 0.168 1 -187.84021 54.036987 -2375.8944 + 1690 0.169 1 -187.83379 54.506178 -2375.8944 + 1700 0.17 1 -187.82846 54.905273 -2375.8944 + 1710 0.171 1 -187.82424 55.231514 -2375.8944 + 1720 0.172 1 -187.82117 55.483104 -2375.8944 + 1730 0.173 1 -187.81922 55.659221 -2375.8944 + 1740 0.174 1 -187.81843 55.760007 -2375.8944 + 1750 0.175 1 -187.81881 55.786556 -2375.8944 + 1760 0.176 1 -187.82029 55.740888 -2375.8944 + 1770 0.177 1 -187.82284 55.625916 -2375.8944 + 1780 0.178 1 -187.82639 55.445397 -2375.8944 + 1790 0.179 1 -187.83088 55.203871 -2375.8944 + 1800 0.18 1 -187.83623 54.906597 -2375.8944 + 1810 0.181 1 -187.84235 54.559471 -2375.8944 + 1820 0.182 1 -187.84913 54.168949 -2375.8944 + 1830 0.183 1 -187.85646 53.741952 -2375.8943 + 1840 0.184 1 -187.86424 53.28578 -2375.8943 + 1850 0.185 1 -187.87239 52.807988 -2375.8943 + 1860 0.186 1 -187.88077 52.3163 -2375.8943 + 1870 0.187 1 -187.88925 51.81851 -2375.8943 + 1880 0.188 1 -187.89772 51.322368 -2375.8943 + 1890 0.189 1 -187.90605 50.835483 -2375.8943 + 1900 0.19 1 -187.91415 50.365218 -2375.8943 + 1910 0.191 1 -187.92189 49.9186 -2375.8943 + 1920 0.192 1 -187.92917 49.502222 -2375.8943 + 1930 0.193 1 -187.93591 49.122167 -2375.8943 + 1940 0.194 1 -187.94198 48.783928 -2375.8943 + 1950 0.195 1 -187.94737 48.492348 -2375.8943 + 1960 0.196 1 -187.95199 48.25154 -2375.8943 + 1970 0.197 1 -187.95576 48.064862 -2375.8943 + 1980 0.198 1 -187.95866 47.934875 -2375.8943 + 1990 0.199 1 -187.96065 47.863314 -2375.8943 + 2000 0.2 1 -187.96171 47.851079 -2375.8943 +Loop time of 4.40076 on 4 procs for 2000 steps with 500 atoms + +Performance: 3.927 ns/day, 6.112 hours/ns, 454.467 timesteps/s +96.2% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2934 | 1.3683 | 1.432 | 4.2 | 31.09 +Neigh | 0.005039 | 0.0053418 | 0.0054908 | 0.2 | 0.12 +Comm | 0.12642 | 0.1922 | 0.26891 | 11.6 | 4.37 +Output | 0.39256 | 0.40875 | 0.43431 | 2.5 | 9.29 +Modify | 2.395 | 2.4202 | 2.4352 | 1.0 | 54.99 +Other | | 0.006007 | | | 0.14 + +Nlocal: 125 ave 130 max 122 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 1324 ave 1330 max 1316 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 6747 ave 6959 max 6652 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +FullNghs: 13494 ave 14060 max 13186 min +Histogram: 2 0 0 1 0 0 0 0 0 1 + +Total # of neighbors = 53976 +Ave neighs/atom = 107.952 +Neighbor list builds = 12 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/iron/Fe_Mishin2006.eam.alloy b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..69231bb7eeed5677009482896fe520f4445413dd --- /dev/null +++ b/examples/SPIN/iron/Fe_Mishin2006.eam.alloy @@ -0,0 +1,15009 @@ +comment 1 +comment 2 +Converted by Ganga P Purja Pun using C++ code on Mon Nov 3 10:48:17 2014 +1 Fe +5001 2.400000000000000e-03 5001 1.134673400048920e-03 5.673367000244601e+00 +26 5.584700000000000e+01 2.855300000000000e+00 BCC + 0.000000000000000e+00 + -2.338738741480766e-02 + -4.628214468925276e-02 + -6.912258036387915e-02 + -9.175603963501618e-02 + -1.141497214000000e-01 + -1.363388222824136e-01 + -1.583226111166723e-01 + -1.800965752913192e-01 + -2.016645989796093e-01 + -2.230289901000000e-01 + -2.441907391820846e-01 + 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-2.316338735426513e-07 + -1.843129441850586e-07 + -1.446395043479685e-07 + -1.117434618507405e-07 + -8.480406305106530e-08 + -6.305553831873507e-08 + -4.578544870958251e-08 + -3.233089380928512e-08 + -2.208448022054805e-08 + -1.449165750478591e-08 + -9.047683233008124e-09 + -5.303766739728543e-09 + -2.863504097386866e-09 + -1.380623394721897e-09 + -5.650641971230870e-10 + -1.790372475752245e-10 + -3.511990521548007e-11 + -8.192061809269277e-13 + 0.000000000000000e+00 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat new file mode 100644 index 0000000000000000000000000000000000000000..58134f244466c5a60bb103b73e6f8ba61414e14b --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_bcc_iron.dat @@ -0,0 +1,5 @@ +2.4824 0.01948336 +2.8665 0.01109 +4.0538 -0.0002176 +4.753 -0.001714 +4.965 -0.001986 diff --git a/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..ccf84fc233bbc4a29bcc01ab4d6336e00ba2ab6d --- /dev/null +++ b/examples/SPIN/iron/exchange_fit_bcc_iron/exchange_fit.py @@ -0,0 +1,32 @@ +#Program fitting the exchange interaction +#Model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +#Definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +#Exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_bcc_iron.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +#Perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +#Print the fitted params +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +#Ploting the result +plt.xlabel('r_ij') +pylab.xlim([0,6.5]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/iron/fe_dd.dat b/examples/SPIN/iron/fe_dd.dat new file mode 100644 index 0000000000000000000000000000000000000000..a4b4c9a0d7c06a14f1a42cd33846405299e368a9 --- /dev/null +++ b/examples/SPIN/iron/fe_dd.dat @@ -0,0 +1,19 @@ + 6 8 + Optimal parameter set + 1 4.100199340884814 F + 2 1.565647547483517 F + 1 0.9332056681088162 T 3.000000000000000 + 2 -1.162558782567700 T 2.866666666666670 + 3 -0.3502026949249225 T 2.733333333333330 + 4 0.4287820835430028 T 2.600000000000000 + 5 4.907925057809273 T 2.400000000000000 + 6 -5.307049068415304 T 2.300000000000000 + 1 -0.1960674387419232 F 4.100000000000000 + 2 0.3687525935422963 F 3.800000000000000 + 3 -1.505333614924853 F 3.500000000000000 + 4 4.948907078156191 T 3.200000000000000 + 5 -4.894613262753399 T 2.900000000000000 + 6 3.468897724782442 T 2.600000000000000 + 7 -1.792218099820337 T 2.400000000000000 + 8 80.22069592246987 T 2.300000000000000 + diff --git a/examples/SPIN/iron/in.spin.iron b/examples/SPIN/iron/in.spin.iron new file mode 100644 index 0000000000000000000000000000000000000000..c2d5082cb6a27751627d72d850ed11ad8feade66 --- /dev/null +++ b/examples/SPIN/iron/in.spin.iron @@ -0,0 +1,56 @@ +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.1 b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..1b27478002833f74c99fc56572e8bc786c9f3b01 --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.1 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.000727415 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.319 | 7.319 | 7.319 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456974 9316.7659 96.663685 -0.86504718 3.1111957 -1070.7504 -1067.6392 + 100 0.01 0.076456983 9488.3743 86.965803 -0.88035771 2.7990619 -1070.4383 -1067.6392 + 150 0.015 0.076456973 9589.0566 72.421197 -0.8996913 2.3309324 -1069.9702 -1067.6392 + 200 0.02 0.076456944 9415.3095 55.633188 -0.921682 1.7905973 -1069.4298 -1067.6392 + 250 0.025 0.076456953 8878.9394 39.802206 -0.94649004 1.2810649 -1068.9203 -1067.6392 + 300 0.03 0.076457027 8203.3388 27.882295 -0.97253854 0.8974133 -1068.5366 -1067.6392 + 350 0.035 0.076457103 7720.309 21.776538 -0.99708692 0.70089477 -1068.3401 -1067.6392 + 400 0.04 0.076457117 7531.0683 21.857102 -1.0190244 0.70348778 -1068.3427 -1067.6392 + 450 0.045 0.076457072 7479.8073 26.959407 -1.0389343 0.86770942 -1068.5069 -1067.6392 + 500 0.05 0.076457001 7461.6683 34.92521 -1.0582008 1.124095 -1068.7633 -1067.6392 + 550 0.055 0.076456962 7396.1112 43.405912 -1.0785156 1.397053 -1069.0363 -1067.6392 + 600 0.06 0.076456997 7121.894 50.544844 -1.102048 1.626825 -1069.2661 -1067.6392 + 650 0.065 0.076457079 6683.4805 55.261218 -1.1296588 1.7786252 -1069.4179 -1067.6392 + 700 0.07 0.076457136 6313.6896 57.25083 -1.1595102 1.8426624 -1069.4819 -1067.6392 + 750 0.075 0.076457132 6199.0363 56.934336 -1.1893875 1.8324758 -1069.4717 -1067.6392 + 800 0.08 0.076457116 6265.997 55.266343 -1.2181223 1.7787901 -1069.418 -1067.6392 + 850 0.085 0.076457116 6326.5886 53.376453 -1.2443326 1.7179626 -1069.3572 -1067.6392 + 900 0.09 0.076457121 6336.1261 52.279557 -1.2676425 1.6826581 -1069.3219 -1067.6392 + 950 0.095 0.076457122 6288.4204 52.667743 -1.2902335 1.6951522 -1069.3344 -1067.6392 + 1000 0.1 0.076457135 6122.1622 54.684094 -1.314147 1.76005 -1069.3993 -1067.6392 + 1050 0.105 0.076457155 5830.2219 57.880399 -1.3392396 1.8629256 -1069.5022 -1067.6392 + 1100 0.11 0.076457162 5477.4214 61.505616 -1.3662331 1.979606 -1069.6188 -1067.6392 + 1150 0.115 0.076457195 5194.1423 64.810972 -1.3984474 2.0859914 -1069.7252 -1067.6392 + 1200 0.12 0.076457219 5096.2484 67.147472 -1.438326 2.1611935 -1069.8004 -1067.6392 + 1250 0.125 0.076457214 5180.7444 67.957533 -1.4822383 2.1872659 -1069.8265 -1067.6392 + 1300 0.13 0.076457208 5332.4483 66.96652 -1.5226303 2.1553694 -1069.7946 -1067.6392 + 1350 0.135 0.076457225 5441.1287 64.471602 -1.5553539 2.0750686 -1069.7143 -1067.6392 + 1400 0.14 0.076457244 5466.8622 61.292592 -1.5804721 1.9727496 -1069.612 -1067.6392 + 1450 0.145 0.07645724 5403.309 58.518161 -1.6006864 1.8834524 -1069.5227 -1067.6392 + 1500 0.15 0.076457224 5275.2171 57.1713 -1.6196756 1.8401027 -1069.4793 -1067.6392 + 1550 0.155 0.076457217 5122.7481 57.878063 -1.6407322 1.8628504 -1069.5021 -1067.6392 + 1600 0.16 0.076457217 4968.5049 60.639452 -1.6657935 1.9517278 -1069.591 -1067.6392 + 1650 0.165 0.076457208 4850.1861 64.668839 -1.690847 2.0814168 -1069.7206 -1067.6392 + 1700 0.17 0.076457217 4809.0194 68.693586 -1.7087416 2.2109564 -1069.8502 -1067.6392 + 1750 0.175 0.076457274 4835.8611 71.611033 -1.7188587 2.3048567 -1069.9441 -1067.6392 + 1800 0.18 0.076457318 4929.7428 72.815077 -1.7280248 2.3436098 -1069.9828 -1067.6392 + 1850 0.185 0.076457279 5036.6365 72.102335 -1.7426092 2.3206696 -1069.9599 -1067.6392 + 1900 0.19 0.076457222 5116.2436 69.579977 -1.7638235 2.2394856 -1069.8787 -1067.6392 + 1950 0.195 0.076457228 5207.2334 65.715745 -1.7895824 2.1151122 -1069.7543 -1067.6392 + 2000 0.2 0.076457288 5216.0413 61.340972 -1.8174915 1.9743068 -1069.6135 -1067.6392 + 2050 0.205 0.076457267 5023.1601 57.468628 -1.8456914 1.8496724 -1069.4889 -1067.6392 + 2100 0.21 0.076457198 4748.7818 55.033266 -1.8742291 1.7712884 -1069.4105 -1067.6392 + 2150 0.215 0.076457199 4558.1302 54.573806 -1.9035225 1.7565003 -1069.3957 -1067.6392 + 2200 0.22 0.076457185 4483.1644 56.074241 -1.9322669 1.804793 -1069.444 -1067.6392 + 2250 0.225 0.076457114 4430.1583 59.0552 -1.9577399 1.9007374 -1069.54 -1067.6392 + 2300 0.23 0.076457092 4353.7973 62.874849 -1.9801275 2.0236758 -1069.6629 -1067.6392 + 2350 0.235 0.076457145 4303.5275 66.892738 -2.0022129 2.1529947 -1069.7922 -1067.6392 + 2400 0.24 0.076457171 4258.6889 70.426826 -2.0233072 2.2667421 -1069.906 -1067.6392 + 2450 0.245 0.076457169 4178.5775 72.910422 -2.0405304 2.3466785 -1069.9859 -1067.6392 + 2500 0.25 0.07645717 4114.786 74.106367 -2.0531755 2.3851709 -1070.0244 -1067.6392 + 2550 0.255 0.076457136 4067.5017 74.169349 -2.0634674 2.3871981 -1070.0264 -1067.6392 + 2600 0.26 0.076457099 4045.3324 73.586199 -2.0755814 2.3684289 -1070.0077 -1067.6392 + 2650 0.265 0.076457099 4137.898 72.914235 -2.0913646 2.3468012 -1069.986 -1067.6392 + 2700 0.27 0.076457106 4332.063 72.583192 -2.1091075 2.3361464 -1069.9754 -1067.6392 + 2750 0.275 0.07645709 4465.1953 72.814559 -2.125099 2.3435931 -1069.9828 -1067.6392 + 2800 0.28 0.076457051 4516.5192 73.652154 -2.1371914 2.3705517 -1070.0098 -1067.6392 + 2850 0.285 0.076457019 4555.5962 75.060211 -2.1489378 2.4158711 -1070.0551 -1067.6392 + 2900 0.29 0.076457069 4544.2734 76.844795 -2.1667679 2.4733094 -1070.1125 -1067.6392 + 2950 0.295 0.076457172 4460.2109 78.48171 -2.1924421 2.5259948 -1070.1652 -1067.6392 + 3000 0.3 0.076457219 4323.2746 79.20682 -2.2209955 2.549333 -1070.1886 -1067.6392 + 3050 0.305 0.076457213 4155.688 78.543529 -2.2505299 2.5279844 -1070.1672 -1067.6392 + 3100 0.31 0.076457203 3969.6188 76.554785 -2.2858382 2.4639752 -1070.1032 -1067.6392 + 3150 0.315 0.076457187 3761.432 73.396149 -2.3245055 2.362312 -1070.0015 -1067.6392 + 3200 0.32 0.076457142 3602.8035 69.313196 -2.3577056 2.230899 -1069.8701 -1067.6392 + 3250 0.325 0.076457116 3505.707 65.032482 -2.3836874 2.0931209 -1069.7324 -1067.6392 + 3300 0.33 0.07645716 3424.8795 61.551539 -2.4057167 1.9810841 -1069.6203 -1067.6392 + 3350 0.335 0.076457236 3335.9672 59.709703 -2.4251844 1.9218031 -1069.561 -1067.6392 + 3400 0.34 0.076457298 3238.0186 60.026953 -2.4425501 1.9320141 -1069.5712 -1067.6392 + 3450 0.345 0.076457297 3185.0674 62.613739 -2.4593531 2.0152718 -1069.6545 -1067.6392 + 3500 0.35 0.07645723 3197.4087 67.011871 -2.4756907 2.1568291 -1069.7961 -1067.6392 + 3550 0.355 0.076457177 3216.1428 72.316209 -2.4911379 2.3275533 -1069.9668 -1067.6392 + 3600 0.36 0.076457165 3241.0326 77.550071 -2.5083858 2.4960092 -1070.1352 -1067.6392 + 3650 0.365 0.076457168 3309.6874 81.877688 -2.5306273 2.6352969 -1070.2745 -1067.6392 + 3700 0.37 0.07645718 3350.748 84.764646 -2.5595247 2.7282159 -1070.3674 -1067.6392 + 3750 0.375 0.07645721 3368.085 86.031781 -2.5938559 2.7689996 -1070.4082 -1067.6392 + 3800 0.38 0.076457208 3425.3173 85.733048 -2.6266899 2.7593847 -1070.3986 -1067.6392 + 3850 0.385 0.076457165 3420.4429 84.240647 -2.6514805 2.7113506 -1070.3506 -1067.6392 + 3900 0.39 0.076457146 3323.0403 82.320886 -2.6700966 2.6495616 -1070.2888 -1067.6392 + 3950 0.395 0.076457179 3273.2625 80.780607 -2.6892405 2.5999865 -1070.2392 -1067.6392 + 4000 0.4 0.076457229 3313.2671 79.92769 -2.709641 2.5725347 -1070.2118 -1067.6392 + 4050 0.405 0.076457272 3381.1117 79.663389 -2.7291493 2.564028 -1070.2033 -1067.6392 + 4100 0.41 0.07645731 3373.3005 79.895158 -2.7514856 2.5714877 -1070.2107 -1067.6392 + 4150 0.415 0.076457296 3279.6989 80.402828 -2.7788004 2.5878274 -1070.2271 -1067.6392 + 4200 0.42 0.076457251 3197.0478 80.770336 -2.8064773 2.599656 -1070.2389 -1067.6392 + 4250 0.425 0.076457243 3160.9065 80.756747 -2.8307967 2.5992186 -1070.2385 -1067.6392 + 4300 0.43 0.076457282 3173.9599 80.446488 -2.852192 2.5892326 -1070.2285 -1067.6392 + 4350 0.435 0.076457289 3185.8003 80.110494 -2.8726607 2.5784184 -1070.2177 -1067.6392 + 4400 0.44 0.076457262 3166.3054 80.045036 -2.8936787 2.5763116 -1070.2155 -1067.6392 + 4450 0.445 0.076457226 3177.4332 80.500194 -2.9171408 2.5909612 -1070.2302 -1067.6392 + 4500 0.45 0.076457174 3238.8362 81.573722 -2.9447352 2.6255135 -1070.2647 -1067.6392 + 4550 0.455 0.07645714 3277.7104 83.104228 -2.975052 2.6747741 -1070.314 -1067.6392 + 4600 0.46 0.076457157 3224.8571 84.845473 -3.0065552 2.7308174 -1070.37 -1067.6392 + 4650 0.465 0.076457215 3112.9952 86.608217 -3.03972 2.7875527 -1070.4268 -1067.6392 + 4700 0.47 0.076457254 3001.141 88.18732 -3.074928 2.8383773 -1070.4776 -1067.6392 + 4750 0.475 0.076457235 2904.0735 89.204263 -3.1082127 2.8711084 -1070.5103 -1067.6392 + 4800 0.48 0.076457195 2832.0276 89.24571 -3.134302 2.8724424 -1070.5117 -1067.6392 + 4850 0.485 0.076457172 2833.7453 88.206351 -3.1541802 2.8389899 -1070.4782 -1067.6392 + 4900 0.49 0.076457184 2941.993 86.310712 -3.1725372 2.7779773 -1070.4172 -1067.6392 + 4950 0.495 0.076457228 3082.4825 84.029047 -3.1931038 2.7045401 -1070.3438 -1067.6392 + 5000 0.5 0.07645727 3155.7095 81.99875 -3.2175967 2.6391934 -1070.2784 -1067.6392 + 5050 0.505 0.076457297 3162.1875 80.72053 -3.2420203 2.5980529 -1070.2373 -1067.6392 + 5100 0.51 0.076457279 3133.3889 80.483768 -3.2606472 2.5904325 -1070.2297 -1067.6392 + 5150 0.515 0.076457223 3144.6361 81.566513 -3.2759117 2.6252815 -1070.2645 -1067.6392 + 5200 0.52 0.076457166 3156.8183 84.062018 -3.2944729 2.7056013 -1070.3448 -1067.6392 + 5250 0.525 0.076457128 3059.9886 87.694328 -3.3209415 2.82251 -1070.4617 -1067.6392 + 5300 0.53 0.076457126 2891.6506 91.782947 -3.3547324 2.9541054 -1070.5933 -1067.6392 + 5350 0.535 0.076457151 2751.9451 95.417928 -3.3914125 3.0711001 -1070.7103 -1067.6392 + 5400 0.54 0.07645725 2681.0265 97.845096 -3.4276651 3.1492204 -1070.7885 -1067.6392 + 5450 0.545 0.076457325 2657.0871 98.736021 -3.4632111 3.1778955 -1070.8171 -1067.6392 + 5500 0.55 0.076457263 2653.1919 98.075727 -3.4957627 3.1566434 -1070.7959 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2476.1857 99.370382 -3.7869326 3.1983129 -1070.8375 -1067.6392 + 6150 0.615 0.076457178 2397.2805 97.465979 -3.8168635 3.1370182 -1070.7763 -1067.6392 + 6200 0.62 0.07645713 2286.8528 94.931714 -3.8450242 3.0554509 -1070.6947 -1067.6392 + 6250 0.625 0.076457116 2250.5238 92.438461 -3.8722441 2.9752036 -1070.6144 -1067.6392 + 6300 0.63 0.076457156 2338.521 90.714356 -3.9006124 2.9197119 -1070.5589 -1067.6392 + 6350 0.635 0.07645717 2433.0115 90.142291 -3.9291158 2.9012996 -1070.5405 -1067.6392 + 6400 0.64 0.076457159 2467.5348 90.771111 -3.9562691 2.9215387 -1070.5608 -1067.6392 + 6450 0.645 0.076457107 2475.8592 92.488016 -3.9828131 2.9767986 -1070.616 -1067.6392 + 6500 0.65 0.0764571 2489.7418 95.127451 -4.0122141 3.0617508 -1070.701 -1067.6392 + 6550 0.655 0.076457169 2500.4747 98.171693 -4.0419177 3.1597321 -1070.799 -1067.6392 + 6600 0.66 0.076457208 2530.7924 100.74938 -4.0631997 3.242697 -1070.8819 -1067.6392 + 6650 0.665 0.076457205 2539.1274 102.26227 -4.0743158 3.2913904 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0.076457184 2101.9996 122.34334 -4.9126837 3.9377155 -1071.5769 -1067.6392 + 8450 0.845 0.076457201 2057.1092 121.73484 -4.921619 3.9181301 -1071.5574 -1067.6392 + 8500 0.85 0.076457149 2005.1132 119.2385 -4.9251343 3.8377838 -1071.477 -1067.6392 + 8550 0.855 0.076457098 1942.6247 115.64537 -4.9291799 3.722136 -1071.3614 -1067.6392 + 8600 0.86 0.076457115 1910.1502 111.98317 -4.9396222 3.6042654 -1071.2435 -1067.6392 + 8650 0.865 0.076457185 1943.3663 109.19353 -4.9603011 3.5144784 -1071.1537 -1067.6392 + 8700 0.87 0.076457254 2019.4182 107.80177 -4.9898541 3.4696837 -1071.1089 -1067.6392 + 8750 0.875 0.076457249 2073.1225 107.76716 -5.0205034 3.4685697 -1071.1078 -1067.6392 + 8800 0.88 0.076457175 2088.6545 108.72646 -5.0437829 3.4994455 -1071.1387 -1067.6392 + 8850 0.885 0.076457093 2077.5406 110.36499 -5.0572565 3.5521827 -1071.1914 -1067.6392 + 8900 0.89 0.076457088 2039.5392 112.51291 -5.0650529 3.6213154 -1071.2605 -1067.6392 + 8950 0.895 0.076457167 2016.6853 114.99374 -5.0744542 3.7011627 -1071.3404 -1067.6392 + 9000 0.9 0.076457241 2000.3012 117.47475 -5.0917242 3.781016 -1071.4202 -1067.6392 + 9050 0.905 0.076457226 1957.0091 119.35854 -5.1139655 3.8416472 -1071.4809 -1067.6392 + 9100 0.91 0.076457166 1923.1545 120.23087 -5.1350957 3.869724 -1071.509 -1067.6392 + 9150 0.915 0.076457128 1933.618 120.11319 -5.1511544 3.8659364 -1071.5052 -1067.6392 + 9200 0.92 0.076457114 1961.4473 119.3017 -5.1596749 3.8398178 -1071.4791 -1067.6392 + 9250 0.925 0.076457136 1962.1 118.34889 -5.1642618 3.8091509 -1071.4484 -1067.6392 + 9300 0.93 0.076457156 1942.9357 117.84262 -5.1720815 3.7928561 -1071.4321 -1067.6392 + 9350 0.935 0.076457138 1911.4886 118.10075 -5.1877615 3.8011641 -1071.4404 -1067.6392 + 9400 0.94 0.076457123 1890.6033 118.99959 -5.2079977 3.830094 -1071.4693 -1067.6392 + 9450 0.945 0.076457145 1911.9879 120.23989 -5.2265042 3.8700141 -1071.5092 -1067.6392 + 9500 0.95 0.076457172 1944.8053 121.67513 -5.2423826 3.9162086 -1071.5554 -1067.6392 + 9550 0.955 0.076457175 1950.6137 123.16708 -5.2566963 3.9642282 -1071.6035 -1067.6392 + 9600 0.96 0.076457174 1953.467 124.46943 -5.2686278 4.0061451 -1071.6454 -1067.6392 + 9650 0.965 0.076457174 1991.321 125.52237 -5.2816008 4.0400348 -1071.6793 -1067.6392 + 9700 0.97 0.076457153 2064.4494 126.48746 -5.3037304 4.0710971 -1071.7103 -1067.6392 + 9750 0.975 0.076457119 2117.0576 127.38593 -5.3401962 4.100015 -1071.7392 -1067.6392 + 9800 0.98 0.076457147 2129.8396 127.90735 -5.38872 4.1167973 -1071.756 -1067.6392 + 9850 0.985 0.076457201 2114.5902 127.47883 -5.4369444 4.103005 -1071.7422 -1067.6392 + 9900 0.99 0.076457216 2054.2807 125.71916 -5.4695662 4.0463688 -1071.6856 -1067.6392 + 9950 0.995 0.076457168 1984.2158 123.01154 -5.4834672 3.9592219 -1071.5985 -1067.6392 + 10000 1 0.076457131 1962.6658 120.32305 -5.4872199 3.8726906 -1071.5119 -1067.6392 + 10050 1.005 0.076457159 1973.2973 118.61523 -5.4922129 3.8177233 -1071.457 -1067.6392 + 10100 1.01 0.076457216 1957.9424 118.36973 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-1067.6392 + 10700 1.07 0.076457242 2058.3043 136.94864 -5.8957766 4.4077983 -1072.047 -1067.6392 + 10750 1.075 0.076457284 2065.4421 138.83647 -5.9266133 4.4685595 -1072.1078 -1067.6392 + 10800 1.08 0.076457341 2054.3284 138.84647 -5.9519915 4.4688815 -1072.1081 -1067.6392 + 10850 1.085 0.076457339 2019.0718 136.8565 -5.9690783 4.4048328 -1072.0441 -1067.6392 + 10900 1.09 0.076457316 1950.5439 133.30535 -5.9772058 4.290536 -1071.9298 -1067.6392 + 10950 1.095 0.076457386 1880.7681 129.31046 -5.9839906 4.1619576 -1071.8012 -1067.6392 + 11000 1.1 0.076457422 1858.5762 126.17301 -5.9991286 4.0609761 -1071.7002 -1067.6392 + 11050 1.105 0.076457344 1895.8864 124.66179 -6.0225804 4.0123366 -1071.6516 -1067.6392 + 11100 1.11 0.076457251 1940.5442 124.88033 -6.0460181 4.0193704 -1071.6586 -1067.6392 + 11150 1.115 0.076457202 1961.4346 126.74742 -6.0683173 4.0794642 -1071.7187 -1067.6392 + 11200 1.12 0.076457268 1940.4836 129.91024 -6.0923522 4.1812618 -1071.8205 -1067.6392 + 11250 1.125 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-17.988379 10.501275 -1078.1405 -1067.6392 + 46500 4.65 0.076457159 948.45576 319.53501 -17.972857 10.284482 -1077.9237 -1067.6392 + 46550 4.655 0.076457197 951.57922 312.18572 -17.950863 10.04794 -1077.6872 -1067.6392 + 46600 4.66 0.076457169 953.72078 306.60692 -17.937745 9.8683816 -1077.5076 -1067.6392 + 46650 4.665 0.07645714 969.19209 304.86187 -17.945815 9.8122157 -1077.4514 -1067.6392 + 46700 4.67 0.076457121 982.50268 307.98161 -17.974576 9.9126272 -1077.5519 -1067.6392 + 46750 4.675 0.076457149 974.5768 314.91384 -18.000917 10.135746 -1077.775 -1067.6392 + 46800 4.68 0.076457222 954.17186 322.2853 -18.003497 10.373003 -1078.0122 -1067.6392 + 46850 4.685 0.076457263 943.539 327.31716 -17.991456 10.534957 -1078.1742 -1067.6392 + 46900 4.69 0.076457272 943.2156 329.68269 -17.979619 10.611093 -1078.2503 -1067.6392 + 46950 4.695 0.076457248 943.45366 330.93325 -17.974243 10.651343 -1078.2906 -1067.6392 + 47000 4.7 0.076457135 949.24404 332.85406 -17.979019 10.713166 -1078.3524 -1067.6392 + 47050 4.705 0.076457109 948.38347 335.49431 -17.990033 10.798145 -1078.4374 -1067.6392 + 47100 4.71 0.076457108 930.57759 336.79293 -18.000912 10.839942 -1078.4792 -1067.6392 + 47150 4.715 0.076457061 927.62433 334.90723 -18.010023 10.779249 -1078.4185 -1067.6392 + 47200 4.72 0.076457026 952.31461 330.77819 -18.012971 10.646353 -1078.2856 -1067.6392 + 47250 4.725 0.076457029 970.41647 328.26943 -18.01237 10.565606 -1078.2048 -1067.6392 + 47300 4.73 0.07645704 968.2995 329.56928 -18.014991 10.607443 -1078.2467 -1067.6392 + 47350 4.735 0.076457096 954.1138 332.31723 -18.02454 10.695888 -1078.3351 -1067.6392 + 47400 4.74 0.07645714 968.01812 333.90938 -18.038354 10.747133 -1078.3864 -1067.6392 + 47450 4.745 0.076457183 1006.2574 334.70242 -18.050106 10.772657 -1078.4119 -1067.6392 + 47500 4.75 0.076457147 1037.4547 335.39669 -18.062338 10.795003 -1078.4342 -1067.6392 + 47550 4.755 0.076457004 1027.5546 333.98227 -18.07862 10.749479 -1078.3887 -1067.6392 + 47600 4.76 0.076457078 986.81013 328.40773 -18.100384 10.570058 -1078.2093 -1067.6392 + 47650 4.765 0.076457236 980.12421 319.46388 -18.120191 10.282193 -1077.9214 -1067.6392 + 47700 4.77 0.076457087 973.75413 310.20532 -18.133538 9.984199 -1077.6234 -1067.6392 + 47750 4.775 0.076456955 944.49227 304.05996 -18.150575 9.7864056 -1077.4256 -1067.6392 + 47800 4.78 0.076457043 934.26558 302.74055 -18.16342 9.7439395 -1077.3832 -1067.6392 + 47850 4.785 0.076457163 946.5867 306.50326 -18.158739 9.8650453 -1077.5043 -1067.6392 + 47900 4.79 0.076457207 956.86274 314.93949 -18.15119 10.136572 -1077.7758 -1067.6392 + 47950 4.795 0.07645715 958.82327 326.06488 -18.164425 10.494651 -1078.1339 -1067.6392 + 48000 4.8 0.076457039 947.13341 336.0645 -18.196245 10.816497 -1078.4557 -1067.6392 + 48050 4.805 0.076457079 939.87276 341.25341 -18.222449 10.983506 -1078.6227 -1067.6392 + 48100 4.81 0.076457027 941.59608 340.87478 -18.232947 10.971319 -1078.6106 -1067.6392 + 48150 4.815 0.076456851 947.69448 337.06143 -18.235444 10.848584 -1078.4878 -1067.6392 + 48200 4.82 0.076456923 945.0083 331.93845 -18.226235 10.683697 -1078.3229 -1067.6392 + 48250 4.825 0.076457065 955.23353 326.88598 -18.206503 10.521079 -1078.1603 -1067.6392 + 48300 4.83 0.076457035 976.25082 323.10993 -18.198786 10.399544 -1078.0388 -1067.6392 + 48350 4.835 0.076456918 980.22652 320.95231 -18.21424 10.330099 -1077.9693 -1067.6392 + 48400 4.84 0.07645681 991.61794 319.56431 -18.236887 10.285425 -1077.9247 -1067.6392 + 48450 4.845 0.076456811 1004.3973 319.00657 -18.259638 10.267474 -1077.9067 -1067.6392 + 48500 4.85 0.076456872 1011.2382 320.78368 -18.281738 10.324672 -1077.9639 -1067.6392 + 48550 4.855 0.076456865 1011.4359 325.48338 -18.293785 10.475935 -1078.1152 -1067.6392 + 48600 4.86 0.076456844 1005.7488 332.46822 -18.305193 10.700748 -1078.34 -1067.6392 + 48650 4.865 0.076456876 989.87609 340.85827 -18.332595 10.970788 -1078.61 -1067.6392 + 48700 4.87 0.07645693 968.07155 348.89288 -18.372402 11.229388 -1078.8686 -1067.6392 + 48750 4.875 0.076456873 954.48433 354.07093 -18.412323 11.396048 -1079.0353 -1067.6392 + 48800 4.88 0.076456838 951.82821 354.8518 -18.445418 11.421181 -1079.0604 -1067.6392 + 48850 4.885 0.076456946 955.18291 351.65785 -18.473652 11.318381 -1078.9576 -1067.6392 + 48900 4.89 0.076457014 961.21122 345.9779 -18.498732 11.135567 -1078.7748 -1067.6392 + 48950 4.895 0.076456863 971.60448 338.99359 -18.517002 10.910772 -1078.55 -1067.6392 + 49000 4.9 0.076456715 983.55102 331.29604 -18.525123 10.66302 -1078.3022 -1067.6392 + 49050 4.905 0.076456793 965.60848 324.24302 -18.535514 10.436013 -1078.0752 -1067.6392 + 49100 4.91 0.076456864 944.53951 319.79955 -18.557009 10.292997 -1077.9322 -1067.6392 + 49150 4.915 0.076456768 947.20225 319.09103 -18.582911 10.270192 -1077.9094 -1067.6392 + 49200 4.92 0.076456734 944.86084 321.47471 -18.607567 10.346913 -1077.9861 -1067.6392 + 49250 4.925 0.076456851 940.6342 324.66116 -18.626242 10.449471 -1078.0887 -1067.6392 + 49300 4.93 0.076456872 950.6162 326.9518 -18.64032 10.523198 -1078.1624 -1067.6392 + 49350 4.935 0.076456643 952.42705 328.08816 -18.649274 10.559772 -1078.199 -1067.6392 + 49400 4.94 0.076456451 940.33548 329.05106 -18.66058 10.590764 -1078.23 -1067.6392 + 49450 4.945 0.076456558 946.93554 331.05799 -18.683544 10.655358 -1078.2946 -1067.6392 + 49500 4.95 0.076456719 968.13429 334.1178 -18.710726 10.753841 -1078.3931 -1067.6392 + 49550 4.955 0.076456712 989.14725 337.02333 -18.733226 10.847357 -1078.4866 -1067.6392 + 49600 4.96 0.076456681 986.97561 338.47429 -18.752155 10.894058 -1078.5333 -1067.6392 + 49650 4.965 0.076456692 980.18259 338.36307 -18.779369 10.890478 -1078.5297 -1067.6392 + 49700 4.97 0.076456776 962.29895 337.41689 -18.815353 10.860024 -1078.4993 -1067.6392 + 49750 4.975 0.076456852 943.47442 335.97999 -18.836611 10.813777 -1078.453 -1067.6392 + 49800 4.98 0.076456829 951.10385 334.29845 -18.839995 10.759655 -1078.3989 -1067.6392 + 49850 4.985 0.076456797 968.57767 333.00568 -18.84792 10.718046 -1078.3573 -1067.6392 + 49900 4.99 0.076456886 973.40031 332.98155 -18.860429 10.71727 -1078.3565 -1067.6392 + 49950 4.995 0.076456914 964.32242 335.13156 -18.853933 10.786469 -1078.4257 -1067.6392 + 50000 5 0.076456921 972.52311 340.63067 -18.841947 10.963463 -1078.6027 -1067.6392 +Loop time of 90.4316 on 1 procs for 50000 steps with 250 atoms + +Performance: 4.777 ns/day, 5.024 hours/ns, 552.904 timesteps/s +99.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.302 | 37.302 | 37.302 | 0.0 | 41.25 +Neigh | 0.386 | 0.386 | 0.386 | 0.0 | 0.43 +Comm | 0.7718 | 0.7718 | 0.7718 | 0.0 | 0.85 +Output | 15.35 | 15.35 | 15.35 | 0.0 | 16.97 +Modify | 36.465 | 36.465 | 36.465 | 0.0 | 40.32 +Other | | 0.1579 | | | 0.17 + +Nlocal: 250 ave 250 max 250 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1327 ave 1327 max 1327 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 7747 ave 7747 max 7747 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 15494 ave 15494 max 15494 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15494 +Ave neighs/atom = 61.976 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:30 diff --git a/examples/SPIN/iron/log.11May18.spin.iron.g++.4 b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..1467f8e2c58a451299cb375773ef76f43a1bb8bc --- /dev/null +++ b/examples/SPIN/iron/log.11May18.spin.iron.g++.4 @@ -0,0 +1,1115 @@ +LAMMPS (11 May 2018) +# bcc iron in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (14.3325 14.3325 14.3325) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 250 atoms + Time spent = 0.00023818 secs + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 + +set group all spin/random 31 2.2 + 250 settings made for spin/random +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 3.5 +pair_coeff * * eam/alloy Fe_Mishin2006.eam.alloy Fe +pair_coeff * * spin/exchange exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +run 50000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.77337 + ghost atom cutoff = 5.77337 + binsize = 2.88668, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.265 | 7.265 | 7.265 Mbytes +Step Time v_magnorm v_tmag Temp v_emag KinEng PotEng TotEng + 0 0 0.076456975 9109.0924 100.00358 -0.85791269 3.2186929 -1070.8579 -1067.6392 + 50 0.005 0.076456995 9402.4007 96.298333 -0.85659448 3.0994366 -1070.7387 -1067.6392 + 100 0.01 0.076457028 9589.1846 86.330828 -0.87003341 2.7786247 -1070.4179 -1067.6392 + 150 0.015 0.076457074 9673.9268 71.603402 -0.89006992 2.3046111 -1069.9438 -1067.6392 + 200 0.02 0.076457106 9509.1148 54.648817 -0.91124541 1.7589146 -1069.3981 -1067.6392 + 250 0.025 0.076457128 9004.27 38.599515 -0.93187522 1.2423553 -1068.8816 -1067.6392 + 300 0.03 0.076457157 8353.4371 26.383018 -0.95082226 0.8491579 -1068.4884 -1067.6392 + 350 0.035 0.076457207 7911.1316 20.01039 -0.96826468 0.64404992 -1068.2833 -1067.6392 + 400 0.04 0.076457243 7775.9492 20.097682 -0.98706373 0.64685949 -1068.2861 -1067.6392 + 450 0.045 0.076457231 7737.1225 25.687511 -1.0095684 0.82677249 -1068.466 -1067.6392 + 500 0.05 0.076457204 7676.9809 34.604697 -1.0349855 1.113779 -1068.753 -1067.6392 + 550 0.055 0.076457196 7550.2809 44.251809 -1.0609123 1.4242788 -1069.0635 -1067.6392 + 600 0.06 0.076457188 7209.7657 52.475202 -1.0880854 1.6889551 -1069.3282 -1067.6392 + 650 0.065 0.07645718 6691.1787 57.926479 -1.1179657 1.8644087 -1069.5036 -1067.6392 + 700 0.07 0.076457185 6276.4003 60.030548 -1.1469999 1.9321298 -1069.5714 -1067.6392 + 750 0.075 0.07645719 6149.9253 59.122504 -1.1721939 1.9029037 -1069.5421 -1067.6392 + 800 0.08 0.076457195 6207.0587 56.349146 -1.1949365 1.813641 -1069.4529 -1067.6392 + 850 0.085 0.076457199 6328.4635 53.154464 -1.2164642 1.7108177 -1069.35 -1067.6392 + 900 0.09 0.076457199 6456.2716 50.837416 -1.2366018 1.6362417 -1069.2755 -1067.6392 + 950 0.095 0.076457222 6495.1064 50.234549 -1.2539657 1.6168379 -1069.2561 -1067.6392 + 1000 0.1 0.076457266 6416.775 51.592727 -1.2671834 1.6605519 -1069.2998 -1067.6392 + 1050 0.105 0.076457256 6305.9015 54.719414 -1.2794824 1.7611868 -1069.4004 -1067.6392 + 1100 0.11 0.076457222 6165.987 59.01343 -1.2960617 1.8993931 -1069.5386 -1067.6392 + 1150 0.115 0.076457194 5941.7807 63.475298 -1.317859 2.0430017 -1069.6822 -1067.6392 + 1200 0.12 0.076457182 5692.0982 67.036713 -1.3432854 2.1576286 -1069.7969 -1067.6392 + 1250 0.125 0.076457217 5543.1736 68.917405 -1.3719994 2.2181602 -1069.8574 -1067.6392 + 1300 0.13 0.076457263 5507.9968 68.753418 -1.4042339 2.2128821 -1069.8521 -1067.6392 + 1350 0.135 0.076457286 5500.7848 66.608286 -1.4385667 2.1438394 -1069.7831 -1067.6392 + 1400 0.14 0.076457254 5523.456 62.967429 -1.4712143 2.0266556 -1069.6659 -1067.6392 + 1450 0.145 0.076457188 5501.5777 58.75732 -1.4990458 1.89115 -1069.5304 -1067.6392 + 1500 0.15 0.076457175 5324.4931 55.246308 -1.5236774 1.7781453 -1069.4174 -1067.6392 + 1550 0.155 0.076457234 5025.5908 53.607297 -1.5492947 1.7253925 -1069.3646 -1067.6392 + 1600 0.16 0.076457297 4742.9546 54.443418 -1.5785798 1.7523036 -1069.3915 -1067.6392 + 1650 0.165 0.076457321 4558.083 57.572305 -1.6113848 1.8530093 -1069.4922 -1067.6392 + 1700 0.17 0.076457304 4479.4352 62.073307 -1.6443595 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347.46226 -18.634634 11.183342 -1078.8226 -1067.6392 + 48450 4.845 0.076457572 985.51176 349.38288 -18.652405 11.245159 -1078.8844 -1067.6392 + 48500 4.85 0.0764575 966.51991 350.00883 -18.680976 11.265306 -1078.9045 -1067.6392 + 48550 4.855 0.076457449 952.81522 348.84984 -18.705088 11.228003 -1078.8672 -1067.6392 + 48600 4.86 0.07645757 956.4504 345.07299 -18.706134 11.106442 -1078.7457 -1067.6392 + 48650 4.865 0.076457648 962.27213 339.6091 -18.687227 10.930583 -1078.5698 -1067.6392 + 48700 4.87 0.076457531 951.28586 335.48047 -18.675207 10.797699 -1078.4369 -1067.6392 + 48750 4.875 0.076457622 939.27346 335.37698 -18.691822 10.794368 -1078.4336 -1067.6392 + 48800 4.88 0.07645763 929.93644 338.62392 -18.723472 10.898874 -1078.5381 -1067.6392 + 48850 4.885 0.07645746 927.0018 341.61788 -18.739309 10.995236 -1078.6345 -1067.6392 + 48900 4.89 0.076457454 933.2133 341.45716 -18.734537 10.990064 -1078.6293 -1067.6392 + 48950 4.895 0.076457525 927.17347 338.03446 -18.732333 10.879901 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4.955 0.076457651 985.5222 322.69351 -18.765732 10.386141 -1078.0254 -1067.6392 + 49600 4.96 0.076457607 966.22788 316.25074 -18.798665 10.178775 -1077.818 -1067.6392 + 49650 4.965 0.076457494 961.04675 313.18195 -18.839015 10.080004 -1077.7192 -1067.6392 + 49700 4.97 0.076457431 960.65868 314.4735 -18.863274 10.121574 -1077.7608 -1067.6392 + 49750 4.975 0.076457515 966.54445 320.68235 -18.880959 10.32141 -1077.9606 -1067.6392 + 49800 4.98 0.076457498 965.47876 331.30789 -18.90627 10.663401 -1078.3026 -1067.6392 + 49850 4.985 0.076457382 964.05595 343.93887 -18.938996 11.069939 -1078.7092 -1067.6392 + 49900 4.99 0.076457357 944.93024 354.89734 -18.970612 11.422646 -1079.0619 -1067.6392 + 49950 4.995 0.076457532 918.77322 361.48317 -18.987516 11.634616 -1079.2739 -1067.6392 + 50000 5 0.07645762 900.51128 363.08297 -18.994661 11.686107 -1079.3253 -1067.6392 +Loop time of 52.5523 on 4 procs for 50000 steps with 250 atoms + +Performance: 8.220 ns/day, 2.920 hours/ns, 951.434 timesteps/s +94.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.242 | 10.478 | 10.799 | 6.3 | 19.94 +Neigh | 0.10368 | 0.10776 | 0.11329 | 1.1 | 0.21 +Comm | 2.4492 | 2.7097 | 2.8852 | 11.0 | 5.16 +Output | 5.5737 | 5.9107 | 6.2742 | 11.8 | 11.25 +Modify | 32.833 | 33.256 | 33.661 | 5.2 | 63.28 +Other | | 0.09063 | | | 0.17 + +Nlocal: 62.5 ave 66 max 57 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 772 ave 785 max 755 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 1931 ave 2025 max 1751 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +FullNghs: 3862 ave 4082 max 3518 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 15448 +Ave neighs/atom = 61.792 +Neighbor list builds = 614 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:52 diff --git a/examples/SPIN/nickel/Ni99.eam.alloy b/examples/SPIN/nickel/Ni99.eam.alloy new file mode 100644 index 0000000000000000000000000000000000000000..458f550462147985aebc64bee947ca587bcb2200 --- /dev/null +++ b/examples/SPIN/nickel/Ni99.eam.alloy @@ -0,0 +1,30006 @@ + Ni EAM from Phys. Rev. B 59, 3393 (1999) in the LAMMPS setfl format. + Conversion by C. A. Becker from Y. Mishin files. + 14 February 2009. http://www.ctcms.nist.gov/potentials + 1 Ni +10000 0.2000000000000000E-03 10000 0.5803750000000001E-03 0.5803750000000000E+01 + 28 0.5871000000E+02 0.3520000000E+01 fcc + -0.3097002992599740E-10 + -0.6727670264584218E-03 + -0.1347243064545615E-02 + -0.2023426205791608E-02 + -0.2701314510756404E-02 + -0.3380906040000000E-02 + -0.4062198854082398E-02 + -0.4745191013563596E-02 + -0.5429880579003596E-02 + -0.6116265610962398E-02 + -0.6804344169999999E-02 + -0.7494114316748643E-02 + -0.8185574112129526E-02 + -0.8878721617136087E-02 + -0.9573554892761765E-02 + -0.1027007200000000E-01 + -0.1096827099948303E-01 + -0.1166814995039830E-01 + -0.1236970691157206E-01 + -0.1307293994183054E-01 + -0.1377784710000000E-01 + -0.1448442644595924E-01 + -0.1519267604379728E-01 + -0.1590259395865570E-01 + -0.1661417825567608E-01 + -0.1732742700000000E-01 + -0.1804233825508002E-01 + -0.1875891007761259E-01 + -0.1947714052260515E-01 + -0.2019702764506515E-01 + 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0.1753659819102016E-05 + 0.1535011699446480E-05 + 0.1335308706819185E-05 + 0.1153698121804797E-05 + 0.9893265964069983E-06 + 0.8413397937480116E-06 + 0.7088819770183164E-06 + 0.5910969229666829E-06 + 0.4871272699961916E-06 + 0.3961146220277366E-06 + 0.3172001065531827E-06 + 0.2495236941769535E-06 + 0.1922246407671419E-06 + 0.1444416614955101E-06 + 0.1053124328882129E-06 + 0.7397412700923994E-07 + 0.4956332050161572E-07 + 0.3121579423557010E-07 + 0.1806692087863425E-07 + 0.9251422554216926E-08 + 0.3903384615269487E-08 + 0.1156542889210542E-08 + 0.1443625144722101E-09 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat new file mode 100644 index 0000000000000000000000000000000000000000..376f6fd16242f4255bd4ba277efb0cfd1e5b4ddc --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni.dat @@ -0,0 +1,5 @@ +2.492 0.0028027 +3.524 0.0000816 +4.316 0.0003537 +4.984 0.0001632 +5.572 0.0000408 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat new file mode 100644 index 0000000000000000000000000000000000000000..4e5aa4765957bd9d196f7543751fb5ce174634b4 --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fcc_ni2.dat @@ -0,0 +1,5 @@ +2.495 8.3 +3.524 -3.99 +4.31 0.998 +4.99 -0.955 +5.56 0.213 diff --git a/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py new file mode 100644 index 0000000000000000000000000000000000000000..4046fa45f7c9dde935e492daf7fdf9453daea82a --- /dev/null +++ b/examples/SPIN/nickel/exchange_fit_fcc_ni/exchange_fit.py @@ -0,0 +1,33 @@ +# program fitting the exchange interaction +# model curve: Bethe-Slater function +import numpy as np, pylab, tkinter +import matplotlib.pyplot as plt +from scipy.optimize import curve_fit +from decimal import * + +print("Loop begin") + +# definition of the Bethe-Slater function +def func(x,a,b,c): + return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2) + +# exchange coeff table (data to fit) +rdata, Jdata = np.loadtxt('exchange_fcc_ni.dat', usecols=(0,1), unpack=True) +plt.plot(rdata, Jdata, 'b-', label='data') + +# perform the fit +popt, pcov = curve_fit(func, rdata, Jdata, bounds=([0.0,-1.0,0.0], [100.,5.,5.])) +plt.plot(rdata, func(rdata, *popt), 'r--', label='fit') + +# print the fitted parameters +print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt)) + +# ploting the result +plt.xlabel('r_ij') +pylab.xlim([0.0,6.5]) +#pylab.ylim([-2.0,10.0]) +plt.ylabel('J_ij') +plt.legend() +plt.show() + +print("Loop end") diff --git a/examples/SPIN/nickel/in.spin.nickel b/examples/SPIN/nickel/in.spin.nickel new file mode 100644 index 0000000000000000000000000000000000000000..ba447b077f24c4ee1213aca34325d370657b1f4e --- /dev/null +++ b/examples/SPIN/nickel/in.spin.nickel @@ -0,0 +1,58 @@ +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 + diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..82f54f4e6b208c946edb445c6ec57b5780912802 --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.1 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000804186 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.384 | 7.384 | 7.384 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733807 0.070491717 101.47879 -56307.038 -2218.1018 + 100 0.01 0.028733815 -0.70937134 101.7311 5851.6355 -2218.1018 + 150 0.015 0.028733823 -1.853981 99.63039 2395.8677 -2218.1018 + 200 0.02 0.028733828 -3.2679239 94.850105 1482.3486 -2218.1018 + 250 0.025 0.028733824 -4.863967 88.444584 1100.7396 -2218.1018 + 300 0.03 0.028733807 -6.5763457 82.689581 899.56642 -2218.1018 + 350 0.035 0.028733783 -8.3489158 80.108798 768.64457 -2218.1018 + 400 0.04 0.028733763 -10.120216 82.374947 670.03091 -2218.1018 + 450 0.045 0.028733755 -11.828932 89.814597 593.77931 -2218.1018 + 500 0.05 0.028733762 -13.423712 101.39613 535.03371 -2218.1018 + 550 0.055 0.028733783 -14.866724 115.07399 489.92024 -2218.1018 + 600 0.06 0.028733801 -16.135279 128.57849 458.66654 -2218.1018 + 650 0.065 0.028733804 -17.222838 140.22402 440.11437 -2218.1018 + 700 0.07 0.028733795 -18.154813 149.61295 425.91356 -2218.1018 + 750 0.075 0.028733781 -18.996903 157.5814 412.82654 -2218.1018 + 800 0.08 0.028733768 -19.804249 164.92075 407.77954 -2218.1018 + 850 0.085 0.028733752 -20.579151 171.67278 406.84726 -2218.1018 + 900 0.09 0.028733728 -21.294277 177.67238 399.69633 -2218.1018 + 950 0.095 0.028733715 -21.943945 183.2621 389.92281 -2218.1018 + 1000 0.1 0.02873374 -22.551277 188.99284 383.19592 -2218.1018 + 1050 0.105 0.028733783 -23.120147 194.51391 375.87245 -2218.1018 + 1100 0.11 0.028733792 -23.602325 198.18631 365.37753 -2218.1018 + 1150 0.115 0.028733774 -23.976048 199.04022 354.04863 -2218.1018 + 1200 0.12 0.02873376 -24.31575 198.41999 346.40397 -2218.1018 + 1250 0.125 0.028733759 -24.718347 198.3669 343.1701 -2218.1018 + 1300 0.13 0.028733765 -25.189073 199.57949 336.90052 -2218.1018 + 1350 0.135 0.028733774 -25.650252 201.45897 329.07023 -2218.1018 + 1400 0.14 0.028733785 -26.042702 203.6926 327.97373 -2218.1018 + 1450 0.145 0.028733791 -26.373965 206.80469 327.38747 -2218.1018 + 1500 0.15 0.028733791 -26.691802 211.43923 322.75885 -2218.1018 + 1550 0.155 0.028733794 -27.021573 217.10969 315.55781 -2218.1018 + 1600 0.16 0.028733792 -27.344066 222.16052 310.6743 -2218.1018 + 1650 0.165 0.028733788 -27.640017 225.28449 310.49671 -2218.1018 + 1700 0.17 0.028733803 -27.907241 226.37676 310.9389 -2218.1018 + 1750 0.175 0.028733828 -28.143477 226.31095 313.28034 -2218.1018 + 1800 0.18 0.028733833 -28.363397 226.43633 317.31668 -2218.1018 + 1850 0.185 0.028733811 -28.58153 227.36287 318.98645 -2218.1018 + 1900 0.19 0.028733796 -28.785208 228.39889 316.9972 -2218.1018 + 1950 0.195 0.028733826 -28.9724 228.84666 309.8027 -2218.1018 + 2000 0.2 0.02873386 -29.175039 228.918 297.88519 -2218.1018 +Loop time of 10.033 on 1 procs for 2000 steps with 500 atoms + +Performance: 1.722 ns/day, 13.935 hours/ns, 199.342 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.909 | 3.909 | 3.909 | 0.0 | 38.96 +Neigh | 0.031031 | 0.031031 | 0.031031 | 0.0 | 0.31 +Comm | 0.046559 | 0.046559 | 0.046559 | 0.0 | 0.46 +Output | 2.4087 | 2.4087 | 2.4087 | 0.0 | 24.01 +Modify | 3.625 | 3.625 | 3.625 | 0.0 | 36.13 +Other | | 0.01268 | | | 0.13 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1956 ave 1956 max 1956 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 19508 ave 19508 max 19508 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 39016 ave 39016 max 39016 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39016 +Ave neighs/atom = 78.032 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..373271459f2e68ede27cbd9b7fa635bc089c917f --- /dev/null +++ b/examples/SPIN/nickel/log.11May18.spin.nickel.g++.4 @@ -0,0 +1,157 @@ +LAMMPS (11 May 2018) +# fcc nickel in a 3d periodic box + +clear +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice fcc 3.524 +Lattice spacing in x,y,z = 3.524 3.524 3.524 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (17.62 17.62 17.62) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000523567 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.69 + +set group all spin/random 31 0.63 + 500 settings made for spin/random +#set group all spin 0.63 0.0 0.0 1.0 +velocity all create 100 4928459 rot yes dist gaussian + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Ni99.eam.alloy Ni +pair_coeff * * spin/exchange exchange 4.0 0.50 0.2280246862 1.229983475 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp v_tmag etotal +thermo 50 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 50 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 2000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.90375 + ghost atom cutoff = 5.90375 + binsize = 2.95187, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.298 | 7.298 | 7.298 Mbytes +Step Time v_magnorm v_emag Temp v_tmag TotEng + 0 0 0.028733803 0.40997576 100.03408 -9550.1342 -2218.1018 + 50 0.005 0.028733805 0.25324083 98.741633 -15727.749 -2218.1018 + 100 0.01 0.028733812 -0.37320751 97.073875 11244.373 -2218.1018 + 150 0.015 0.028733819 -1.3971549 94.073447 3250.0517 -2218.1018 + 200 0.02 0.028733825 -2.7238372 89.419944 1838.752 -2218.1018 + 250 0.025 0.028733829 -4.2684428 84.07494 1304.3675 -2218.1018 + 300 0.03 0.028733824 -5.9636712 80.06368 1025.7815 -2218.1018 + 350 0.035 0.02873381 -7.7386326 79.366702 844.49729 -2218.1018 + 400 0.04 0.028733802 -9.5148059 83.052751 715.20758 -2218.1018 + 450 0.045 0.028733806 -11.234935 91.282747 621.75552 -2218.1018 + 500 0.05 0.02873381 -12.875184 103.49836 550.04479 -2218.1018 + 550 0.055 0.028733808 -14.413473 118.16526 495.70417 -2218.1018 + 600 0.06 0.028733803 -15.812466 132.83837 461.35805 -2218.1018 + 650 0.065 0.028733808 -17.061311 145.41049 444.38951 -2218.1018 + 700 0.07 0.028733818 -18.181903 154.83414 438.85866 -2218.1018 + 750 0.075 0.028733823 -19.176259 160.58645 436.90462 -2218.1018 + 800 0.08 0.028733825 -20.035157 163.02829 429.73193 -2218.1018 + 850 0.085 0.028733825 -20.806548 164.4197 419.73763 -2218.1018 + 900 0.09 0.028733829 -21.571419 167.8571 411.59699 -2218.1018 + 950 0.095 0.028733825 -22.365879 175.00875 402.66175 -2218.1018 + 1000 0.1 0.028733821 -23.133464 184.68305 391.05824 -2218.1018 + 1050 0.105 0.028733833 -23.770507 193.83795 379.23354 -2218.1018 + 1100 0.11 0.02873385 -24.249882 200.5039 372.08521 -2218.1018 + 1150 0.115 0.028733864 -24.630489 204.46984 367.92135 -2218.1018 + 1200 0.12 0.028733877 -24.956281 205.96624 363.72367 -2218.1018 + 1250 0.125 0.028733884 -25.227332 205.18503 361.09236 -2218.1018 + 1300 0.13 0.028733877 -25.43568 202.76969 359.10924 -2218.1018 + 1350 0.135 0.028733868 -25.588748 199.85462 358.69556 -2218.1018 + 1400 0.14 0.028733866 -25.723582 197.99165 360.27856 -2218.1018 + 1450 0.145 0.028733851 -25.866283 198.30283 360.46623 -2218.1018 + 1500 0.15 0.028733812 -26.014569 200.95517 354.66722 -2218.1018 + 1550 0.155 0.02873379 -26.192673 205.95485 348.37935 -2218.1018 + 1600 0.16 0.028733795 -26.444059 212.87557 345.53576 -2218.1018 + 1650 0.165 0.028733838 -26.75551 219.86449 338.9224 -2218.1018 + 1700 0.17 0.028733868 -27.068513 224.47868 327.81241 -2218.1018 + 1750 0.175 0.028733862 -27.344118 225.62318 319.85486 -2218.1018 + 1800 0.18 0.028733849 -27.57563 224.07463 320.07064 -2218.1018 + 1850 0.185 0.028733852 -27.774274 221.70618 323.12599 -2218.1018 + 1900 0.19 0.028733864 -27.967999 220.53947 322.9504 -2218.1018 + 1950 0.195 0.028733863 -28.173041 221.61407 318.63401 -2218.1018 + 2000 0.2 0.028733853 -28.362177 224.22281 310.55185 -2218.1018 +Loop time of 3.95094 on 4 procs for 2000 steps with 500 atoms + +Performance: 4.374 ns/day, 5.487 hours/ns, 506.208 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0289 | 1.0467 | 1.0811 | 2.0 | 26.49 +Neigh | 0.0079527 | 0.0081946 | 0.0084369 | 0.2 | 0.21 +Comm | 0.094456 | 0.13311 | 0.15138 | 6.2 | 3.37 +Output | 0.69702 | 0.71998 | 0.74483 | 2.1 | 18.22 +Modify | 2.0107 | 2.0383 | 2.0598 | 1.3 | 51.59 +Other | | 0.004668 | | | 0.12 + +Nlocal: 125 ave 132 max 120 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 1099 ave 1104 max 1092 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 4876.5 ave 5100 max 4721 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +FullNghs: 9753 ave 10296 max 9362 min +Histogram: 2 0 0 0 0 1 0 0 0 1 + +Total # of neighbors = 39012 +Ave neighs/atom = 78.024 +Neighbor list builds = 21 +Dangerous builds = 0 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy new file mode 120000 index 0000000000000000000000000000000000000000..6a47c9eebef2dc333daa871fc882f2afc038bd4c --- /dev/null +++ b/examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy @@ -0,0 +1 @@ +../cobalt_fcc/Co_PurjaPun_2012.eam.alloy \ No newline at end of file diff --git a/examples/SPIN/read_restart/Norm_randXY_8x8x32.data b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data new file mode 100644 index 0000000000000000000000000000000000000000..d239bb6ca07359deb45bf37e6fbbb7447fa8458a --- /dev/null +++ b/examples/SPIN/read_restart/Norm_randXY_8x8x32.data @@ -0,0 +1,8207 @@ +LAMMPS data file via write_data, version 4 May 2017, timestep = 0 + +8192 atoms +1 atom types + +0.0000000000000000e+00 2.8320000000000000e+01 xlo xhi +0.0000000000000000e+00 2.8320000000000000e+01 ylo yhi +0.0000000000000000e+00 1.1328000000000000e+02 zlo zhi + +Masses + +1 58.93 + +Atoms # spin + +1 1 1.72 0.0 0.0 0.0 0.52887 -0.848703 1.0 +2 1 1.72 1.77 1.77 0.0 -0.745115 -0.666936 1.0 +3 1 1.72 1.77 0.0 1.77 -0.989437 -0.144964 1.0 +4 1 1.72 0.0 1.77 1.77 0.999926 -0.0121449 1.0 +5 1 1.72 3.54 0.0 0.0 0.377063 -0.926188 1.0 +6 1 1.72 5.31 1.77 0.0 0.412944 0.910756 1.0 +7 1 1.72 5.31 0.0 1.77 -0.999979 0.00650985 1.0 +8 1 1.72 3.54 1.77 1.77 0.535453 -0.844565 1.0 +9 1 1.72 7.0799999 0.0 0.0 -0.986135 0.165942 1.0 +10 1 1.72 8.8500004 1.77 0.0 -0.37352 -0.927622 1.0 +11 1 1.72 8.8500004 0.0 1.77 -0.926878 0.375363 1.0 +12 1 1.72 7.0799999 1.77 1.77 -0.690063 -0.72375 1.0 +13 1 1.72 10.6199999 0.0 0.0 -0.7204 -0.693559 1.0 +14 1 1.72 12.3900004 1.77 0.0 -0.832046 -0.554707 1.0 +15 1 1.72 12.3900004 0.0 1.77 0.23719 0.971463 1.0 +16 1 1.72 10.6199999 1.77 1.77 0.456617 -0.889663 1.0 +17 1 1.72 14.1599999 0.0 0.0 -0.661715 0.749755 1.0 +18 1 1.72 15.9300004 1.77 0.0 -0.847309 -0.531099 1.0 +19 1 1.72 15.9300004 0.0 1.77 -0.956536 0.291614 1.0 +20 1 1.72 14.1599999 1.77 1.77 -0.770778 -0.637104 1.0 +21 1 1.72 17.7000008 0.0 0.0 -0.896558 -0.442927 1.0 +22 1 1.72 19.4699993 1.77 0.0 0.557673 0.830061 1.0 +23 1 1.72 19.4699993 0.0 1.77 0.983224 0.182403 1.0 +24 1 1.72 17.7000008 1.77 1.77 -0.939201 0.343368 1.0 +25 1 1.72 21.2399998 0.0 0.0 0.894393 0.447281 1.0 +26 1 1.72 23.0100002 1.77 0.0 0.484661 0.874702 1.0 +27 1 1.72 23.0100002 0.0 1.77 0.525609 -0.850726 1.0 +28 1 1.72 21.2399998 1.77 1.77 0.551899 0.833911 1.0 +29 1 1.72 24.7800007 0.0 0.0 -0.307979 0.951393 1.0 +30 1 1.72 26.5499993 1.77 0.0 -0.993353 -0.115107 1.0 +31 1 1.72 26.5499993 0.0 1.77 0.786777 -0.617237 1.0 +32 1 1.72 24.7800007 1.77 1.77 -0.646691 0.762752 1.0 +33 1 1.72 0.0 3.54 0.0 0.119106 -0.992881 1.0 +34 1 1.72 1.77 5.31 0.0 0.719383 0.694614 1.0 +35 1 1.72 1.77 3.54 1.77 -0.704699 0.709506 1.0 +36 1 1.72 0.0 5.31 1.77 0.795511 -0.605939 1.0 +37 1 1.72 3.54 3.54 0.0 -0.97 -0.243107 1.0 +38 1 1.72 5.31 5.31 0.0 0.976076 0.217428 1.0 +39 1 1.72 5.31 3.54 1.77 0.735471 -0.677556 1.0 +40 1 1.72 3.54 5.31 1.77 -0.319137 -0.947708 1.0 +41 1 1.72 7.0799999 3.54 0.0 -0.610942 0.791675 1.0 +42 1 1.72 8.8500004 5.31 0.0 -0.679543 0.733635 1.0 +43 1 1.72 8.8500004 3.54 1.77 0.983607 -0.180324 1.0 +44 1 1.72 7.0799999 5.31 1.77 -0.217118 -0.976145 1.0 +45 1 1.72 10.6199999 3.54 0.0 -0.997762 0.0668716 1.0 +46 1 1.72 12.3900004 5.31 0.0 0.275194 -0.961389 1.0 +47 1 1.72 12.3900004 3.54 1.77 -0.828419 -0.560108 1.0 +48 1 1.72 10.6199999 5.31 1.77 0.118246 -0.992984 1.0 +49 1 1.72 14.1599999 3.54 0.0 0.737418 0.675437 1.0 +50 1 1.72 15.9300004 5.31 0.0 0.723539 -0.690283 1.0 +51 1 1.72 15.9300004 3.54 1.77 0.445177 0.895443 1.0 +52 1 1.72 14.1599999 5.31 1.77 -0.0224847 -0.999747 1.0 +53 1 1.72 17.7000008 3.54 0.0 -0.0340097 0.999422 1.0 +54 1 1.72 19.4699993 5.31 0.0 -0.842076 -0.539358 1.0 +55 1 1.72 19.4699993 3.54 1.77 0.628732 -0.777622 1.0 +56 1 1.72 17.7000008 5.31 1.77 -0.710873 -0.70332 1.0 +57 1 1.72 21.2399998 3.54 0.0 -0.997492 0.0707798 1.0 +58 1 1.72 23.0100002 5.31 0.0 -0.643338 -0.765582 1.0 +59 1 1.72 23.0100002 3.54 1.77 -0.891542 0.452938 1.0 +60 1 1.72 21.2399998 5.31 1.77 -0.576343 -0.817208 1.0 +61 1 1.72 24.7800007 3.54 0.0 0.915658 -0.401959 1.0 +62 1 1.72 26.5499993 5.31 0.0 -0.674018 -0.738715 1.0 +63 1 1.72 26.5499993 3.54 1.77 -0.92775 -0.373203 1.0 +64 1 1.72 24.7800007 5.31 1.77 -0.336441 0.941705 1.0 +65 1 1.72 0.0 7.0799999 0.0 0.499974 0.86604 1.0 +66 1 1.72 1.77 8.8500004 0.0 -0.582403 0.8129 1.0 +67 1 1.72 1.77 7.0799999 1.77 0.46326 -0.886222 1.0 +68 1 1.72 0.0 8.8500004 1.77 0.812676 -0.582716 1.0 +69 1 1.72 3.54 7.0799999 0.0 0.572515 0.819894 1.0 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109.7399979 0.945592 -0.325356 1.0 +8087 1 1.72 19.4699993 14.1599999 111.5100022 0.237079 -0.97149 1.0 +8088 1 1.72 17.7000008 15.9300004 111.5100022 0.541095 -0.840961 1.0 +8089 1 1.72 21.2399998 14.1599999 109.7399979 0.547786 0.836619 1.0 +8090 1 1.72 23.0100002 15.9300004 109.7399979 -0.810246 0.58609 1.0 +8091 1 1.72 23.0100002 14.1599999 111.5100022 -0.0396045 -0.999215 1.0 +8092 1 1.72 21.2399998 15.9300004 111.5100022 0.999244 0.0388725 1.0 +8093 1 1.72 24.7800007 14.1599999 109.7399979 -0.995393 -0.0958841 1.0 +8094 1 1.72 26.5499993 15.9300004 109.7399979 0.707666 -0.706547 1.0 +8095 1 1.72 26.5499993 14.1599999 111.5100022 -0.857797 0.513989 1.0 +8096 1 1.72 24.7800007 15.9300004 111.5100022 0.688346 0.725383 1.0 +8097 1 1.72 0.0 17.7000008 109.7399979 0.453695 0.891157 1.0 +8098 1 1.72 1.77 19.4699993 109.7399979 -0.869991 0.493068 1.0 +8099 1 1.72 1.77 17.7000008 111.5100022 -0.828945 0.55933 1.0 +8100 1 1.72 0.0 19.4699993 111.5100022 -0.578312 -0.815815 1.0 +8101 1 1.72 3.54 17.7000008 109.7399979 -0.474111 -0.880465 1.0 +8102 1 1.72 5.31 19.4699993 109.7399979 -0.953145 0.302515 1.0 +8103 1 1.72 5.31 17.7000008 111.5100022 -0.662482 0.749078 1.0 +8104 1 1.72 3.54 19.4699993 111.5100022 -0.673709 0.738997 1.0 +8105 1 1.72 7.0799999 17.7000008 109.7399979 0.703708 0.71049 1.0 +8106 1 1.72 8.8500004 19.4699993 109.7399979 -0.962777 0.270298 1.0 +8107 1 1.72 8.8500004 17.7000008 111.5100022 -0.409325 0.912389 1.0 +8108 1 1.72 7.0799999 19.4699993 111.5100022 0.992278 0.12403 1.0 +8109 1 1.72 10.6199999 17.7000008 109.7399979 -0.256869 -0.966446 1.0 +8110 1 1.72 12.3900004 19.4699993 109.7399979 -0.81811 0.575062 1.0 +8111 1 1.72 12.3900004 17.7000008 111.5100022 0.944442 -0.328678 1.0 +8112 1 1.72 10.6199999 19.4699993 111.5100022 -0.790776 0.612106 1.0 +8113 1 1.72 14.1599999 17.7000008 109.7399979 0.99885 0.047945 1.0 +8114 1 1.72 15.9300004 19.4699993 109.7399979 -0.75767 0.652638 1.0 +8115 1 1.72 15.9300004 17.7000008 111.5100022 0.104479 -0.994527 1.0 +8116 1 1.72 14.1599999 19.4699993 111.5100022 -0.366155 -0.930554 1.0 +8117 1 1.72 17.7000008 17.7000008 109.7399979 -0.100712 0.994916 1.0 +8118 1 1.72 19.4699993 19.4699993 109.7399979 0.20119 -0.979552 1.0 +8119 1 1.72 19.4699993 17.7000008 111.5100022 0.7043 -0.709902 1.0 +8120 1 1.72 17.7000008 19.4699993 111.5100022 0.995221 -0.0976515 1.0 +8121 1 1.72 21.2399998 17.7000008 109.7399979 0.0913868 0.995815 1.0 +8122 1 1.72 23.0100002 19.4699993 109.7399979 -0.783334 0.6216 1.0 +8123 1 1.72 23.0100002 17.7000008 111.5100022 0.762993 0.646407 1.0 +8124 1 1.72 21.2399998 19.4699993 111.5100022 0.969106 -0.246644 1.0 +8125 1 1.72 24.7800007 17.7000008 109.7399979 -0.99318 -0.116594 1.0 +8126 1 1.72 26.5499993 19.4699993 109.7399979 0.751321 -0.659937 1.0 +8127 1 1.72 26.5499993 17.7000008 111.5100022 -0.41311 -0.910681 1.0 +8128 1 1.72 24.7800007 19.4699993 111.5100022 -0.231533 0.972827 1.0 +8129 1 1.72 0.0 21.2399998 109.7399979 -0.638342 -0.769753 1.0 +8130 1 1.72 1.77 23.0100002 109.7399979 -0.358386 -0.933574 1.0 +8131 1 1.72 1.77 21.2399998 111.5100022 0.0433983 -0.999058 1.0 +8132 1 1.72 0.0 23.0100002 111.5100022 -0.986115 -0.166067 1.0 +8133 1 1.72 3.54 21.2399998 109.7399979 0.996583 0.082601 1.0 +8134 1 1.72 5.31 23.0100002 109.7399979 -0.865815 0.500364 1.0 +8135 1 1.72 5.31 21.2399998 111.5100022 0.446465 0.894801 1.0 +8136 1 1.72 3.54 23.0100002 111.5100022 0.701589 -0.712582 1.0 +8137 1 1.72 7.0799999 21.2399998 109.7399979 0.994388 0.105798 1.0 +8138 1 1.72 8.8500004 23.0100002 109.7399979 0.779675 0.626184 1.0 +8139 1 1.72 8.8500004 21.2399998 111.5100022 -0.913378 0.407112 1.0 +8140 1 1.72 7.0799999 23.0100002 111.5100022 -0.974435 0.22467 1.0 +8141 1 1.72 10.6199999 21.2399998 109.7399979 0.0180628 0.999837 1.0 +8142 1 1.72 12.3900004 23.0100002 109.7399979 -0.393018 0.919531 1.0 +8143 1 1.72 12.3900004 21.2399998 111.5100022 0.171283 -0.985222 1.0 +8144 1 1.72 10.6199999 23.0100002 111.5100022 0.853928 0.520391 1.0 +8145 1 1.72 14.1599999 21.2399998 109.7399979 -0.893534 -0.448996 1.0 +8146 1 1.72 15.9300004 23.0100002 109.7399979 0.783901 0.620886 1.0 +8147 1 1.72 15.9300004 21.2399998 111.5100022 -0.636441 0.771326 1.0 +8148 1 1.72 14.1599999 23.0100002 111.5100022 -0.62653 0.779398 1.0 +8149 1 1.72 17.7000008 21.2399998 109.7399979 -0.426717 -0.904385 1.0 +8150 1 1.72 19.4699993 23.0100002 109.7399979 0.150477 -0.988614 1.0 +8151 1 1.72 19.4699993 21.2399998 111.5100022 0.993032 -0.117843 1.0 +8152 1 1.72 17.7000008 23.0100002 111.5100022 -0.858474 -0.512857 1.0 +8153 1 1.72 21.2399998 21.2399998 109.7399979 0.671527 -0.74098 1.0 +8154 1 1.72 23.0100002 23.0100002 109.7399979 0.724398 -0.689382 1.0 +8155 1 1.72 23.0100002 21.2399998 111.5100022 -0.533734 -0.845652 1.0 +8156 1 1.72 21.2399998 23.0100002 111.5100022 0.446337 0.894865 1.0 +8157 1 1.72 24.7800007 21.2399998 109.7399979 0.100506 -0.994936 1.0 +8158 1 1.72 26.5499993 23.0100002 109.7399979 0.663547 -0.748135 1.0 +8159 1 1.72 26.5499993 21.2399998 111.5100022 -0.838999 0.544134 1.0 +8160 1 1.72 24.7800007 23.0100002 111.5100022 -0.412355 -0.911023 1.0 +8161 1 1.72 0.0 24.7800007 109.7399979 -0.768577 -0.639757 1.0 +8162 1 1.72 1.77 26.5499993 109.7399979 0.876973 -0.480539 1.0 +8163 1 1.72 1.77 24.7800007 111.5100022 0.940988 0.33844 1.0 +8164 1 1.72 0.0 26.5499993 111.5100022 -0.739484 -0.673174 1.0 +8165 1 1.72 3.54 24.7800007 109.7399979 0.463964 0.885854 1.0 +8166 1 1.72 5.31 26.5499993 109.7399979 0.834599 0.550857 1.0 +8167 1 1.72 5.31 24.7800007 111.5100022 -0.414423 -0.910084 1.0 +8168 1 1.72 3.54 26.5499993 111.5100022 0.209991 0.977703 1.0 +8169 1 1.72 7.0799999 24.7800007 109.7399979 -0.200071 -0.979781 1.0 +8170 1 1.72 8.8500004 26.5499993 109.7399979 -0.593916 0.804527 1.0 +8171 1 1.72 8.8500004 24.7800007 111.5100022 -0.976341 -0.216238 1.0 +8172 1 1.72 7.0799999 26.5499993 111.5100022 0.892014 -0.452008 1.0 +8173 1 1.72 10.6199999 24.7800007 109.7399979 0.262541 0.964921 1.0 +8174 1 1.72 12.3900004 26.5499993 109.7399979 -0.541535 -0.840678 1.0 +8175 1 1.72 12.3900004 24.7800007 111.5100022 0.789328 0.613972 1.0 +8176 1 1.72 10.6199999 26.5499993 111.5100022 0.500046 0.865999 1.0 +8177 1 1.72 14.1599999 24.7800007 109.7399979 0.353277 0.935519 1.0 +8178 1 1.72 15.9300004 26.5499993 109.7399979 0.604788 0.796387 1.0 +8179 1 1.72 15.9300004 24.7800007 111.5100022 0.840508 -0.541799 1.0 +8180 1 1.72 14.1599999 26.5499993 111.5100022 0.296351 -0.955079 1.0 +8181 1 1.72 17.7000008 24.7800007 109.7399979 -0.957237 0.289304 1.0 +8182 1 1.72 19.4699993 26.5499993 109.7399979 0.344119 -0.938926 1.0 +8183 1 1.72 19.4699993 24.7800007 111.5100022 -0.989355 -0.145521 1.0 +8184 1 1.72 17.7000008 26.5499993 111.5100022 0.787109 0.616813 1.0 +8185 1 1.72 21.2399998 24.7800007 109.7399979 -0.321766 0.946819 1.0 +8186 1 1.72 23.0100002 26.5499993 109.7399979 -0.647284 -0.762249 1.0 +8187 1 1.72 23.0100002 24.7800007 111.5100022 -0.999094 0.0425548 1.0 +8188 1 1.72 21.2399998 26.5499993 111.5100022 -0.33438 0.942438 1.0 +8189 1 1.72 24.7800007 24.7800007 109.7399979 0.960667 -0.277704 1.0 +8190 1 1.72 26.5499993 26.5499993 109.7399979 0.822147 -0.569276 1.0 +8191 1 1.72 26.5499993 24.7800007 111.5100022 0.915832 -0.401561 1.0 +8192 1 1.72 24.7800007 26.5499993 111.5100022 -0.746316 -0.665592 1.0 diff --git a/examples/SPIN/read_restart/in.spin.read_data b/examples/SPIN/read_restart/in.spin.read_data new file mode 100644 index 0000000000000000000000000000000000000000..80de0366616956ab9b505be148d19fadf3a0bdae --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.read_data @@ -0,0 +1,45 @@ +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.restart b/examples/SPIN/read_restart/in.spin.restart new file mode 100644 index 0000000000000000000000000000000000000000..a1198ccf9351e07e8ae6784a49edece5dcbeab39 --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.restart @@ -0,0 +1,49 @@ +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 diff --git a/examples/SPIN/read_restart/in.spin.write_restart b/examples/SPIN/read_restart/in.spin.write_restart new file mode 100644 index 0000000000000000000000000000000000000000..84fea24611540156a0fdd9d1863d1b745aae67ef --- /dev/null +++ b/examples/SPIN/read_restart/in.spin.write_restart @@ -0,0 +1,55 @@ +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +write_restart restart_hcp_cobalt.equil + diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..405be50bd987b18e6353ae8bd00bc6788c208247 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.1 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 18.68 | 18.68 | 18.68 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249102 -2984.9466433509 51.7121203365409 0 -38881.8459242429 + 10 0.001 0.980832325038224 -2984.94800197308 52.2550760237226 0.00128259392155095 -38881.8459243688 + 20 0.002 0.980832322622779 -2984.95196908579 53.4253029071033 0.0050206854169363 -38881.8459246487 + 30 0.003 0.980832317889283 -2984.95826684048 55.1488791221993 0.0109316238061975 -38881.8459250502 + 40 0.004 0.980832310888481 -2984.96649810512 57.3217709603901 0.0186091353316915 -38881.8459255204 + 50 0.005 0.980832301939686 -2984.97619813381 59.8271487572311 0.0275752699737783 -38881.8459260027 + 60 0.006 0.980832291654664 -2984.98688847988 62.5518654049861 0.0373348857300743 -38881.8459264498 + 70 0.007 0.980832280861627 -2984.99812400566 65.3978892661935 0.0474235455824994 -38881.845926824 + 80 0.008 0.980832270462785 -2985.00952679611 68.286219599829 0.0574425858114516 -38881.8459271072 + 90 0.009 0.980832261284587 -2985.02080458573 71.1539714621652 0.0670788260497413 -38881.8459272915 + 100 0.01 0.980832253960703 -2985.03175506188 73.9486358176052 0.0761100787140068 -38881.8459273845 +Loop time of 12.4286 on 1 procs for 100 steps with 8192 atoms + +Performance: 0.070 ns/day, 345.239 hours/ns, 8.046 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0123 | 4.0123 | 4.0123 | 0.0 | 32.28 +Neigh | 3.005 | 3.005 | 3.005 | 0.0 | 24.18 +Comm | 0.041798 | 0.041798 | 0.041798 | 0.0 | 0.34 +Output | 1.8465 | 1.8465 | 1.8465 | 0.0 | 14.86 +Modify | 3.5157 | 3.5157 | 3.5157 | 0.0 | 28.29 +Other | | 0.007261 | | | 0.06 + +Nlocal: 8192 ave 8192 max 8192 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 14621 ave 14621 max 14621 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 573440 ave 573440 max 573440 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:12 diff --git a/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..56fed3530760762fa2131929f31cb8343daac0e0 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.read_data.g++.4 @@ -0,0 +1,112 @@ +LAMMPS (11 May 2018) +units metal +dimension 3 +boundary p p p + +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array +read_data Norm_randXY_8x8x32.data + orthogonal box = (0 0 0) to (28.32 28.32 113.28) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 8192 atoms + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs and computes + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 10 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 8 8 31 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.994 | 8.25 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 0 0 0.980832325249103 -2984.9466433509 51.7121203365411 0 -38881.8459242507 + 10 0.001 0.980832325329477 -2984.94800197307 52.2550778515409 0.00128259391683994 -38881.8459243698 + 20 0.002 0.980832324654401 -2984.95196908569 53.4253110612179 0.00502068532291255 -38881.8459246487 + 30 0.003 0.98083232312993 -2984.95826683995 55.148898005011 0.0109316232931419 -38881.84592505 + 40 0.004 0.980832320808156 -2984.9664981035 57.3218040934977 0.0186091337978305 -38881.8459255198 + 50 0.005 0.980832317596783 -2984.97619813016 59.827198436387 0.0275752665472358 -38881.8459260035 + 60 0.006 0.980832313514709 -2984.98688847322 62.5519331668858 0.037334879488755 -38881.84592645 + 70 0.007 0.980832309220414 -2984.99812399537 65.3979760533737 0.0474235360022736 -38881.8459268243 + 80 0.008 0.980832304490479 -2985.00952678209 68.2863250613635 0.0574425728014485 -38881.8459271068 + 90 0.009 0.980832299379824 -2985.02080456789 71.1540940309591 0.0670788096168283 -38881.8459272917 + 100 0.01 0.980832294622694 -2985.03175503971 73.9487734241296 0.0761100584457276 -38881.8459273851 +Loop time of 3.6612 on 4 procs for 100 steps with 8192 atoms + +Performance: 0.236 ns/day, 101.700 hours/ns, 27.313 timesteps/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0622 | 1.076 | 1.0936 | 1.1 | 29.39 +Neigh | 0.77462 | 0.79542 | 0.81798 | 1.9 | 21.73 +Comm | 0.024701 | 0.066122 | 0.10261 | 11.1 | 1.81 +Output | 0.50304 | 0.51253 | 0.52111 | 0.9 | 14.00 +Modify | 1.2006 | 1.2082 | 1.2205 | 0.7 | 33.00 +Other | | 0.002962 | | | 0.08 + +Nlocal: 2048 ave 2095 max 1981 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 5765 ave 5832 max 5718 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Neighs: 143360 ave 146361 max 139058 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +FullNghs: 286720 ave 293300 max 277340 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 1146880 +Ave neighs/atom = 140 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..16eb7c3f5e9ccf9d72f69b6ac90a2a43cfe6d33b --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.1 @@ -0,0 +1,117 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.315 | 6.315 | 6.315 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448938 5244.87332482316 0 -2206.81097898043 + 1010 0.001 0.106120047478105 -11.8198467887534 5263.87502105137 0.136650312456579 -2206.81097929055 + 1020 0.002 0.106120026430373 -11.8460960518731 5267.29822866382 0.542282409605327 -2206.81098022997 + 1030 0.003 0.106120005015917 -11.8891434078861 5252.95323564256 1.204018338139 -2206.81098172551 + 1040 0.004 0.106119988532653 -11.9479778701641 5220.88508622311 2.10120884995911 -2206.81098371047 + 1050 0.005 0.10611998133687 -12.021242685853 5172.58549378915 3.20622445795757 -2206.81098610701 + 1060 0.006 0.10611998489458 -12.107271344148 5110.57395203849 4.48535975411235 -2206.81098879725 + 1070 0.007 0.106119996964771 -12.204156761765 5038.48903231346 5.9003121044977 -2206.81099161183 + 1080 0.008 0.106120013042521 -12.3098695046152 4961.0327167967 7.4104497466856 -2206.81099434653 + 1090 0.009 0.106120029236234 -12.4224157835754 4883.3210922213 8.97568980540163 -2206.81099680117 + 1100 0.01 0.106120044071404 -12.5400036896932 4809.88136080052 10.559459821976 -2206.81099883104 +Loop time of 0.833234 on 1 procs for 100 steps with 500 atoms + +Performance: 1.037 ns/day, 23.145 hours/ns, 120.014 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.26558 | 0.26558 | 0.26558 | 0.0 | 31.87 +Neigh | 0.21352 | 0.21352 | 0.21352 | 0.0 | 25.62 +Comm | 0.0057988 | 0.0057988 | 0.0057988 | 0.0 | 0.70 +Output | 0.12463 | 0.12463 | 0.12463 | 0.0 | 14.96 +Modify | 0.22275 | 0.22275 | 0.22275 | 0.0 | 26.73 +Other | | 0.0009537 | | | 0.11 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2534 ave 2534 max 2534 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 36500 ave 36500 max 36500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 73000 ave 73000 max 73000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..f93605a10a2e28eb923241d1fc629eea81ecf31f --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.restart.g++.4 @@ -0,0 +1,118 @@ +LAMMPS (11 May 2018) +# start a spin-lattice simulation from a data file +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +read_restart restart_hcp_cobalt.equil +WARNING: Restart file used different # of processors (../read_restart.cpp:723) + restoring atom style spin from restart + orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid + restoring pair style spin/exchange from restart + 500 atoms + +# setting mass, mag. moments, and interactions + +mass 1 58.93 + +pair_style hybrid/overlay eam/alloy spin/exchange 4.0 +pair_coeff * * eam/alloy Co_PurjaPun_2012.eam.alloy Co +pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 1.0 bin +neigh_modify every 1 check no delay 0 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 0.0 0.0 21 + +fix 3 all nve/spin lattice yes +timestep 0.0001 + +# define outputs + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 10 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.49954 + ghost atom cutoff = 7.49954 + binsize = 3.74977, bins = 4 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair eam/alloy, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes +Step Time v_magnorm v_emag v_tmag Temp TotEng + 1000 0 0.106120063678768 -11.8110267448939 5244.87332482316 0 -2206.81097898003 + 1010 0.001 0.106120030254187 -11.8198467883806 5263.87550015043 0.136650306637598 -2206.81097929055 + 1020 0.002 0.106119996655714 -11.8460960476455 5267.299198699 0.542282344092749 -2206.81098022997 + 1030 0.003 0.106119967407682 -11.8891433919665 5252.95473019843 1.20401809237154 -2206.81098172552 + 1040 0.004 0.106119960016585 -11.9479778326021 5220.88686874944 2.10120827278397 -2206.81098371049 + 1050 0.005 0.106119961252471 -12.0212426191481 5172.58712301374 3.20622343988728 -2206.81098610703 + 1060 0.006 0.106119967598995 -12.1072712483404 5110.57504803718 4.48535830705751 -2206.81098879724 + 1070 0.007 0.106119967669058 -12.2041566468564 5038.48927079832 5.90031039867811 -2206.81099161179 + 1080 0.008 0.106119969263395 -12.3098693905406 4961.03212459716 7.41044810751949 -2206.8109943465 + 1090 0.009 0.106119960964075 -12.4224156966204 4883.31968289062 8.97568865379831 -2206.81099680112 + 1100 0.01 0.106119945605273 -12.5400036591612 4809.87930844463 10.5594596175303 -2206.81099883101 +Loop time of 0.304678 on 4 procs for 100 steps with 500 atoms + +Performance: 2.836 ns/day, 8.463 hours/ns, 328.215 timesteps/s +98.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.071445 | 0.073018 | 0.074151 | 0.4 | 23.97 +Neigh | 0.054448 | 0.055709 | 0.057528 | 0.5 | 18.28 +Comm | 0.0061178 | 0.0074609 | 0.0090766 | 1.2 | 2.45 +Output | 0.037489 | 0.038586 | 0.039952 | 0.5 | 12.66 +Modify | 0.12826 | 0.12954 | 0.13065 | 0.3 | 42.52 +Other | | 0.0003686 | | | 0.12 + +Nlocal: 125 ave 129 max 120 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 1387 ave 1392 max 1383 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 9125 ave 9428 max 8740 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 18250 ave 18834 max 17520 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 73000 +Ave neighs/atom = 146 +Neighbor list builds = 100 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c3be90cb505bace4db678ff8fb4f94d5dce948d2 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.00027585 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.446 | 6.446 | 6.446 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.079107243 0.56368447 0 0.56368447 + 200 0.02 0.08225862 -0.42421042 0 -0.42421042 + 300 0.03 0.08397714 -1.4964948 0 -1.4964948 + 400 0.04 0.084704989 -2.6740652 0 -2.6740652 + 500 0.05 0.087486342 -4.2043382 0 -4.2043382 + 600 0.06 0.09187261 -5.6687169 0 -5.6687169 + 700 0.07 0.096925249 -6.937499 0 -6.937499 + 800 0.08 0.098988236 -8.2456715 0 -8.2456715 + 900 0.09 0.10434092 -10.111953 0 -10.111953 + 1000 0.1 0.10612006 -11.811027 0 -11.811027 +Loop time of 2.60215 on 1 procs for 1000 steps with 500 atoms + +Performance: 3.320 ns/day, 7.228 hours/ns, 384.297 timesteps/s +99.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.35178 | 0.35178 | 0.35178 | 0.0 | 13.52 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014421 | 0.014421 | 0.014421 | 0.0 | 0.55 +Output | 1.2046 | 1.2046 | 1.2046 | 0.0 | 46.29 +Modify | 1.0274 | 1.0274 | 1.0274 | 0.0 | 39.48 +Other | | 0.004006 | | | 0.15 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1221 ave 1221 max 1221 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 10000 ave 10000 max 10000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..e54299b9ddbef2d6328c7d4cc1b62c212ddcc019 --- /dev/null +++ b/examples/SPIN/read_restart/log.11May18.spin.write_restart.g++.4 @@ -0,0 +1,119 @@ +LAMMPS (11 May 2018) +# fcc cobalt in a 3d periodic box + +units metal +atom_style spin + +dimension 3 +boundary p p p + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice hcp 2.5071 +Lattice spacing in x,y,z = 2.5071 4.34242 4.09408 +region box block 0.0 5.0 0.0 5.0 0.0 5.0 +create_box 1 box +Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 500 atoms + Time spent = 0.000257969 secs + +# setting mass, mag. moments, and interactions for cobalt + +mass 1 58.93 + +set group all spin/random 31 1.72 + 500 settings made for spin/random + +pair_style spin/exchange 4.0 +pair_coeff * * exchange 4.0 0.3593 1.135028015e-05 1.064568567 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0 +fix 2 all langevin/spin 100.0 0.01 21 + +fix 3 all nve/spin lattice no +timestep 0.0001 + +# compute and output options + +compute out_mag all compute/spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo_style custom step time v_magnorm v_emag temp etotal +thermo 100 + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +run 1000 +Neighbor list info ... + update every 10 steps, delay 20 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.1 + ghost atom cutoff = 4.1 + binsize = 2.05, bins = 7 11 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair spin/exchange, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.367 | 6.367 | 6.367 Mbytes +Step Time v_magnorm v_emag Temp TotEng + 0 0 0.076558814 1.7982359 0 1.7982359 + 100 0.01 0.081414414 0.70545723 0 0.70545723 + 200 0.02 0.084519539 -0.33171078 0 -0.33171078 + 300 0.03 0.089334139 -1.3988283 0 -1.3988283 + 400 0.04 0.092873722 -2.8519371 0 -2.8519371 + 500 0.05 0.0970839 -4.1531164 0 -4.1531164 + 600 0.06 0.099626132 -5.7993765 0 -5.7993765 + 700 0.07 0.10467169 -7.3011333 0 -7.3011333 + 800 0.08 0.10893493 -8.6918141 0 -8.6918141 + 900 0.09 0.11389657 -10.236174 0 -10.236174 + 1000 0.1 0.1180057 -11.896933 0 -11.896933 +Loop time of 1.05012 on 4 procs for 1000 steps with 500 atoms + +Performance: 8.228 ns/day, 2.917 hours/ns, 952.272 timesteps/s +98.1% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.08972 | 0.090456 | 0.091872 | 0.3 | 8.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016958 | 0.018047 | 0.019791 | 0.8 | 1.72 +Output | 0.36286 | 0.37483 | 0.38975 | 1.6 | 35.69 +Modify | 0.55131 | 0.56541 | 0.57702 | 1.3 | 53.84 +Other | | 0.001374 | | | 0.13 + +Nlocal: 125 ave 125 max 125 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 597.5 ave 600 max 595 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2500 ave 2500 max 2500 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10000 +Ave neighs/atom = 20 +Neighbor list builds = 0 +Dangerous builds = 0 +write_restart restart_hcp_cobalt.equil + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/SPIN/vmd/prepare_vmd.sh b/examples/SPIN/vmd/prepare_vmd.sh new file mode 100755 index 0000000000000000000000000000000000000000..fa62c6e109d75315abbd26bb4467d7c5d02c9cb3 --- /dev/null +++ b/examples/SPIN/vmd/prepare_vmd.sh @@ -0,0 +1,91 @@ +#!/bin/bash +# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj +# you will get a return file + +echo "vmd script for file $1 is preparing..." + +timestamp(){ + date +%s +} + +TS=$(timestamp) +FILE=view_${TS}.vmd + +cat >${FILE} <] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength \$args] < 3} { + error "wrong # args: should be \$usage" + } + set mol [lindex \$args 0] + set center [lindex \$args 1] + set vector [lindex \$args 2] + if {[llength \$center] != 3 || [llength \$vector] != 3} { + error "wrong type of args: should be \$usage" + } + + foreach {flag value} [lrange \$args 3 end] { + switch -glob \$flag { + scale {set scale \$value} + res* {set res \$value} + rad* {set radius \$value} + fill* {set filled \$value} + default {error "unknown option '\$flag': should be \$usage" } + } + } + + set vechalf [vecscale [expr \$scale * 0.5] \$vector] + return [list \\ + [graphics \$mol color yellow]\\ + [graphics \$mol cylinder [vecsub \$center \$vechalf]\\ + [vecadd \$center [vecscale 0.7 \$vechalf]] \\ + radius \$radius resolution \$res filled \$filled] \\ + [graphics \$mol color orange]\\ + [graphics \$mol cone [vecadd \$center [vecscale 0.6 \$vechalf]] \\ + [vecadd \$center \$vechalf] radius [expr \$radius * 2.5] \\ + resolution \$res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics \$molid delete all + set frame [molinfo \$molid get frame] + set natoms [molinfo \$molid get numatoms] + for {set i 0} {\$i < \$natoms} {incr i} { + set sel [atomselect top "index \$i"] + set coords [lindex [\$sel get {x y z}] \$molid] + set velocities [lindex [\$sel get {vx vy vz}] \$molid] + draw vector \$coords \$velocities + set uvx [lindex [\$sel get {vx}] \$molid] + set uvy [lindex [\$sel get {vy}] \$molid] + set uvz [lindex [\$sel get {vz}] \$molid] + \$sel set user [vecadd [vecadd [vecscale \$uvy \$uvy] [vecscale \$uvz \$uvz] ] [vecscale \$uvx \$uvx]] + \$sel set user \$uvy + #draw vector \$coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin +} + +set molid [mol addfile {$1} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace +EOF +echo "$FILE is ready..." diff --git a/examples/SPIN/vmd/vmd_nano.vmd b/examples/SPIN/vmd/vmd_nano.vmd new file mode 100644 index 0000000000000000000000000000000000000000..f9e345427076250c5c98e96a9f9b625c6354947d --- /dev/null +++ b/examples/SPIN/vmd/vmd_nano.vmd @@ -0,0 +1,79 @@ +proc vmd_draw_arrow {mol start end} { + set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]] + graphics $mol cylinder $start $middle radius 0.05 + graphics $mol cone $middle $end radius 0.01 color 3 +} + +proc vmd_draw_vector {args} { + set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale ] [resolution ] [radius ] [filled ]"} + # defaults + set scale 2.0 + set res 50 + set radius 0.1 + set filled yes + + if {[llength $args] < 3} { + error "wrong # args: should be $usage" + } + set mol [lindex $args 0] + set center [lindex $args 1] + set vector [lindex $args 2] + if {[llength $center] != 3 || [llength $vector] != 3} { + error "wrong type of args: should be $usage" + } + + foreach {flag value} [lrange $args 3 end] { + switch -glob $flag { + scale {set scale $value} + res* {set res $value} + rad* {set radius $value} + fill* {set filled $value} + default {error "unknown option '$flag': should be $usage" } + } + } + + set vechalf [vecscale [expr $scale * 0.5] $vector] + return [list \ + [graphics $mol color yellow]\ + [graphics $mol cylinder [vecsub $center $vechalf]\ + [vecadd $center [vecscale 0.7 $vechalf]] \ + radius $radius resolution $res filled $filled] \ + [graphics $mol color orange]\ + [graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \ + [vecadd $center $vechalf] radius [expr $radius * 2.5] \ + resolution $res]] +} + +proc vmd_draw_spin {args} { + global molid + graphics $molid delete all + set frame [molinfo $molid get frame] + set natoms [molinfo $molid get numatoms] + for {set i 0} {$i < $natoms} {incr i} { + set sel [atomselect top "index $i"] +# set sel [atomselect top "index 1200"] + set coords [lindex [$sel get {x y z}] $molid] + set velocities [lindex [$sel get {vx vy vz}] $molid] + draw vector $coords $velocities + set uvx [lindex [$sel get {vx}] $molid] + set uvy [lindex [$sel get {vy}] $molid] + set uvz [lindex [$sel get {vz}] $molid] + $sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]] + $sel set user $uvy + #draw vector $coords {0.0 uvy 0.0} + } + #pbc box -color 3 +} + +proc enable_trace {} { + global vmd_frame + trace variable vmd_frame([molinfo top]) w vmd_draw_spin + } + +set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all] +scale by 0.5 +animate style Loop +enable_trace + + + diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/BulkNi.in index a18163175cf35f9d125307df4dc8c7534d5526a5..0fa9c1b74c2c41d9917d21b7167d4761403a2c2b 100644 --- a/examples/USER/diffraction/BulkNi.in +++ b/examples/USER/diffraction/BulkNi.in @@ -20,7 +20,7 @@ compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 1 0 0 c 0.025 0.025 0.025 & dR_Ewald 0.05 echo manual -fix 1 all ave/histo 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & mode vector file $A.hist.xrd fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed diff --git a/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs new file mode 100644 index 0000000000000000000000000000000000000000..76ecae7b44401c7a2dc6380514ab33b9fc05f29a --- /dev/null +++ b/examples/USER/misc/entropy/Na_MendelevM_2014.eam.fs @@ -0,0 +1,6006 @@ +Source: M.I. Mendelev, unpublished +Contact information: mendelev@ameslab.gov +Tuesday, Sep 2, 2014 The potential was taken from v1_4_bcc (in C:\SIMULATION.MD\Na\Results\v1_4) +1 Na +10000 1.00000000000000E-0002 10000 9.20000000000000E-0004 9.20000000000000E+0000 +11 2.29897700000000E+0001 4.22786798098572E+0000 bcc +0 -1.00000000000000E-0001 -1.41421356237310E-0001 -1.73205080756888E-0001 -2.00000000000000E-0001 +-2.23606797749979E-0001 -2.44948974278318E-0001 -2.64575131106459E-0001 -2.82842712474619E-0001 -3.00000000000000E-0001 +-3.16227766016838E-0001 -3.31662479035540E-0001 -3.46410161513775E-0001 -3.60555127546399E-0001 -3.74165738677394E-0001 +-3.87298334620742E-0001 -4.00000000000000E-0001 -4.12310562561766E-0001 -4.24264068711929E-0001 -4.35889894354067E-0001 +-4.47213595499958E-0001 -4.58257569495584E-0001 -4.69041575982343E-0001 -4.79583152331272E-0001 -4.89897948556636E-0001 +-5.00000000000000E-0001 -5.09901951359279E-0001 -5.19615242270663E-0001 -5.29150262212918E-0001 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5.3475882301508628e+00 -4.2408022628023092e+00 2.8635136565717958e+00 +3635 4.4614680716667365e+00 6.2902271235152298e+00 -5.0718257577217107e-01 +3697 -2.3133908750710659e+00 4.8943513150812494e+00 1.9433222354694877e+00 +3850 -2.3520082780840483e+00 -4.1382139646522829e+00 -4.2313549631213059e+00 +3572 5.2887124760018267e+00 -4.3056356137804634e+00 6.9026361811244985e-01 +2624 1.7265686526178390e+00 -1.5412180689889587e+00 -3.0934661542201152e+00 +3807 -5.4848006405032041e+00 2.8242358170289159e+00 4.0218318776038071e+00 +4057 -1.9436173231502683e+00 -6.4379617617013585e-01 2.9422585763085856e+00 +3575 4.8405797034935167e+00 1.8151525525656706e-01 -1.7336806690066728e+00 +3533 6.2985102473952148e+00 -3.8737828734077979e+00 5.9554831944004860e-01 +3749 -2.3060762715548426e+00 -1.5566670264415590e+00 7.6409930776677175e+00 +3628 1.1047697174211357e+00 4.5872009773756268e+00 -4.3312248695892714e+00 +3463 -4.0202543908176064e-01 1.0543123597897606e+00 -4.5095953260218593e+00 +3339 4.4461045576277334e+00 2.7023074862421219e+00 6.5761907532557173e-01 +3605 -1.9130986635970524e+00 3.9668547188660113e+00 -6.3242395502805584e+00 +3643 4.2561654139359133e+00 2.7079886942829829e+00 2.7399717274611493e+00 +3679 -2.1411701998224424e+00 -1.6132315381071032e+00 7.2516729511827427e-01 +3324 -8.2027537927136707e-01 -2.7694148205687066e+00 2.4736641085737388e+00 +3274 -4.4417852313637960e+00 -3.1061873476270003e+00 -4.2202494315305700e-01 +3779 -6.8867094633379926e+00 8.9727449535086627e+00 2.8636972542619379e+00 +621 3.0864972952518466e+00 -7.7377722234997837e-01 1.2106492653280587e-01 +3759 4.2946340382075698e+00 -2.7309518923249305e+00 -7.9384037173415658e+00 +3903 5.6188342028914784e+00 -2.7814248255132510e+00 -7.5133775402016285e+00 +3247 -1.6193326128196186e+00 -1.7233073750291210e+00 1.2558642428529292e+00 +3620 3.1413258846560623e+00 4.1189507481056093e+00 -6.3921202343711521e+00 +3984 1.3917530918758356e+00 -2.3497816055013883e+00 -1.4662677833340403e+00 +3359 -9.7958489915505709e-01 -7.9530975508665236e-01 3.6113761736403754e-01 +3728 4.3499495062909288e+00 -3.0962919910136191e+00 2.5291553497464387e+00 +3105 -2.1324777268885367e+00 4.6999502576160301e+00 -1.1831903765756278e+00 +2913 9.6792227860968549e-01 -8.2454190909792562e+00 -3.4600835572456634e+00 +105 1.1598974321010078e+00 6.6642846330522749e+00 -3.1397454859758240e+00 +3786 2.4337460674831185e-01 1.7007163465914101e+00 2.5520406588866820e+00 +4072 -4.0958048708482792e-01 1.1106824876365642e+00 3.0788300199054586e+00 +3160 -5.4524347356962517e+00 4.3156482789948143e+00 -1.3707562648323310e+00 +167 -3.7846180163481380e+00 6.0688805089413700e+00 -9.3209569588631103e-01 +193 -2.2590274085362330e+00 -3.0825410238075674e+00 2.7055352419861740e+00 +848 7.0018093775573365e-01 2.8058409327943159e+00 -2.8664598081555570e+00 +3993 -2.1133573700213573e+00 -3.5509555580404868e+00 1.6428703567042029e+00 +3781 -9.8115460551194134e-01 -3.3293080663104027e+00 -4.8282826681026414e+00 +9 -5.7488885085826680e-01 -3.8370861619809009e+00 -7.2892619744045950e+00 +3599 5.2833107352107955e+00 -8.2925617792090145e-01 -2.5358574431762029e+00 +3518 4.0580253230452010e+00 -3.0945361122357586e+00 -8.8323796705297763e-01 +4089 7.2248060554373073e+00 9.0480655644191388e-01 -9.6284911590930766e-01 +2593 3.2503133857492319e+00 -4.1972151630470256e+00 -1.7952974231313504e-01 diff --git a/examples/USER/misc/entropy/in.entropy b/examples/USER/misc/entropy/in.entropy new file mode 100644 index 0000000000000000000000000000000000000000..2c25dac3205d885b2b84aa4c3aff7df5420bce74 --- /dev/null +++ b/examples/USER/misc/entropy/in.entropy @@ -0,0 +1,34 @@ +echo both + +units metal +atom_style full + +read_data data.interface +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 + diff --git a/examples/USER/misc/entropy/log.entropy b/examples/USER/misc/entropy/log.entropy new file mode 100644 index 0000000000000000000000000000000000000000..c380c62a731b77c6c83d3a36fc822b52843f8c17 --- /dev/null +++ b/examples/USER/misc/entropy/log.entropy @@ -0,0 +1,124 @@ +LAMMPS (30 Mar 2018) + +units metal +atom_style full + +read_data data.interface +Reading data file ... + triclinic box = (0 0 0) to (138.4 34.57 34.57) with tilt (0 0 0) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 4096 atoms + reading velocities ... + 4096 velocities +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +mass 1 22.98977 + +neigh_modify delay 10 every 1 +pair_style eam/fs +pair_coeff * * Na_MendelevM_2014.eam.fs Na +timestep 0.002 +thermo 500 + +neighbor 4. bin + +# Define computes +# Global density, no average +compute 1 all entropy/atom 0.25 7.75 +# Local density, no average +compute 2 all entropy/atom 0.25 7.75 local yes +# Global density, average over neighbors +compute 3 all entropy/atom 0.25 7.75 avg yes 5. +# Local density, average over neighbors +compute 4 all entropy/atom 0.25 7.75 avg yes 5. local yes + +dump myDump all custom 500 dump.interface id type x y z c_1 c_2 c_3 c_4 + + +fix 1 all nph x 1. 1. 10. +fix 2 all temp/csvr 350. 350. 0.1 64582 + +run 1000 +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.2 + ghost atom cutoff = 13.2 + binsize = 6.6, bins = 21 6 6 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair eam/fs, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard + (2) compute entropy/atom, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard + (3) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (4) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none + (5) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on, ghost + pair build: copy + stencil: none + bin: none +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.002 +Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75 + 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18 + 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18 +Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms + +Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95 +Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00 +Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96 +Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06 +Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66 +Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16 +Other | | 0.01161 | | | 0.22 + +Nlocal: 1024 ave 1040 max 1001 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 4614.25 ave 4700 max 4540 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 121747 ave 126398 max 116931 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +FullNghs: 243494 ave 252523 max 233842 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 973974 +Ave neighs/atom = 237.787 +Ave special neighs/atom = 0 +Neighbor list builds = 13 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/body/data.cubes b/examples/body/data.cubes new file mode 100644 index 0000000000000000000000000000000000000000..c1323ca3503bb10745df9a9bc176ce531850a4eb --- /dev/null +++ b/examples/body/data.cubes @@ -0,0 +1,76 @@ +LAMMPS data file for polygons: cubes, moment of inertia I = m edge^2/ 6 +2 atoms +2 bodies +1 atom types +0 6 xlo xhi +0 6 ylo yhi +0 6 zlo zhi + +Atoms + +1 1 1 1 1.5 1.5 1.5 +2 1 1 1 4.0 4.0 4.0 + +Bodies + +1 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 +2 3 79 +8 12 6 +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/data.squares b/examples/body/data.squares new file mode 100755 index 0000000000000000000000000000000000000000..6b198fd422dc0e5d8f736d70bcd9906ca133898e --- /dev/null +++ b/examples/body/data.squares @@ -0,0 +1,32 @@ +LAMMPS data file for polygons: squares of edge length L: Izz = 1/6mL^2 +2 atoms +2 bodies +1 atom types +0 12 xlo xhi +0 12 ylo yhi +-0.5 0.5 zlo zhi + +Atoms + +1 1 1 1 4 5 0 +2 1 1 1 9 6 0 + +Bodies + +1 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 +2 1 19 +4 +1 1 2.67 0 0 0 +-2 -2 0 +-2 2 0 +2 2 0 +2 -2 0 +0.5 + diff --git a/examples/body/in.body b/examples/body/in.body index 5879ed5e45bc8810e82df81fdac0928306ae9e23..815b8531545a4348fb54dd1553abcfb642f44bf5 100644 --- a/examples/body/in.body +++ b/examples/body/in.body @@ -8,7 +8,7 @@ read_data data.body velocity all create 1.44 87287 loop geom -pair_style body 5.0 +pair_style body/nparticle 5.0 pair_coeff * * 1.0 1.0 neighbor 0.5 bin diff --git a/examples/body/in.cubes b/examples/body/in.cubes new file mode 100644 index 0000000000000000000000000000000000000000..a22599fe9607873aab7bc2214f59b8268415814d --- /dev/null +++ b/examples/body/in.cubes @@ -0,0 +1,53 @@ +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + +replicate $r $r $r + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} + diff --git a/examples/body/in.pour3d b/examples/body/in.pour3d new file mode 100644 index 0000000000000000000000000000000000000000..bcba950e593606065837cdbaeb85a4376fd0c4c4 --- /dev/null +++ b/examples/body/in.pour3d @@ -0,0 +1,57 @@ +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 & + molecule.rod3d toff 2 molecule.point3d toff 3 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object & + molfrac 0.25 0.25 0.25 0.25 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type & +# zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} + + diff --git a/examples/body/in.squares b/examples/body/in.squares new file mode 100755 index 0000000000000000000000000000000000000000..3b05b5cead88cd6265b17ce2772873b97c475383 --- /dev/null +++ b/examples/body/in.squares @@ -0,0 +1,55 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 & + y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/in.wall2d b/examples/body/in.wall2d new file mode 100755 index 0000000000000000000000000000000000000000..04e7f31cb6810151570f164353f683ac6b675afa --- /dev/null +++ b/examples/body/in.wall2d @@ -0,0 +1,57 @@ +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + +replicate $r $r 1 + +velocity all create $T ${seed} dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_coeff * * ${k_n} ${k_na} + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 & +# adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} diff --git a/examples/body/log.9Jul18.body.cubes.g++.1 b/examples/body/log.9Jul18.body.cubes.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c9a799c0b51192a5420fb75fb8aeaa32a0b1a3df --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 1 by 1 MPI processor grid + 54 atoms + Time spent = 0.000217915 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 38.5686 on 1 procs for 10000 steps with 54 atoms + +Performance: 22401.653 tau/day, 259.278 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 38.426 | 38.426 | 38.426 | 0.0 | 99.63 +Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01 +Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12 +Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00 +Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22 +Other | | 0.007761 | | | 0.02 + +Nlocal: 54 ave 54 max 54 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 96 ave 96 max 96 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:38 diff --git a/examples/body/log.9Jul18.body.cubes.g++.4 b/examples/body/log.9Jul18.body.cubes.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..e2407e972532938d39ba0e62964d74dc9c69740f --- /dev/null +++ b/examples/body/log.9Jul18.body.cubes.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (29 Jun 2018) +# 3d rounded cubes + +variable r index 3 +variable steps index 10000 + +units lj +dimension 3 + +atom_style body rounded/polyhedron 1 10 + +read_data data.cubes + orthogonal box = (0 0 0) to (6 6 6) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r $r +replicate 3 $r $r +replicate 3 3 $r +replicate 3 3 3 + orthogonal box = (0 0 0) to (18 18 18) + 1 by 2 by 2 MPI processor grid + 54 atoms + Time spent = 0.00103807 secs + +velocity all create 1.2 187287 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 1 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 1 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +fix 1 all nvt/body temp 1.2 1.2 0.1 +#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0 + +compute p2 all pressure 1_temp + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4] + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15 +#dump_modify 2 pad 6 + +thermo_style custom step ke pe etotal c_p2 c_1_temp + +thermo 1000 + +run ${steps} +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.9641 + ghost atom cutoff = 3.9641 + binsize = 1.98205, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.879 | 5.068 | 5.256 Mbytes +Step KinEng PotEng TotEng c_p2 c_1_temp + 0 1.7666667 0 1.7666667 0.01090535 0.59439252 + 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 + 2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624 + 3000 3.090491 0.16511199 3.255603 0.018691142 1.23672 + 4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839 + 5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154 + 6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839 + 7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326 + 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 + 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 + 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 +Loop time of 20.5306 on 4 procs for 10000 steps with 54 atoms + +Performance: 42083.509 tau/day, 487.078 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98 +Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01 +Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66 +Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00 +Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23 +Other | | 0.023 | | | 0.11 + +Nlocal: 13.5 ave 17 max 9 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 63.5 ave 68 max 58 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 25 ave 38 max 6 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 100 +Ave neighs/atom = 1.85185 +Neighbor list builds = 268 +Dangerous builds = 0 + +Total wall time: 0:00:20 diff --git a/examples/body/log.9Jul18.body.pour3d.g++.1 b/examples/body/log.9Jul18.body.pour3d.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..213dd2e18fa9959a87ca922760e53508cace973d --- /dev/null +++ b/examples/body/log.9Jul18.body.pour3d.g++.1 @@ -0,0 +1,138 @@ +LAMMPS (29 Jun 2018) +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg +Created orthogonal box = (0 0 0) to (50 50 50) + 1 by 1 by 1 MPI processor grid + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 5 + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 +Read molecule object: + 1 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 2 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 3 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 4 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 +Particle insertion: 134 every 4472 steps, 500 by step 13417 + +fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL + +#compute 1 all body/local type 1 2 3 +#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] +#dump 10 all custom 1000 tmp.dump id type x y z radius + +thermo_style custom step atoms ke pe etotal press + +thermo 1000 + +#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15 +#dump_modify 2 pad 6 + +run ${steps} +run 6000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5 + ghost atom cutoff = 5 + binsize = 2.5, bins = 20 20 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polyhedron, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes +Step Atoms KinEng PotEng TotEng Press + 0 0 -0 0 0 0 + 1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06 + 2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08 + 3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11 + 4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13 + 5000 268 -0 0.014969705 0.014969705 3.0797164e-05 + 6000 268 -0 0.042467887 0.042467887 0.00056148005 +Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms + +Performance: 816716.196 tau/day, 9452.734 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21 +Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66 +Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49 +Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02 +Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09 +Other | | 0.009719 | | | 1.53 + +Nlocal: 268 ave 268 max 268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 68 ave 68 max 68 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 68 +Ave neighs/atom = 0.253731 +Neighbor list builds = 168 +Dangerous builds = 0 + + +Total wall time: 0:00:00 diff --git a/examples/body/log.9Jul18.body.squares.g++.1 b/examples/body/log.9Jul18.body.squares.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..7b539797bd6d399ade37eeb28d580447c8721d9e --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.1 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00020504 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864838 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836655 0.62936359 0.016852121 + 15000 0.41895506 0.019513348 0.43846841 0.015225695 + 16000 0.55799421 0.1564559 0.71445011 0.011703561 + 17000 0.59391964 0.034450221 0.62836986 0.026215002 + 18000 0.75911858 0.030885726 0.7900043 0.018396366 + 19000 0.64417995 0.12110912 0.76528907 0.010247952 + 20000 0.57751435 0.16965651 0.74717086 0.023392323 + 21000 0.7613368 0.13405354 0.89539034 0.021498982 + 22000 0.57676692 0.18011879 0.75688571 0.024469161 + 23000 0.54043723 0.11842026 0.65885749 0.019799067 + 24000 0.62276061 0.038967924 0.66172853 0.019080086 + 25000 0.53157536 0.11651937 0.64809473 0.017019298 + 26000 0.72213293 0.039012448 0.76114538 0.015434904 + 27000 0.62157832 0.13697494 0.75855326 0.028711011 + 28000 0.41323738 0.16301101 0.57624839 0.041792632 + 29000 0.45774328 0.17569066 0.63343394 0.019975231 + 30000 0.78901796 0.099791386 0.88880934 0.024116947 + 31000 0.85205397 0.11977547 0.97182945 0.026667489 + 32000 0.37137095 0.1232622 0.49463315 0.00087637364 + 33000 0.26860871 0.26056381 0.52917252 0.036110517 + 34000 0.3018636 0.21336905 0.51523265 0.040315549 + 35000 0.39915129 0.28245957 0.68161085 0.034876856 + 36000 0.25761236 0.2352705 0.49288286 0.022772767 + 37000 0.1071233 0.31692858 0.42405188 0.017994666 + 38000 0.083729577 0.28473145 0.36846103 -0.0045370431 + 39000 0.070355565 0.26682083 0.33717639 0.017921556 + 40000 0.075894079 0.20077896 0.27667304 0.014873186 + 41000 0.05891028 0.15989064 0.21880092 0.025547873 + 42000 0.1225107 0.16583605 0.28834675 0.038842785 + 43000 0.17049189 0.14323991 0.3137318 0.029550161 + 44000 0.26823939 0.15208257 0.42032196 0.028113612 + 45000 0.10172203 0.1729706 0.27469264 -0.013769913 + 46000 0.14841355 0.19085074 0.33926429 -0.00073741985 + 47000 0.27654927 0.19097937 0.46752864 0.04021431 + 48000 0.53432331 0.080769923 0.61509323 0.029932845 + 49000 0.69111634 0.13064951 0.82176585 0.028985406 + 50000 0.24520806 0.18317453 0.42838258 0.05179746 + 51000 0.23541368 0.14281364 0.37822732 0.071884238 + 52000 0.25464996 0.095730242 0.3503802 0.034488204 + 53000 0.53677633 0.1058745 0.64265084 0.059932498 + 54000 0.32970921 0.27979128 0.60950049 0.062869716 + 55000 0.49094054 0.096735015 0.58767556 0.04728005 + 56000 0.54398249 0.2216472 0.76562969 0.056712022 + 57000 0.60869068 0.2338422 0.84253288 0.077143302 + 58000 0.72175509 0.18687368 0.90862877 0.019357656 + 59000 0.79442757 0.092502981 0.88693055 0.066882632 + 60000 0.6810555 0.077699385 0.75875488 0.095975173 + 61000 0.63178834 0.05071143 0.68249977 0.043586668 + 62000 0.76589344 0.044615704 0.81050914 0.085718411 + 63000 0.84815889 0.030527848 0.87868674 0.053072795 + 64000 0.7309043 0.051938637 0.78284294 0.058887766 + 65000 0.62498816 0.034474465 0.65946262 0.068446407 + 66000 0.69817494 0.068546004 0.76672094 0.062634433 + 67000 0.86444275 0.010184259 0.87462701 0.073635055 + 68000 0.77820319 0.0079319524 0.78613515 0.090330925 + 69000 0.56938919 0.0092629332 0.57865213 0.061838729 + 70000 0.61870712 0.010047381 0.6287545 0.066501338 + 71000 0.71651803 0.0088366199 0.72535465 0.079136316 + 72000 0.76278925 0.008828151 0.77161741 0.063672771 + 73000 0.75447428 0.0083985526 0.76287283 0.078256913 + 74000 0.66185251 0.0091910052 0.67104351 0.069840511 + 75000 0.58458829 0.0097671568 0.59435544 0.076123422 + 76000 0.7487564 0.0100022 0.7587586 0.076171741 + 77000 0.89505465 0.009250681 0.90430533 0.074921699 + 78000 0.73738164 0.0092029279 0.74658457 0.078835344 + 79000 0.65735281 0.010099528 0.66745233 0.077940627 + 80000 0.70247542 0.010306464 0.71278189 0.079560093 + 81000 0.74839505 0.010199092 0.75859415 0.080835104 + 82000 0.75193767 0.010274058 0.76221173 0.081086684 + 83000 0.71392598 0.010495573 0.72442156 0.082746145 + 84000 0.58498928 0.011027388 0.59601667 0.08356465 + 85000 0.59022869 0.011729474 0.60195817 0.084519397 + 86000 0.81753578 0.011208964 0.82874475 0.085490261 + 87000 0.83480682 0.010542579 0.8453494 0.086268527 + 88000 0.67322538 0.011170734 0.68439611 0.08751623 + 89000 0.62637389 0.012033316 0.6384072 0.088548094 + 90000 0.92828557 0.011750388 0.94003596 0.089199823 + 91000 0.96072564 0.010324509 0.97105015 0.090204803 + 92000 0.72105071 0.011484152 0.73253486 0.09140819 + 93000 0.65762527 0.012558219 0.67018349 0.092453474 + 94000 0.73991591 0.01261909 0.752535 0.093373477 + 95000 0.91791653 0.011980455 0.92989699 0.094182136 + 96000 0.76562561 0.011807085 0.7774327 0.095323684 + 97000 0.57292104 0.013610205 0.58653124 0.096505977 + 98000 0.68141076 0.013863204 0.69527396 0.097380069 + 99000 0.82390969 0.013002341 0.83691203 0.098235926 + 100000 0.77639728 0.012989342 0.78938662 0.099274147 +Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms + +Performance: 2221655.884 tau/day, 25713.610 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58 +Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13 +Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35 +Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03 +Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98 +Other | | 0.03616 | | | 0.93 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 1445 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/body/log.9Jul18.body.squares.g++.4 b/examples/body/log.9Jul18.body.squares.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..56d7734b7ba2a1919c1581799bb2eb83660aa4c9 --- /dev/null +++ b/examples/body/log.9Jul18.body.squares.g++.4 @@ -0,0 +1,221 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000324011 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 + 2000 0.42284177 0.01346585 0.43630762 0.0029377883 + 3000 0.58154405 0.011321689 0.59286574 0.003667871 + 4000 0.73518304 0.034603175 0.76978621 0.0018689207 + 5000 0.84367476 0.025292163 0.86896692 0.0089161373 + 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 + 7000 0.56206452 0.10453031 0.66659483 0.010255161 + 8000 0.64538994 0.088817673 0.73420761 0.0037633655 + 9000 0.90540819 0.063696004 0.96910419 0.0077673359 + 10000 0.68632042 0.093265016 0.77958544 0.0057864837 + 11000 0.59118074 0.025654748 0.61683549 0.012518759 + 12000 0.67522767 0.038176401 0.71340407 0.01741153 + 13000 0.7644843 0.10429844 0.86878274 0.013161339 + 14000 0.56152694 0.067836656 0.6293636 0.016852113 + 15000 0.41895505 0.019513353 0.43846841 0.015225696 + 16000 0.55799443 0.15645637 0.7144508 0.011703646 + 17000 0.59385248 0.03451986 0.62837234 0.025482966 + 18000 0.75902169 0.031103586 0.79012527 0.018263354 + 19000 0.64266826 0.12535314 0.76802141 0.014884119 + 20000 0.57836261 0.16581188 0.74417449 0.024667165 + 21000 0.78281936 0.11877527 0.90159464 -0.0090089213 + 22000 0.5312006 0.13300874 0.66420934 0.025797278 + 23000 0.56458861 0.084369128 0.64895774 0.024630917 + 24000 0.65126875 0.06122992 0.71249867 0.034377198 + 25000 0.55173441 0.15694886 0.70868327 0.021634086 + 26000 0.59121615 0.17071182 0.76192797 0.024758366 + 27000 0.6394843 0.17442949 0.81391378 0.034919937 + 28000 0.31144221 0.41243036 0.72387256 0.074115225 + 29000 0.13516917 0.3075419 0.44271107 0.023861298 + 30000 0.14094934 0.24407203 0.38502137 0.037030438 + 31000 0.26313749 0.087395422 0.35053291 0.042347005 + 32000 0.51602457 0.063012079 0.57903664 0.018550299 + 33000 0.55628829 0.200213 0.75650129 0.026507686 + 34000 0.97399408 0.082504517 1.0564986 0.037889878 + 35000 0.64710533 0.17662002 0.82372535 0.058295508 + 36000 0.45769083 0.08241194 0.54010277 0.014957415 + 37000 0.72850105 0.053874061 0.78237512 0.037194593 + 38000 0.44177995 0.28939498 0.73117493 0.045194029 + 39000 0.46828451 0.077630686 0.54591519 0.089849009 + 40000 0.46786451 0.092828423 0.56069294 0.028042052 + 41000 0.71861856 0.097085715 0.81570427 0.036473296 + 42000 0.74121021 0.10553127 0.84674148 0.054058843 + 43000 0.62945489 0.12770673 0.75716161 0.047267994 + 44000 0.49900638 0.085150056 0.58415644 0.054798793 + 45000 0.70199572 0.063415877 0.7654116 0.038363546 + 46000 0.49513142 0.10649384 0.60162526 0.059392561 + 47000 0.3858898 0.079458749 0.46534855 0.051825764 + 48000 0.62585854 0.028585902 0.65444444 0.054074424 + 49000 0.65934482 0.51865062 1.1779954 -0.035272836 + 50000 0.5420438 0.082056756 0.62410056 0.031187494 + 51000 0.36685223 0.14224019 0.50909241 0.073790397 + 52000 0.19044627 0.15368389 0.34413016 0.059034266 + 53000 0.26847678 0.075693324 0.3441701 0.032276915 + 54000 0.3593711 0.19034549 0.54971659 0.070827883 + 55000 0.21659198 0.1929074 0.40949939 0.035916364 + 56000 0.28242715 0.12313241 0.40555956 0.062083926 + 57000 0.34067475 0.14711992 0.48779467 0.059321458 + 58000 0.4842796 0.16143425 0.64571385 0.059048247 + 59000 0.84438871 0.076546849 0.92093556 0.048046901 + 60000 0.92794849 0.054331626 0.98228012 0.058392272 + 61000 0.6916736 0.076168342 0.76784194 0.058654987 + 62000 0.63317965 0.094506389 0.72768604 0.061044719 + 63000 0.63317266 0.038785593 0.67195825 0.097236147 + 64000 0.81696668 0.121811 0.93877769 0.064935373 + 65000 0.82644758 0.25188344 1.078331 0.093352359 + 66000 0.64975019 0.17930857 0.82905876 0.058805254 + 67000 0.63487678 0.16877059 0.80364737 0.070254696 + 68000 0.79140717 0.11631004 0.9077172 0.064646394 + 69000 0.85687272 0.057835331 0.91470805 0.071057291 + 70000 0.67785976 0.040686768 0.71854653 0.074687222 + 71000 0.60594577 0.032193155 0.63813893 0.069349268 + 72000 0.77586745 0.024068533 0.79993598 0.083394193 + 73000 0.88877625 0.025746326 0.91452258 0.081511105 + 74000 0.73507888 0.036574786 0.77165367 0.075360233 + 75000 0.68787782 0.042098622 0.72997644 0.068651098 + 76000 0.72515745 0.04360868 0.76876613 0.069594624 + 77000 0.77580944 0.041826702 0.81763614 0.071937144 + 78000 0.76640394 0.039285046 0.80568899 0.074274921 + 79000 0.62504309 0.039593585 0.66463667 0.076443295 + 80000 0.60001642 0.043468215 0.64348464 0.094547719 + 81000 0.82175037 0.045608873 0.86735924 0.080186295 + 82000 0.85783276 0.042692576 0.90052534 0.081576548 + 83000 0.71367707 0.042172193 0.75584926 0.08256625 + 84000 0.68532406 0.044724759 0.73004882 0.083672013 + 85000 0.72576789 0.046982462 0.77275035 0.084789331 + 86000 0.75597701 0.04765086 0.80362787 0.085758056 + 87000 0.74190598 0.047629096 0.78953507 0.086679976 + 88000 0.60967704 0.049906172 0.65958321 0.085526191 + 89000 0.54490288 0.054768238 0.59967112 0.090604027 + 90000 0.75398341 0.057153453 0.81113686 0.091900858 + 91000 0.84577472 0.052753512 0.89852823 0.091913909 + 92000 0.7176235 0.050677427 0.76830093 0.092032507 + 93000 0.61699446 0.054097013 0.67109147 0.092071275 + 94000 0.76330752 0.057398618 0.82070614 0.092435043 + 95000 0.98754458 0.053801311 1.0413459 0.093526707 + 96000 0.7405897 0.052135628 0.79272533 0.095011929 + 97000 0.65587599 0.057011962 0.71288795 0.096692123 + 98000 0.72345634 0.060700171 0.78415651 0.097510345 + 99000 0.88283624 0.061795247 0.94463149 0.09799633 + 100000 0.86303812 0.058912988 0.92195111 0.09892993 +Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms + +Performance: 3084895.573 tau/day, 35704.810 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94 +Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06 +Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42 +Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03 +Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06 +Other | | 0.1536 | | | 5.48 + +Nlocal: 8 ave 10 max 4 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 17.25 ave 19 max 15 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 13.5 ave 21 max 5 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 54 +Ave neighs/atom = 1.6875 +Neighbor list builds = 1443 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.1 b/examples/body/log.9Jul18.body.wall2d.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..f22c3663802a487158fffc74c13931f9d83a9416 --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.1 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.00029707 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079782e-05 + 11000 0.41529308 0.13619284 0.55148592 -0.0067482285 + 12000 0.43274718 0.071315497 0.50406268 0.007006378 + 13000 0.4748331 0.069904647 0.54473775 0.0010384372 + 14000 0.6287791 0.12721033 0.75598943 0.0047792448 + 15000 0.4692413 0.12344005 0.59268136 0.018033616 + 16000 0.43157074 0.14306789 0.57463862 0.042356676 + 17000 0.53085999 0.22126296 0.75212294 0.027509646 + 18000 0.52688968 0.13225282 0.6591425 0.0021558013 + 19000 0.55032328 0.12513047 0.67545375 0.025036251 + 20000 0.48465097 0.1431055 0.62775647 0.017193781 + 21000 0.53166734 0.21928574 0.75095307 0.011564317 + 22000 0.62177353 0.09296159 0.71473512 0.017660922 + 23000 0.6972939 0.12434123 0.82163514 0.024432327 + 24000 0.42767372 0.22152311 0.64919684 -0.013712449 + 25000 0.4816037 0.19272865 0.67433236 0.052386055 + 26000 0.72642579 0.19697046 0.92339625 0.020407694 + 27000 0.39649144 0.15058326 0.5470747 0.023705766 + 28000 0.44896324 0.18500106 0.6339643 -0.0089410286 + 29000 0.5565759 0.11085772 0.66743362 0.048437166 + 30000 0.58173584 0.21773281 0.79946865 0.0057357773 + 31000 0.49199415 0.23601982 0.72801397 0.046744152 + 32000 0.55665496 0.20542161 0.76207658 -0.0038756805 + 33000 0.62730739 0.24460524 0.87191263 0.045330682 + 34000 0.58107044 0.16395278 0.74502322 -0.0049496051 + 35000 0.56838849 0.21842922 0.78681771 0.0062086036 + 36000 0.45910273 0.28464172 0.74374445 -0.011700747 + 37000 0.37092037 0.27646862 0.647389 0.022305679 + 38000 0.7278047 0.30674438 1.0345491 0.07698342 + 39000 0.5132923 0.27395066 0.78724295 0.026898634 + 40000 0.62348649 0.24424644 0.86773293 0.039403899 + 41000 0.3658401 0.15512326 0.52096337 0.022559003 + 42000 0.4912253 0.35712978 0.84835508 -0.010336341 + 43000 0.70225957 0.36314638 1.0654059 0.004148866 + 44000 0.56958157 0.25488927 0.82447084 0.067537066 + 45000 0.45854352 0.30149439 0.76003791 -0.017002401 + 46000 0.62787247 0.34567995 0.97355242 0.11894801 + 47000 0.61348914 0.29378625 0.90727539 0.067873976 + 48000 0.71301829 0.34135284 1.0543711 0.021077736 + 49000 0.53520804 0.30593196 0.84113999 0.0059257647 + 50000 0.44966403 0.35370793 0.80337195 0.0020395669 + 51000 0.5236113 0.32296924 0.84658054 -0.051011506 + 52000 0.53905573 0.351771 0.89082672 0.013720106 + 53000 0.55978158 0.41293947 0.97272106 0.068558589 + 54000 0.52170459 0.2718066 0.7935112 0.0093138985 + 55000 0.61078876 0.43353897 1.0443277 0.045377392 + 56000 0.51300655 0.33182278 0.84482933 -0.018418487 + 57000 0.54882822 0.38380093 0.93262915 0.10249946 + 58000 0.72106212 0.45361279 1.1746749 0.030313481 + 59000 0.55871447 0.63823029 1.1969448 0.019079703 + 60000 0.49395192 0.58283102 1.0767829 0.0179349 + 61000 0.45991079 0.62540573 1.0853165 0.074398804 + 62000 0.4655788 0.60862262 1.0742014 0.11472976 + 63000 0.55634524 0.63069255 1.1870378 -0.0025676135 + 64000 0.57688903 0.45435264 1.0312417 0.0083813852 + 65000 0.57168922 0.42217005 0.99385927 0.044931269 + 66000 0.6206044 0.46727538 1.0878798 0.019686229 + 67000 0.61037155 0.41840109 1.0287726 0.0195109 + 68000 0.63848598 0.41305347 1.0515395 0.072940144 + 69000 0.49244916 0.3834095 0.87585866 0.07963677 + 70000 0.41847062 0.51907975 0.93755037 0.18447904 + 71000 0.45198986 0.52973709 0.98172695 0.078419371 + 72000 0.47064262 0.37808165 0.84872427 -0.00046308054 + 73000 0.6690143 0.37549359 1.0445079 0.061208432 + 74000 0.60444955 0.33779636 0.94224592 -0.068840321 + 75000 0.61762382 0.3916421 1.0092659 0.16253292 + 76000 0.63657961 0.50277989 1.1393595 0.013857508 + 77000 0.52524028 0.43597896 0.96121924 -0.03296482 + 78000 0.43803533 0.33172284 0.76975817 0.078763029 + 79000 0.67156089 0.55272177 1.2242827 0.080822223 + 80000 0.68678238 0.46061627 1.1473987 0.0027036992 + 81000 0.64956678 0.44959229 1.0991591 0.11201483 + 82000 0.51060477 0.43508342 0.9456882 0.028000608 + 83000 0.59550548 0.69026083 1.2857663 -0.0015809004 + 84000 0.64222145 0.38768816 1.0299096 0.014153173 + 85000 0.7661229 0.43445261 1.2005755 0.048034534 + 86000 0.60025257 0.53027929 1.1305319 0.0056865157 + 87000 0.46220939 0.47470035 0.93690974 0.075311946 + 88000 0.54123847 0.62899839 1.1702369 0.13260162 + 89000 0.61212272 0.6114241 1.2235468 0.033284822 + 90000 0.63924773 0.6916249 1.3308726 0.045088296 + 91000 0.49316865 0.51037033 1.003539 0.023203598 + 92000 0.57572123 0.43496319 1.0106844 0.297092 + 93000 0.65187559 0.56815972 1.2200353 0.1538215 + 94000 0.64107331 0.58948521 1.2305585 0.031117778 + 95000 0.64584158 0.6364688 1.2823104 0.096154676 + 96000 0.60509093 0.601487 1.2065779 0.03457172 + 97000 0.68837218 0.77974186 1.468114 0.17801164 + 98000 0.62725266 0.64137144 1.2686241 0.17449001 + 99000 0.46861221 0.67000291 1.1386151 0.2429588 + 100000 0.5879119 0.7140612 1.3019731 0.064634257 +Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms + +Performance: 3447804.126 tau/day, 39905.140 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41 +Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35 +Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35 +Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05 +Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34 +Other | | 0.03781 | | | 1.51 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 20 ave 20 max 20 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 57 ave 57 max 57 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 57 +Ave neighs/atom = 1.78125 +Neighbor list builds = 2705 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.4 b/examples/body/log.9Jul18.body.wall2d.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..7239fd4dcd4fc6a55886d0bfd11a401ab3e97f23 --- /dev/null +++ b/examples/body/log.9Jul18.body.wall2d.g++.4 @@ -0,0 +1,223 @@ +LAMMPS (29 Jun 2018) +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000386 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.49241101 0.0031318767 0.49554289 0.017768281 + 2000 0.56118632 0.0026068888 0.56379321 0.003410416 + 3000 0.75565115 0.025578366 0.78122951 0.0071862988 + 4000 0.72298647 0.093150646 0.81613712 0.003190158 + 5000 0.51684166 0.049164868 0.56600653 0.0096960168 + 6000 0.56627905 0.048132853 0.6144119 0.020733586 + 7000 0.58122129 0.018223718 0.59944501 0.0038160759 + 8000 0.64297977 0.025934821 0.66891459 0.0041091784 + 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 + 10000 0.35738377 0.078487805 0.43587158 3.9079865e-05 + 11000 0.41529307 0.13619284 0.55148591 -0.0067482285 + 12000 0.43274718 0.071315527 0.50406271 0.007006369 + 13000 0.4748324 0.069905666 0.54473807 0.0010385254 + 14000 0.62603727 0.098905625 0.7249429 0.0048876764 + 15000 0.44512086 0.10415235 0.54927321 0.01902062 + 16000 0.47460177 0.18053316 0.65513493 0.045013976 + 17000 0.52742676 0.10110706 0.62853382 0.013615471 + 18000 0.46111734 0.096118795 0.55723613 0.0073676834 + 19000 0.59668439 0.13652292 0.73320731 0.029403553 + 20000 0.46840192 0.11611719 0.58451911 -0.00034412499 + 21000 0.53550533 0.096457461 0.6319628 0.0019785732 + 22000 0.46599715 0.13206373 0.59806087 0.031970672 + 23000 0.49280776 0.20404726 0.69685501 0.03657433 + 24000 0.60901688 0.18255214 0.79156902 0.044955017 + 25000 0.47345185 0.13671357 0.61016542 0.020313539 + 26000 0.47653832 0.12448225 0.60102057 0.01878099 + 27000 0.50008212 0.24740634 0.74748845 0.021862639 + 28000 0.41627204 0.2519463 0.66821834 0.054683701 + 29000 0.55608273 0.23100212 0.78708485 -0.0043318497 + 30000 0.53884537 0.3001584 0.83900377 -0.012838186 + 31000 0.53036238 0.2300328 0.76039518 -0.0061688449 + 32000 0.42666792 0.20536256 0.63203048 0.045305282 + 33000 0.62908185 0.1652033 0.79428515 0.0072777588 + 34000 0.47028154 0.388736 0.85901754 0.04332288 + 35000 0.54602322 0.2775624 0.82358562 0.02898206 + 36000 0.59860544 0.21824655 0.81685199 0.0025936194 + 37000 0.62467827 0.11983499 0.74451326 0.050052743 + 38000 0.72594229 0.36584781 1.0917901 0.04280621 + 39000 0.51129656 0.23859043 0.74988699 0.050817447 + 40000 0.53263836 0.24212889 0.77476725 0.036245922 + 41000 0.50288088 0.36668283 0.86956371 0.018381415 + 42000 0.46653688 0.21974887 0.68628574 0.012661062 + 43000 0.61738785 0.32131037 0.93869821 0.012709433 + 44000 0.56603903 0.26515554 0.83119457 0.03315102 + 45000 0.56231638 0.32111693 0.88343331 0.06079756 + 46000 0.7096208 0.2570131 0.96663391 0.048770468 + 47000 0.588755 0.1880748 0.7768298 0.035962604 + 48000 0.56296339 0.25783519 0.82079858 0.053019928 + 49000 0.419885 0.42328618 0.84317118 0.038105269 + 50000 0.63073351 0.41426285 1.0449964 0.0015271048 + 51000 0.59357935 0.184222 0.77780136 0.015996218 + 52000 0.60608471 0.36247533 0.96856003 0.10984665 + 53000 0.5227842 0.27686739 0.79965159 0.02761699 + 54000 0.39435923 0.34197355 0.73633278 0.061183263 + 55000 0.46748455 0.34230903 0.80979358 0.077441382 + 56000 0.59819827 0.29212061 0.89031889 0.043772353 + 57000 0.61682559 0.32788566 0.94471124 0.03992069 + 58000 0.52702478 0.24891506 0.77593984 0.058480883 + 59000 0.66925719 0.4109031 1.0801603 0.072434423 + 60000 0.66807714 0.39233068 1.0604078 0.082370324 + 61000 0.5724275 0.43308567 1.0055132 0.0072945426 + 62000 0.49433556 0.38453743 0.87887299 0.0036097443 + 63000 0.57575143 0.54067119 1.1164226 0.073339638 + 64000 0.68045383 0.38246533 1.0629192 0.025314593 + 65000 0.59843527 0.42928622 1.0277215 -0.030096445 + 66000 0.60274797 0.50186417 1.1046121 0.069797184 + 67000 0.47450407 0.52689807 1.0014021 0.008758012 + 68000 0.5514135 0.64113187 1.1925454 0.093863314 + 69000 0.52008074 0.45749565 0.97757639 -0.066061381 + 70000 0.69042662 0.50416006 1.1945867 0.014128617 + 71000 0.63925854 0.35153425 0.9907928 -0.01134957 + 72000 0.52088835 0.47626986 0.99715821 0.10198133 + 73000 0.46333852 0.5515537 1.0148922 0.00060582772 + 74000 0.53481418 0.50409531 1.0389095 0.00919451 + 75000 0.67182749 0.50380162 1.1756291 0.043301985 + 76000 0.70492289 0.4112122 1.1161351 0.14880484 + 77000 0.59781817 0.50197661 1.0997948 -0.057111711 + 78000 0.51677429 0.4348232 0.95159749 -0.0074619446 + 79000 0.50663297 0.55000424 1.0566372 0.0052071216 + 80000 0.59392006 0.48394003 1.0778601 -0.018990234 + 81000 0.66323593 0.40358336 1.0668193 -0.02961345 + 82000 0.61596979 0.49177944 1.1077492 0.1314853 + 83000 0.63917554 0.61656584 1.2557414 0.11908351 + 84000 0.49305291 0.46161646 0.95466937 0.033558488 + 85000 0.52552044 0.54250555 1.068026 0.13015174 + 86000 0.55140914 0.38924725 0.94065638 0.047412499 + 87000 0.60952504 0.52603688 1.1355619 0.039230066 + 88000 0.50119735 0.547539 1.0487364 0.019659933 + 89000 0.40331401 0.50331134 0.90662535 -0.056906034 + 90000 0.47067839 0.51306911 0.9837475 0.11918166 + 91000 0.45564995 0.38693455 0.8425845 0.12040045 + 92000 0.64163032 0.34232532 0.98395564 0.0057051641 + 93000 0.70375593 0.53646186 1.2402178 0.16044241 + 94000 0.53378112 0.51971406 1.0534952 0.11389004 + 95000 0.47055342 0.50396004 0.97451346 0.079424215 + 96000 0.59543473 0.40204536 0.99748009 0.096813093 + 97000 0.64821917 0.50051728 1.1487365 0.054071312 + 98000 0.55723937 0.4945909 1.0518303 0.047316424 + 99000 0.56044424 0.50773312 1.0681774 0.0149959 + 100000 0.68254229 0.32704484 1.0095871 0.0069212661 +Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms + +Performance: 3926501.701 tau/day, 45445.622 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80 +Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14 +Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88 +Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05 +Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78 +Other | | 0.1618 | | | 7.36 + +Nlocal: 8 ave 9 max 7 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 12.75 ave 14 max 12 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 11 ave 19 max 5 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 44 +Ave neighs/atom = 1.375 +Neighbor list builds = 2663 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/body/molecule.cube b/examples/body/molecule.cube new file mode 100644 index 0000000000000000000000000000000000000000..2a8a7bca5023155889095b303b22d3aef201d2cc --- /dev/null +++ b/examples/body/molecule.cube @@ -0,0 +1,52 @@ +# 3d polygon body: cubes, moment of inertia I = m edge^2/ 6 + +1 atoms +3 79 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +8 12 6 + +Body Doubles + +0.667 0.667 0.667 0 0 0 +1 1 1 +1 -1 1 +-1 -1 1 +-1 1 1 +1 1 -1 +1 -1 -1 +-1 -1 -1 +-1 1 -1 +0 1 +1 2 +2 3 +3 0 +4 5 +5 6 +6 7 +7 4 +0 4 +1 5 +2 6 +3 7 +0 1 2 3 +4 5 6 7 +0 1 5 4 +1 2 6 5 +2 3 7 6 +3 0 4 7 +0.5 + diff --git a/examples/body/molecule.point3d b/examples/body/molecule.point3d new file mode 100644 index 0000000000000000000000000000000000000000..d22bfbe6fa9d58e0df10b2cba22dd1b402185e9a --- /dev/null +++ b/examples/body/molecule.point3d @@ -0,0 +1,26 @@ +# 2d polygon body: disks Izz = 1/2 m radius^2 + +1 atoms +3 10 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +1 0 0 + +Body Doubles + +1 1 1.125 0 0 0 +0 0 0 +3.0 diff --git a/examples/body/molecule.rod3d b/examples/body/molecule.rod3d new file mode 100644 index 0000000000000000000000000000000000000000..1c8a0a8cd3eecfa325d2a1c99a38edca26d0a789 --- /dev/null +++ b/examples/body/molecule.rod3d @@ -0,0 +1,27 @@ +# 2d polygon body: rods Izz = 1/12 m length^2 + +1 atoms +3 13 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +2 1 0 + +Body Doubles + +1 1 1.333 0 0 0 +-2 0 0 +2 0 0 +0.5 diff --git a/examples/body/molecule.tetra b/examples/body/molecule.tetra new file mode 100644 index 0000000000000000000000000000000000000000..d67ec906c64868521eaae59f8284697e18ff7d72 --- /dev/null +++ b/examples/body/molecule.tetra @@ -0,0 +1,39 @@ +# 3d polygon body: regular tetrahedra, moment of inertia I = m edge^2/ 20 + +1 atoms +3 47 body + +Coords + +1 0 0 0 + +Types + +1 1 + +Masses + +1 1.0 + +Body Integers + +4 6 4 + +Body Doubles + +0.4 0.4 0.4 0 0 0 +1 1 1 +1 -1 -1 +-1 1 -1 +-1 -1 1 +0 1 +0 2 +0 3 +1 2 +2 3 +3 1 +0 1 2 -1 +0 1 3 -1 +0 2 3 -1 +1 2 3 -1 +0.5 diff --git a/examples/latte/data.ch4 b/examples/latte/data.ch4 new file mode 100644 index 0000000000000000000000000000000000000000..fc8d48d244305c0b4f64c523bb7021418ea4c439 --- /dev/null +++ b/examples/latte/data.ch4 @@ -0,0 +1,23 @@ + LAMMPS Description + + 5 atoms + + 2 atom types + + 0.0000000000000000 19.523000000000000 xlo xhi + 0.0000000000000000 12.757999999999999 ylo yhi + 0.0000000000000000 11.692000000000000 zlo zhi + 0.0000000000000000 0.0000000000000000 0.0000000000000000 xy xz yz + + Masses + + 1 12.010000000000000 + 2 1.0078250169754028 + + Atoms + + 1 1 1 0.0 -9.16600 2.05200 0.00000 + 2 1 2 0.0 -8.09600 2.05200 0.00000 + 3 1 2 0.0 -9.52300 2.75800 -0.72000 + 4 1 2 0.0 -9.52300 2.32200 0.97200 + 5 1 2 0.0 -9.52300 1.07500 -0.25200 diff --git a/examples/latte/data.graphene b/examples/latte/data.graphene new file mode 100644 index 0000000000000000000000000000000000000000..5455a2eeb6cc1756e6c5ad5af01069aa5f01d866 --- /dev/null +++ b/examples/latte/data.graphene @@ -0,0 +1,49 @@ + LAMMPS Description + + 32 atoms + + 1 atom types + + 0.0000000000000000 10.000000000000000 xlo xhi + 0.0000000000000000 8.0000000000000000 ylo yhi + 0.0000000000000000 20.000000000000000 zlo zhi + 4.8985871965894128E-016 1.2246467991473533E-015 1.2246467991473533E-015 xy xz yz + + Masses + + 1 12.010000000000000 + + Atoms + + 1 1 1 0.0 4.93100 4.25000 0.00500 + 2 1 1 0.0 8.62100 2.12100 0.14000 + 3 1 1 0.0 3.70700 2.12600 0.14700 + 4 1 1 0.0 7.38200 4.25400 0.07800 + 5 1 1 0.0 2.47900 4.25400 0.08000 + 6 1 1 0.0 6.15800 6.37400 -0.01000 + 7 1 1 0.0 1.23700 6.38300 0.06600 + 8 1 1 0.0 1.24000 2.12100 0.14600 + 9 1 1 0.0 6.15500 2.12600 0.12900 + 10 1 1 0.0 0.00700 4.25200 0.12200 + 11 1 1 0.0 8.62100 6.38500 0.04100 + 12 1 1 0.0 3.70000 6.37400 -0.01000 + 13 1 1 0.0 0.00600 1.41600 0.13000 + 14 1 1 0.0 4.93000 1.40800 0.14700 + 15 1 1 0.0 8.61800 3.54600 0.11500 + 16 1 1 0.0 3.70800 3.55300 0.08400 + 17 1 1 0.0 7.39400 5.68000 0.03500 + 18 1 1 0.0 2.46500 5.68000 0.03500 + 19 1 1 0.0 6.16000 7.80500 0.02700 + 20 1 1 0.0 1.23800 7.81100 0.06000 + 21 1 1 0.0 2.47300 1.41800 0.16100 + 22 1 1 0.0 7.38900 1.41700 0.14800 + 23 1 1 0.0 1.24200 3.54700 0.12600 + 24 1 1 0.0 6.15300 3.55300 0.07400 + 25 1 1 0.0 0.00700 5.67800 0.09700 + 26 1 1 0.0 4.93100 5.66800 -0.03100 + 27 1 1 0.0 8.62000 7.81300 0.03900 + 28 1 1 0.0 3.70100 7.80200 0.03700 + 29 1 1 0.0 0.00700 -0.01000 0.08900 + 30 1 1 0.0 4.93100 -0.01500 0.16100 + 31 1 1 0.0 2.47300 -0.01200 0.14400 + 32 1 1 0.0 7.38900 -0.01300 0.14800 diff --git a/examples/latte/in.graphene.boxrel b/examples/latte/in.graphene.boxrel new file mode 100644 index 0000000000000000000000000000000000000000..721b7f014f0981bdc8672e2d1bdc2f7bb9f6932d --- /dev/null +++ b/examples/latte/in.graphene.boxrel @@ -0,0 +1,44 @@ +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 diff --git a/examples/latte/in.latte.multiple b/examples/latte/in.latte.multiple new file mode 100644 index 0000000000000000000000000000000000000000..4888d14ebc6fe862b8d98e2520879cdd11488f01 --- /dev/null +++ b/examples/latte/in.latte.multiple @@ -0,0 +1,65 @@ +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + diff --git a/examples/latte/in.latte.sucrose.md b/examples/latte/in.latte.sucrose.md new file mode 100644 index 0000000000000000000000000000000000000000..a10dae5c5ea9451d7733de60d695d559cd340b78 --- /dev/null +++ b/examples/latte/in.latte.sucrose.md @@ -0,0 +1,40 @@ +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/in.latte.water.md b/examples/latte/in.latte.water.md new file mode 100644 index 0000000000000000000000000000000000000000..e1185602b43ec5990e27f904cb97cfc2f725a3df --- /dev/null +++ b/examples/latte/in.latte.water.md @@ -0,0 +1,40 @@ +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/in.latte.water.min b/examples/latte/in.latte.water.min index 503e45a300b25802bde6ae646d317c15774dd355..173afee96a8b8d5987a7bd92ebda8ddb24996408 100644 --- a/examples/latte/in.latte.water.min +++ b/examples/latte/in.latte.water.min @@ -37,5 +37,6 @@ thermo_style custom step temp pe etotal press # minimization thermo 10 -min_style fire -minimize 1.0e-9 1.0e-9 500 500 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 diff --git a/examples/latte/latte.in b/examples/latte/latte.in index b8b214b78b4847ee4a58c0a03e6f8a94adc78e4b..f927313457cafdf39b762db9b73ec10dd77a82ab 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -9,9 +9,8 @@ LATTE INPUT FILE #General controls CONTROL{ - xControl= 1 + XCONTROL= 1 BASISTYPE= NONORTHO - COORDSFILE= "./coords.dat" PARAMPATH= "./TBparam" KBT= 0.0 ENTROPYKIND= 1 @@ -22,9 +21,8 @@ CONTROL{ BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL FULLQCONV= 1 QITER= 3 QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25 - SPARSEON= 1 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 + SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 MSPARSE= 1500 - RELAX= 0 RELAXTYPE= SD MAXITER= 100000 RLXFTOL= 0.0000001 SKIN= 1.0 CHARGE= 0 XBO= 1 @@ -32,9 +30,3 @@ CONTROL{ XBODISORDER= 5 KON= 0 } - -#Controls for QMD (if using lammps MAXITER must be set to -1) -MDCONTROL{ - MAXITER= -1 -} - diff --git a/examples/latte/log.19Sep17.latte.sucrose.g++.1 b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 similarity index 100% rename from examples/latte/log.19Sep17.latte.sucrose.g++.1 rename to examples/latte/log.19Sep17.latte.sucrose.md.g++.1 diff --git a/examples/latte/log.19Sep17.latte.water.g++.1 b/examples/latte/log.19Sep17.latte.water.md.g++.1 similarity index 100% rename from examples/latte/log.19Sep17.latte.water.g++.1 rename to examples/latte/log.19Sep17.latte.water.md.g++.1 diff --git a/examples/latte/log.19Sep17.latte.water.min.g++.1 b/examples/latte/log.19Sep17.latte.water.min.g++.1 deleted file mode 100644 index 4b96bd26682bcb3162250bc48ecd8cd3eb60387d..0000000000000000000000000000000000000000 --- a/examples/latte/log.19Sep17.latte.water.min.g++.1 +++ /dev/null @@ -1,152 +0,0 @@ -LAMMPS (1 Sep 2017) -# simple water model with LATTE - -units metal -atom_style full -atom_modify sort 0 0.0 # turn off sorting of the coordinates - -read_data data.water - orthogonal box = (0 0 0) to (6.267 6.267 6.267) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 24 atoms - 0 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -# replicate system if requested - -variable x index 1 -variable y index 1 -variable z index 1 - -variable nrep equal v_x*v_y*v_z -if "${nrep} > 1" then "replicate $x $y $z" - -# initialize system - -velocity all create 0.0 87287 loop geom - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.00025 - -fix 1 all nve - -fix 2 all latte NULL -fix_modify 2 energy yes - -thermo_style custom step temp pe etotal press - -# minimization - -thermo 10 -min_style fire -minimize 1.0e-9 1.0e-9 500 500 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes -Step Temp PotEng TotEng Press - 0 0 -104.95614 -104.95614 48229.712 - 10 349.44219 -105.50971 -104.47083 62149.591 - 20 1253.6752 -107.00898 -103.28182 116444.44 - 30 134.63588 -107.56184 -107.16157 59854.143 - 40 2.4043703 -108.15301 -108.14586 32685.77 - 50 162.13426 -108.40551 -107.92349 62104.273 - 60 134.03149 -108.70118 -108.30271 49400.525 - 70 64.159014 -108.78034 -108.5896 37243.303 - 80 240.49926 -109.10766 -108.39266 42158.884 - 90 0.60467192 -109.61818 -109.61639 14107.515 - 100 1.4691163 -109.65556 -109.65119 21596.775 - 110 30.500628 -109.69267 -109.602 16104.639 - 120 120.62379 -109.83749 -109.47888 9474.971 - 130 8.4742975 -109.99986 -109.97467 10104.102 - 140 3.4732679 -110.01209 -110.00176 11990.442 - 150 24.749482 -110.04313 -109.96955 10851.569 - 160 4.1106505 -110.13288 -110.12066 8257.3969 - 170 0.0065628716 -110.18061 -110.18059 7876.8748 - 180 2.0542078 -110.1837 -110.17759 7996.0533 - 190 20.134782 -110.21071 -110.15085 7556.1811 - 200 2.3397267 -110.3244 -110.31745 3767.062 - 210 4.3544709 -110.34438 -110.33143 4889.145 - 220 1.1872367 -110.37457 -110.37104 4162.6543 - 230 2.2798399 -110.38081 -110.37403 4321.0943 - 240 11.835907 -110.39611 -110.36092 4187.5757 - 250 0.13741849 -110.41453 -110.41412 3720.7527 - 260 4.2283185 -110.42036 -110.40779 3743.3494 - 270 0.47243724 -110.44349 -110.44208 3172.1866 - 280 0.06090137 -110.45428 -110.4541 3065.9348 - 290 5.3413962 -110.46285 -110.44697 3121.2924 - 300 8.2032986 -110.48519 -110.4608 2705.5001 - 310 2.0783529 -110.48807 -110.48189 2740.7989 - 320 16.629185 -110.51002 -110.46058 2581.7434 - 330 0.19723065 -110.53444 -110.53385 1942.0228 - 340 6.2758334 -110.54361 -110.52495 1924.0965 - 350 1.4539052 -110.59108 -110.58676 -449.41056 - 360 0.0514233 -110.60143 -110.60128 1284.8259 - 370 1.7240145 -110.60394 -110.59881 1468.0004 - 380 13.28516 -110.62337 -110.58387 1573.4714 - 390 1.2247432 -110.63525 -110.63161 1113.4557 - 400 0.3946985 -110.63694 -110.63576 1083.0801 - 410 2.9831433 -110.641 -110.63213 1112.419 - 420 0.068550589 -110.66029 -110.66009 897.09211 - 430 0.83976182 -110.66259 -110.66009 918.69832 - 440 4.4760907 -110.66844 -110.65513 915.24435 - 450 1.2841241 -110.67482 -110.671 953.30422 - 460 2.5707455 -110.68509 -110.67745 775.21273 - 470 0.99721544 -110.68646 -110.6835 812.74984 - 480 6.8379261 -110.69468 -110.67435 787.9705 - 490 0.18134438 -110.69628 -110.69574 675.52792 - 500 2.0946523 -110.69918 -110.69295 696.82065 -Loop time of 31.775 on 1 procs for 500 steps with 24 atoms - -884.8% CPU use with 1 MPI tasks x no OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -104.95614332 -110.698546127 -110.699182193 - Force two-norm initial, final = 19.119 0.234621 - Force max component initial, final = 11.7759 0.0903198 - Final line search alpha, max atom move = 0 0 - Iterations, force evaluations = 500 500 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.00 -Bond | 2.8372e-05 | 2.8372e-05 | 2.8372e-05 | 0.0 | 0.00 -Neigh | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00 -Comm | 0.00060034 | 0.00060034 | 0.00060034 | 0.0 | 0.00 -Output | 0.00057817 | 0.00057817 | 0.00057817 | 0.0 | 0.00 -Modify | 31.771 | 31.771 | 31.771 | 0.0 | 99.99 -Other | | 0.002469 | | | 0.01 - -Nlocal: 24 ave 24 max 24 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 27 ave 27 max 27 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 27 -Ave neighs/atom = 1.125 -Ave special neighs/atom = 0 -Neighbor list builds = 2 -Dangerous builds = 0 -Total wall time: 0:00:31 diff --git a/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..3a37136fd36595826ab3e5d51b5ef31bca1f3b96 --- /dev/null +++ b/examples/latte/log.21Jun18.latte.graphene.boxrelax.g++.1 @@ -0,0 +1,170 @@ +LAMMPS (11 May 2018) +# Simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.graphene.boxrel + triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 32 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all box/relax iso 0.0 vmax 0.001 + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom etotal + +# minimization + +thermo 1 +fix 3 all print 1 "Total Energy =" +min_style cg +min_modify dmax 0.1 +min_modify line quadratic +minimize 1.0e-4 1.0e-4 10000 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 11 9 20 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes +TotEng + -247.46002 + -247.67224 + -247.87937 + -248.08148 + -248.27865 + -248.47096 + -248.65851 + -248.84137 + -249.01964 + -249.19342 + -249.36281 + -249.52791 + -249.68883 + -249.8457 + -249.99865 + -250.1478 + -250.29332 + -250.43535 + -250.57409 + -250.70972 + -250.84247 + -250.97258 + -251.10035 + -251.2261 + -251.35021 + -251.47314 + -251.59543 + -251.71776 + -251.84096 + -251.9661 + -252.09459 + -252.22833 + -252.37003 + -252.52371 + -252.69578 + -252.89752 + -253.15197 + -253.52044 + -254.31418 + -255.6175 + -256.8162 + -258.1227 + -259.38401 + -260.74831 + -262.03991 + -263.5463 + -264.70486 + -267.69144 + -267.88682 + -269.03519 + -270.60187 + -270.65382 + -270.74279 + -271.55883 + -271.81248 + -271.87529 + -273.01494 + -273.23948 + -273.28719 + -273.35272 + -273.41591 + -273.46274 + -273.54755 + -273.58318 + -273.73111 + -273.75754 +Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms + +1582.4% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -247.460020579 -273.731112592 -273.757543461 + Force two-norm initial, final = 201.608 9.43485 + Force max component initial, final = 188.924 2.41297 + Final line search alpha, max atom move = 0.000223273 0.00053875 + Iterations, force evaluations = 65 65 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00 +Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00 +Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00 +Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00 +Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00 +Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99 +Other | | 0.00127 | | | 0.00 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 48 ave 48 max 48 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 48 +Ave neighs/atom = 1.5 +Ave special neighs/atom = 0 +Neighbor list builds = 1 +Dangerous builds = 0 +Total wall time: 0:00:40 diff --git a/examples/latte/log.21Jun18.latte.multiple.g++.1 b/examples/latte/log.21Jun18.latte.multiple.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..2c624e4371277f587328241857e38a7e354e719a --- /dev/null +++ b/examples/latte/log.21Jun18.latte.multiple.g++.1 @@ -0,0 +1,171 @@ +LAMMPS (22 Jun 2018) +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95596 -104.95596 48235.442 + 10 336.53107 -105.96027 -104.95977 97996.851 +Loop time of 0.912921 on 1 procs for 10 steps with 24 atoms + +Performance: 0.237 ns/day, 101.436 hours/ns, 10.954 timesteps/s +6614.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.3392e-05 | 4.3392e-05 | 4.3392e-05 | 0.0 | 0.00 +Bond | 3.8862e-05 | 3.8862e-05 | 3.8862e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00036955 | 0.00036955 | 0.00036955 | 0.0 | 0.04 +Output | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.01 +Modify | 0.91199 | 0.91199 | 0.91199 | 0.0 | 99.90 +Other | | 0.0003812 | | | 0.04 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.54167 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 20 13 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes +Step Temp PotEng TotEng Press + 0 0 -23.980353 -23.980353 348.02716 + 10 19.123149 -23.990297 -23.98041 18.774332 +Loop time of 0.0415399 on 1 procs for 10 steps with 5 atoms + +Performance: 5.200 ns/day, 4.616 hours/ns, 240.732 timesteps/s +6674.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.722e-06 | 5.722e-06 | 5.722e-06 | 0.0 | 0.01 +Bond | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.02 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.8358e-05 | 1.8358e-05 | 1.8358e-05 | 0.0 | 0.04 +Output | 2.0981e-05 | 2.0981e-05 | 2.0981e-05 | 0.0 | 0.05 +Modify | 0.041394 | 0.041394 | 0.041394 | 0.0 | 99.65 +Other | | 9.322e-05 | | | 0.22 + +Nlocal: 5 ave 5 max 5 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7 ave 7 max 7 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 10 +Ave neighs/atom = 2 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/latte/log.21Jun18.latte.sucrose.g++.1 b/examples/latte/log.21Jun18.latte.sucrose.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..cb4526587cccc40da331b1dceed633550e87158f --- /dev/null +++ b/examples/latte/log.21Jun18.latte.sucrose.g++.1 @@ -0,0 +1,103 @@ +LAMMPS (11 May 2018) +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose + orthogonal box = (0 0 0) to (17.203 18.009 21.643) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 45 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 18 19 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes +Step Temp PotEng TotEng Press + 0 0 -251.26617 -251.26617 16.617234 + 10 0.025263709 -251.26631 -251.26617 8.0576708 + 20 0.034232467 -251.26636 -251.26617 1.6673442 + 30 0.059079556 -251.2665 -251.26617 11.058458 + 40 0.055499766 -251.26648 -251.26617 14.837775 + 50 0.058499509 -251.2665 -251.26617 6.7183113 + 60 0.071094535 -251.26657 -251.26617 6.6133687 + 70 0.084309439 -251.26665 -251.26617 12.372721 + 80 0.1089929 -251.26679 -251.26617 8.8355516 + 90 0.11378257 -251.26681 -251.26617 5.1177922 + 100 0.13003966 -251.26691 -251.26617 8.2431185 +Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms + +Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s +1799.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00 +Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00 +Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 +Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00 +Other | | 0.0005403 | | | 0.00 + +Nlocal: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 59 ave 59 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 59 +Ave neighs/atom = 1.31111 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:28 diff --git a/examples/latte/log.21Jun18.latte.water.g++.1 b/examples/latte/log.21Jun18.latte.water.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..0decce1f985aa32cd18220ae15f9ca07373748ef --- /dev/null +++ b/examples/latte/log.21Jun18.latte.water.g++.1 @@ -0,0 +1,103 @@ +LAMMPS (11 May 2018) +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95594 -104.95594 48236.006 + 10 336.5303 -105.96026 -104.95976 97997.303 + 20 529.06385 -106.53021 -104.95731 131520.49 + 30 753.62616 -107.1995 -104.95898 49297.371 + 40 716.6565 -107.08802 -104.95741 28307.272 + 50 824.04417 -107.40822 -104.95835 102167.48 + 60 933.56056 -107.73478 -104.95932 92508.792 + 70 851.18518 -107.48766 -104.95711 13993.28 + 80 999.80265 -107.93146 -104.95906 36700.417 + 90 998.77707 -107.92569 -104.95634 107233.7 + 100 1281.4446 -108.76961 -104.95989 49703.193 +Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms + +Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s +6459.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00 +Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00 +Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00 +Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00 +Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00 +Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99 +Other | | 0.00052 | | | 0.00 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 77 ave 77 max 77 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31 +Ave neighs/atom = 1.29167 +Ave special neighs/atom = 0 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:10 diff --git a/examples/latte/log.21Jun18.latte.water.min.g++.1 b/examples/latte/log.21Jun18.latte.water.min.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..1c8921fd60cdb482ffb3650e14bb3250ee83e011 --- /dev/null +++ b/examples/latte/log.21Jun18.latte.water.min.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (11 May 2018) +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + orthogonal box = (0 0 0) to (6.267 6.267 6.267) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 24 atoms + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# minimization + +thermo 10 + +min_style fire +minimize 1.0e-4 1.0e-4 500 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes +Step Temp PotEng TotEng Press + 0 0 -104.95594 -104.95594 48236.006 + 10 349.4534 -105.50948 -104.47056 62157.729 + 20 1253.6636 -107.00863 -103.28151 116456.71 + 30 134.64051 -107.56155 -107.16127 59864.196 + 40 2.4044989 -108.1527 -108.14556 32695.648 + 47 137.26885 -108.30413 -107.89603 60177.442 +Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms + +6481.9% CPU use with 1 MPI tasks x no OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -104.955944301 -108.302982895 -108.304126127 + Force two-norm initial, final = 19.119 3.44609 + Force max component initial, final = 11.7758 1.3408 + Final line search alpha, max atom move = 0 0 + Iterations, force evaluations = 47 47 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00 +Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00 +Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00 +Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99 +Other | | 0.0004699 | | | 0.01 + +Nlocal: 24 ave 24 max 24 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37 ave 37 max 37 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37 +Ave neighs/atom = 1.54167 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index 21663ad85cb161c5acf97ee0463f295beaf58c17..0d7214260da804c79a26413b51458623f71c078a 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -79,7 +79,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ - $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \ @@ -137,7 +140,10 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \ $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \ $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \ - $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h + $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \ + $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h all: $(OBJ_DIR) $(GPU_LIB) $(EXECS) @@ -837,6 +843,42 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_ $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h $(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_coul_long_cs.cu + +$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin + $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu + +$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin + $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu + +$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin + $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda diff --git a/lib/gpu/Nvidia.makefile_multi b/lib/gpu/Nvidia.makefile_multi index 5fb35cce3c30cdb55f5ca5ff76dcb0569c8d3920..94cfd4af6b8cd376a2c4497011f8ab71a7b63b5f 100644 --- a/lib/gpu/Nvidia.makefile_multi +++ b/lib/gpu/Nvidia.makefile_multi @@ -79,7 +79,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ - $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \ @@ -137,7 +140,10 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \ $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \ $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \ - $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h + $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \ + $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \ + $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h all: $(OBJ_DIR) $(GPU_LIB) $(EXECS) @@ -837,6 +843,42 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_ $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h $(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu + +$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin + $(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu + +$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin + $(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h + $(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu + +$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin + $(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile index 3e73e6256c7b998c449a60e32e2a3974f636b227..86991a1e98f09ef30217e0c003239b9fcff8f11c 100644 --- a/lib/gpu/Opencl.makefile +++ b/lib/gpu/Opencl.makefile @@ -68,7 +68,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \ $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \ $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \ $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \ - $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o + $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \ + $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \ + $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/neighbor_cpu_cl.h $(OBJ_DIR)/pppm_cl.h \ @@ -98,7 +101,8 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \ $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h \ $(OBJ_DIR)/ufm_cl.h $(OBJ_DIR)/dipole_long_lj_cl.h \ - $(OBJ_DIR)/lj_expand_coul_long_cl.h + $(OBJ_DIR)/lj_expand_coul_long_cl.h $(OBJ_DIR)/coul_long_cs_cl.h \ + $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h OCL_EXECS = $(BIN_DIR)/ocl_get_devices @@ -609,6 +613,33 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_ $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h $(OCL) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/coul_long_cs_cl.h: lal_coul_long_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh coul_long_cs $(PRE1_H) lal_coul_long_cs.cu $(OBJ_DIR)/coul_long_cs_cl.h; + +$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o + $(OCL) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h + $(OCL) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_long_cs_cl.h: lal_born_coul_long_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh born_coul_long_cs $(PRE1_H) lal_born_coul_long_cs.cu $(OBJ_DIR)/born_coul_long_cs_cl.h; + +$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/born_coul_long_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o + $(OCL) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h + $(OCL) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/born_coul_wolf_cs_cl.h: lal_born_coul_wolf_cs.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh born_coul_wolf_cs $(PRE1_H) lal_born_coul_wolf_cs.cu $(OBJ_DIR)/born_coul_wolf_cs_cl.h; + +$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/born_coul_wolf_cs_cl.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o + $(OCL) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h + $(OCL) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) + $(BIN_DIR)/ocl_get_devices: ./geryon/ucl_get_devices.cpp $(OCL_H) $(OCL) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_OPENCL $(OCL_LINK) diff --git a/lib/gpu/geryon/nvd_device.h b/lib/gpu/geryon/nvd_device.h index 2d2a751f85b47dbef4e08bb0ec69858a8ecc4798..129bdbbdef7b6af52792ccec44fb0446744e7c0e 100644 --- a/lib/gpu/geryon/nvd_device.h +++ b/lib/gpu/geryon/nvd_device.h @@ -260,6 +260,9 @@ class UCL_Device { /// List all devices along with all properties inline void print_all(std::ostream &out); + /// Select the platform that has accelerators (for compatibility with OpenCL) + inline int set_platform_accelerator(int pid=-1) { return UCL_SUCCESS; } + private: int _device, _num_devices; std::vector _properties; diff --git a/lib/gpu/geryon/ocl_device.h b/lib/gpu/geryon/ocl_device.h index 2b2367545e837427527cad44843a5cb31fd09d30..14455e38a50740784fe2c28fc3ae5a6673c85796 100644 --- a/lib/gpu/geryon/ocl_device.h +++ b/lib/gpu/geryon/ocl_device.h @@ -165,8 +165,8 @@ class UCL_Device { /// Get the current OpenCL device name inline std::string name() { return name(_device); } /// Get the OpenCL device name - inline std::string name(const int i) - { return std::string(_properties[i].name); } + inline std::string name(const int i) { + return std::string(_properties[i].name); } /// Get a string telling the type of the current device inline std::string device_type_name() { return device_type_name(_device); } @@ -281,7 +281,7 @@ class UCL_Device { inline cl_device_id & cl_device() { return _cl_device; } /// Select the platform that has accelerators - inline void set_platform_accelerator(int pid=-1); + inline int set_platform_accelerator(int pid=-1); private: int _num_platforms; // Number of platforms @@ -324,6 +324,7 @@ UCL_Device::~UCL_Device() { void UCL_Device::clear() { _properties.clear(); + _cl_devices.clear(); if (_device>-1) { for (size_t i=0; i<_cq.size(); i++) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq.back())); @@ -520,8 +521,6 @@ int UCL_Device::device_type(const int i) { // Set the CUDA device to the specified device number int UCL_Device::set(int num) { - clear(); - cl_device_id *device_list = new cl_device_id[_num_devices]; cl_uint n; CL_SAFE_CALL(clGetDeviceIDs(_cl_platform,CL_DEVICE_TYPE_ALL,_num_devices, @@ -612,7 +611,7 @@ void UCL_Device::print_all(std::ostream &out) { // Select the platform that is associated with accelerators // if pid < 0, select the first platform -void UCL_Device::set_platform_accelerator(int pid) { +int UCL_Device::set_platform_accelerator(int pid) { if (pid < 0) { int found = 0; for (int n=0; n<_num_platforms; n++) { @@ -625,10 +624,11 @@ void UCL_Device::set_platform_accelerator(int pid) { break; } } - if (found) break; + if (found) return UCL_SUCCESS; } + return UCL_ERROR; } else { - set_platform(pid); + return set_platform(pid); } } diff --git a/lib/gpu/geryon/ocl_timer.h b/lib/gpu/geryon/ocl_timer.h index 66b79dcab101db3cbc31bbaa00263d5b563081f8..1f56aeb364ccc73c3b6ce22fa2644f0c9413f64b 100644 --- a/lib/gpu/geryon/ocl_timer.h +++ b/lib/gpu/geryon/ocl_timer.h @@ -49,8 +49,6 @@ class UCL_Timer { inline void clear() { if (_initialized) { CL_DESTRUCT_CALL(clReleaseCommandQueue(_cq)); - clReleaseEvent(start_event); - clReleaseEvent(stop_event); _initialized=false; _total_time=0.0; } @@ -107,6 +105,8 @@ class UCL_Timer { CL_SAFE_CALL(clGetEventProfilingInfo(start_event, CL_PROFILING_COMMAND_END, sizeof(cl_ulong), &tstart, NULL)); + clReleaseEvent(start_event); + clReleaseEvent(stop_event); return (tend-tstart)*t_factor; } diff --git a/lib/gpu/lal_atom.h b/lib/gpu/lal_atom.h index f6a0b109f2143889e5cde02f546de6e017d15561..57880d7ca976c029ab7006b9c2a5035da8018cfc 100644 --- a/lib/gpu/lal_atom.h +++ b/lib/gpu/lal_atom.h @@ -322,10 +322,12 @@ class Atom { // Copy charges to device asynchronously inline void add_q_data() { + time_q.start(); if (_q_avail==false) { q.update_device(_nall,true); _q_avail=true; } + time_q.stop(); } // Cast quaternions to write buffer @@ -347,10 +349,12 @@ class Atom { // Copy quaternions to device /** Copies nall()*4 elements **/ inline void add_quat_data() { + time_quat.start(); if (_quat_avail==false) { quat.update_device(_nall*4,true); _quat_avail=true; } + time_quat.stop(); } /// Cast velocities and tags to write buffer diff --git a/lib/gpu/lal_born_coul_long.cpp b/lib/gpu/lal_born_coul_long.cpp index 68695c49380ea9a0810a98ca0273686c6d3eb61c..116d44d58fd340e13b75439dab4d380dd13de89b 100644 --- a/lib/gpu/lal_born_coul_long.cpp +++ b/lib/gpu/lal_born_coul_long.cpp @@ -57,7 +57,7 @@ int BornCoulLongT::init(const int ntypes, double **host_cutsq, double **host_rho const double g_ewald) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,born_coul_long,"k_born_long"); + _screen,born_coul_long,"k_born_coul_long"); if (success!=0) return success; diff --git a/lib/gpu/lal_born_coul_long.cu b/lib/gpu/lal_born_coul_long.cu index 4cb4ea448fbf74374ce8b7ca7bd95b7cfda6505a..71e5e0ae502e8847bc006788deaf82da9477868d 100644 --- a/lib/gpu/lal_born_coul_long.cu +++ b/lib/gpu/lal_born_coul_long.cu @@ -29,7 +29,7 @@ texture q_tex; #define q_tex q_ #endif -__kernel void k_born_long(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_long(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1, const __global numtyp4 *restrict coeff2, const int lj_types, @@ -110,7 +110,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul); } else forcecoul = (numtyp)0.0; - if (rsq < cutsq_sigma[mtype].y) { + if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq numtyp r = ucl_sqrt(rsq); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); r6inv = r2inv*r2inv*r2inv; @@ -127,7 +127,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, if (eflag>0) { if (rsq < cut_coulsq) e_coul += prefactor*(_erfc-factor_coul); - if (rsq < coeff1[mtype].w) { + if (rsq < cutsq_sigma[mtype].y) { numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + coeff2[mtype].z*r2inv*r6inv; energy+=factor_lj*(e-coeff2[mtype].w); @@ -149,7 +149,7 @@ __kernel void k_born_long(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_born_long_fast(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_long_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1_in, const __global numtyp4 *restrict coeff2_in, const __global numtyp *restrict sp_lj_in, @@ -232,7 +232,7 @@ __kernel void k_born_long_fast(const __global numtyp4 *restrict x_, forcecoul = prefactor * (_erfc + EWALD_F*grij*expm2-factor_coul); } else forcecoul = (numtyp)0.0; - if (rsq < cutsq_sigma[mtype].y) { + if (rsq < cutsq_sigma[mtype].y) { // cut_ljsq numtyp r = ucl_sqrt(rsq); rexp = ucl_exp((cutsq_sigma[mtype].z-r)*coeff1[mtype].x); r6inv = r2inv*r2inv*r2inv; @@ -249,7 +249,7 @@ __kernel void k_born_long_fast(const __global numtyp4 *restrict x_, if (eflag>0) { if (rsq < cut_coulsq) e_coul += prefactor*(_erfc-factor_coul); - if (rsq < coeff1[mtype].w) { + if (rsq < cutsq_sigma[mtype].y) { numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + coeff2[mtype].z*r2inv*r6inv; energy+=factor_lj*(e-coeff2[mtype].w); diff --git a/lib/gpu/lal_born_coul_long.h b/lib/gpu/lal_born_coul_long.h index e0de27c71cc19091887d0c162af5861e37759df0..d236b7b57feca914beb028aae304c91eddda1ff3 100644 --- a/lib/gpu/lal_born_coul_long.h +++ b/lib/gpu/lal_born_coul_long.h @@ -78,7 +78,7 @@ class BornCoulLong : public BaseCharge { numtyp _cut_coulsq, _qqrd2e, _g_ewald; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_born_coul_long_cs.cpp b/lib/gpu/lal_born_coul_long_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e7fb946f148949f3b4d50dc71e662458f32977fd --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.cpp @@ -0,0 +1,95 @@ +/*************************************************************************** + born_coul_long_cs.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifdef USE_OPENCL +#include "born_coul_long_cs_cl.h" +#elif defined(USE_CUDART) +const char *born_coul_long_cs=0; +#else +#include "born_coul_long_cs_cubin.h" +#endif + +#include "lal_born_coul_long_cs.h" +#include +using namespace LAMMPS_AL; +#define BornCoulLongCST BornCoulLongCS + +extern Device device; + +template +int BornCoulLongCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,born_coul_long_cs,"k_born_coul_long_cs"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; icoeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv, + host_born1,host_born2,host_born3); + + this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c, + host_d,host_offset); + + this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq, + host_cut_ljsq,host_sigma); + + this->sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(this->sp_lj,host_write,8,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_g_ewald=g_ewald; + + this->_allocated=true; + this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes() + +this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes(); + return 0; +} + +template class BornCoulLongCS; diff --git a/lib/gpu/lal_born_coul_long_cs.cu b/lib/gpu/lal_born_coul_long_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..b3e79d9ec841afd0d31cf64b5af1c74f9469a811 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.cu @@ -0,0 +1,325 @@ +// ************************************************************************** +// born_coul_long_cs.cu +// ------------------- +// Trung Dac Nguyen (Northwestern) +// +// Device code for acceleration of the born/coul/long/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : June 2018 +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +// Note: EWALD_P is different from that in lal_preprocessor.h +// acctyp is needed for these parameters +#define CS_EWALD_P (acctyp)9.95473818e-1 +#define B0 (acctyp)-0.1335096380159268 +#define B1 (acctyp)-2.57839507e-1 +#define B2 (acctyp)-1.37203639e-1 +#define B3 (acctyp)-8.88822059e-3 +#define B4 (acctyp)-5.80844129e-3 +#define B5 (acctyp)1.14652755e-1 + +#define EPSILON (acctyp)(1.0e-20) +#define EPS_EWALD (acctyp)(1.0e-6) +#define EPS_EWALD_SQR (acctyp)(1.0e-12) + +__kernel void k_born_coul_long_cs(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1, + const __global numtyp4 *restrict coeff2, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + if (rsq < cut_coulsq) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_born_coul_long_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1_in, + const __global numtyp4 *restrict coeff2_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + coeff2[tid]=coeff2_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) { + if (rsq < cut_coulsq) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_born_coul_long_cs.h b/lib/gpu/lal_born_coul_long_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..df0fa0fcd41c790932fd9f4bedd2eb8e982c4865 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs.h @@ -0,0 +1,53 @@ +/*************************************************************************** + born_coul_long_cs.h + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_BORN_COUL_LONG_CS_H +#define LAL_BORN_COUL_LONG_CS_H + +#include "lal_born_coul_long.h" + +namespace LAMMPS_AL { + +template +class BornCoulLongCS : public BornCoulLong { + public: + BornCoulLongCS() {} + ~BornCoulLongCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +}; + +} + +#endif diff --git a/lib/gpu/lal_born_coul_long_cs_ext.cpp b/lib/gpu/lal_born_coul_long_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..badc8b0808488569685a7d11c5224beb720ce534 --- /dev/null +++ b/lib/gpu/lal_born_coul_long_cs_ext.cpp @@ -0,0 +1,132 @@ +/*************************************************************************** + born_coul_long_cs_ext.cpp + ------------------- + Trung Dac Nguyen (ORNL) + + Functions for LAMMPS access to born/coul/long/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_born_coul_long_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static BornCoulLongCS BCLCSMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int bornclcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **sigma, double **offset, double *special_lj, + const int inum, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, int &gpu_mode, + FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double g_ewald) { + BCLCSMF.clear(); + gpu_mode=BCLCSMF.device->gpu_mode(); + double gpu_split=BCLCSMF.device->particle_split(); + int first_gpu=BCLCSMF.device->first_device(); + int last_gpu=BCLCSMF.device->last_device(); + int world_me=BCLCSMF.device->world_me(); + int gpu_rank=BCLCSMF.device->gpu_rank(); + int procs_per_gpu=BCLCSMF.device->procs_per_gpu(); + + BCLCSMF.device->init_message(screen,"born/coul/long/cs",first_gpu,last_gpu); + + bool message=false; + if (BCLCSMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=BCLCSMF.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2, + host_born3, host_a, host_c, host_d, sigma, offset, + special_lj, inum, nall, 300, maxspecial, cell_size, + gpu_split, screen, host_cut_ljsq, host_cut_coulsq, + host_special_coul, qqrd2e, g_ewald); + + BCLCSMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + BCLCSMF.estimate_gpu_overhead(); + return init_ok; +} + +void bornclcs_gpu_clear() { + BCLCSMF.clear(); +} + +int** bornclcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return BCLCSMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void bornclcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + BCLCSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double bornclcs_gpu_bytes() { + return BCLCSMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_born_coul_wolf.cpp b/lib/gpu/lal_born_coul_wolf.cpp index 7ebd7b744fd6501a2710c3ad7143112aa9cf520e..c44b8414635abcb6a872b46544e52c1fa5a738da 100644 --- a/lib/gpu/lal_born_coul_wolf.cpp +++ b/lib/gpu/lal_born_coul_wolf.cpp @@ -57,7 +57,7 @@ int BornCoulWolfT::init(const int ntypes, double **host_cutsq, double **host_rho const double alf, const double e_shift, const double f_shift) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,born_coul_wolf,"k_born_wolf"); + _screen,born_coul_wolf,"k_born_coul_wolf"); if (success!=0) return success; diff --git a/lib/gpu/lal_born_coul_wolf.cu b/lib/gpu/lal_born_coul_wolf.cu index 0dc7d08c638d93bd9d0a5f0c1e37cd26e963e593..2c2249feeb7a34bdc899195aad60284aef51551a 100644 --- a/lib/gpu/lal_born_coul_wolf.cu +++ b/lib/gpu/lal_born_coul_wolf.cu @@ -31,7 +31,7 @@ texture q_tex; #define MY_PIS (acctyp)1.77245385090551602729 -__kernel void k_born_wolf(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_wolf(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1, const __global numtyp4 *restrict coeff2, const int lj_types, @@ -165,7 +165,7 @@ __kernel void k_born_wolf(const __global numtyp4 *restrict x_, } // if ii } -__kernel void k_born_wolf_fast(const __global numtyp4 *restrict x_, +__kernel void k_born_coul_wolf_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict coeff1_in, const __global numtyp4 *restrict coeff2_in, const __global numtyp *restrict sp_lj_in, diff --git a/lib/gpu/lal_born_coul_wolf.h b/lib/gpu/lal_born_coul_wolf.h index 4b2406b989be7d41d57c3b6cb66c035d491d937d..4b817ee0ced7df7d975c14de7cf20fa2410cdea3 100644 --- a/lib/gpu/lal_born_coul_wolf.h +++ b/lib/gpu/lal_born_coul_wolf.h @@ -13,8 +13,8 @@ email : nguyentd@ornl.gov ***************************************************************************/ -#ifndef LAL_BORN_COUL_LONG_H -#define LAL_BORN_COUL_LONG_H +#ifndef LAL_BORN_COUL_WOLF_H +#define LAL_BORN_COUL_WOLF_H #include "lal_base_charge.h" @@ -79,7 +79,7 @@ class BornCoulWolf : public BaseCharge { numtyp _cut_coulsq,_qqrd2e,_alf,_e_shift,_f_shift; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_born_coul_wolf_cs.cpp b/lib/gpu/lal_born_coul_wolf_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..bdb1c31e557b9f91f9308036cdf31ee46d87271f --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.cpp @@ -0,0 +1,97 @@ +/*************************************************************************** + born_coul_wolf_cs.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/wolf/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifdef USE_OPENCL +#include "born_coul_wolf_cs_cl.h" +#elif defined(USE_CUDART) +const char *born_coul_wolf_cs=0; +#else +#include "born_coul_wolf_cs_cubin.h" +#endif + +#include "lal_born_coul_wolf_cs.h" +#include +using namespace LAMMPS_AL; +#define BornCoulWolfCST BornCoulWolfCS + +extern Device device; + +template +int BornCoulWolfCST::init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, + double *host_special_lj, const int nlocal, + const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + double **host_cut_ljsq, const double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double alf, const double e_shift, const double f_shift) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, + _screen,born_coul_wolf_cs,"k_born_coul_wolf_cs"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; icoeff1.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff1,host_write,host_rhoinv, + host_born1,host_born2,host_born3); + + this->coeff2.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->coeff2,host_write,host_a,host_c, + host_d,host_offset); + + this->cutsq_sigma.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,lj_types,this->cutsq_sigma,host_write,host_cutsq, + host_cut_ljsq,host_sigma); + + this->sp_lj.alloc(8,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_lj[i]; + host_write[i+4]=host_special_coul[i]; + } + ucl_copy(this->sp_lj,host_write,8,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_alf=alf; + this->_e_shift=e_shift; + this->_f_shift=f_shift; + + this->_allocated=true; + this->_max_bytes=this->coeff1.row_bytes()+this->coeff2.row_bytes() + +this->cutsq_sigma.row_bytes()+this->sp_lj.row_bytes(); + return 0; +} + +template class BornCoulWolfCS; diff --git a/lib/gpu/lal_born_coul_wolf_cs.cu b/lib/gpu/lal_born_coul_wolf_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..847387bfe8c1adbe2e1f3f2a3ed21964d08c5989 --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.cu @@ -0,0 +1,306 @@ +// ************************************************************************** +// born_coul_wolf_cs.cu +// ------------------- +// Trung Dac Nguyen (Northwestern) +// +// Device code for acceleration of the born/coul/wolf/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +#define EPSILON (acctyp)(1.0e-20) +#define MY_PIS (acctyp)1.77245385090551602729 + +__kernel void k_born_coul_wolf_cs(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1, + const __global numtyp4 *restrict coeff2, + const int lj_types, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp alf, const numtyp e_shift, + const numtyp f_shift, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_lj[8]; + sp_lj[0]=sp_lj_in[0]; + sp_lj[1]=sp_lj_in[1]; + sp_lj[2]=sp_lj_in[2]; + sp_lj[3]=sp_lj_in[3]; + sp_lj[4]=sp_lj_in[4]; + sp_lj[5]=sp_lj_in[5]; + sp_lj[6]=sp_lj_in[6]; + sp_lj[7]=sp_lj_in[7]; + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) * + qtmp*qtmp*qqrd2e/(acctyp)t_per_atom; + e_coul += (acctyp)2.0*e_self; + } + + for ( ; nbor0) { + if (rsq < cut_coulsq) { + acctyp e=v_sh; + if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_born_coul_wolf_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict coeff1_in, + const __global numtyp4 *restrict coeff2_in, + const __global numtyp *restrict sp_lj_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const __global numtyp4 *restrict cutsq_sigma, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp alf, const numtyp e_shift, + const numtyp f_shift, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp4 coeff1[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_lj[8]; + if (tid<8) + sp_lj[tid]=sp_lj_in[tid]; + if (tid0) + coeff2[tid]=coeff2_in[tid]; + } + + acctyp energy=(acctyp)0; + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) { + acctyp e_self = -((acctyp)0.5*e_shift + alf/MY_PIS) * + qtmp*qtmp*qqrd2e/(acctyp)t_per_atom; + e_coul += (acctyp)2.0*e_self; + } + + for ( ; nbor0) { + if (rsq < cut_coulsq) { + acctyp e=v_sh; + if (factor_coul < (numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (rsq < cutsq_sigma[mtype].y) { + numtyp e=coeff2[mtype].x*rexp - coeff2[mtype].y*r6inv + + coeff2[mtype].z*r2inv*r6inv; + energy+=factor_lj*(e-coeff2[mtype].w); + } + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_born_coul_wolf_cs.h b/lib/gpu/lal_born_coul_wolf_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..1d9de0a457f04027118aebe5e9f4c1c6c6561ad3 --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs.h @@ -0,0 +1,54 @@ +/*************************************************************************** + born_coul_wolf_cs.h + ------------------- + Trung Dac Nguyen (Northwestern) + + Class for acceleration of the born/coul/wolf/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_BORN_COUL_WOLF_CS_H +#define LAL_BORN_COUL_WOLF_CS_H + +#include "lal_born_coul_wolf.h" + +namespace LAMMPS_AL { + +template +class BornCoulWolfCS : public BornCoulWolf { + public: + BornCoulWolfCS() {} + ~BornCoulWolfCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **host_cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **host_sigma, double **host_offset, double *host_special_lj, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, double **host_cut_ljsq, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double alf, const double e_shift, + const double f_shift); +}; + +} + +#endif diff --git a/lib/gpu/lal_born_coul_wolf_cs_ext.cpp b/lib/gpu/lal_born_coul_wolf_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e2211644af1f5b662a4750686ae5afa28216441c --- /dev/null +++ b/lib/gpu/lal_born_coul_wolf_cs_ext.cpp @@ -0,0 +1,134 @@ +/*************************************************************************** + born_coul_wolf_cs_ext.cpp + ------------------- + Trung Dac Nguyen (Northwestern) + + Functions for LAMMPS access to born/coul/wolf/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_born_coul_wolf_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static BornCoulWolfCS BornCWCST; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int borncwcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, double **host_born3, + double **host_a, double **host_c, double **host_d, + double **sigma, double **offset, double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double alf, const double e_shift, const double f_shift) { + BornCWCST.clear(); + gpu_mode=BornCWCST.device->gpu_mode(); + double gpu_split=BornCWCST.device->particle_split(); + int first_gpu=BornCWCST.device->first_device(); + int last_gpu=BornCWCST.device->last_device(); + int world_me=BornCWCST.device->world_me(); + int gpu_rank=BornCWCST.device->gpu_rank(); + int procs_per_gpu=BornCWCST.device->procs_per_gpu(); + + BornCWCST.device->init_message(screen,"born/coul/wolf/cs",first_gpu,last_gpu); + + bool message=false; + if (BornCWCST.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=BornCWCST.init(ntypes, cutsq, host_rhoinv, host_born1, host_born2, + host_born3, host_a, host_c, host_d, sigma, + offset, special_lj, inum, nall, 300, + maxspecial, cell_size, gpu_split, screen, host_cut_ljsq, + host_cut_coulsq, host_special_coul, qqrd2e, + alf, e_shift, f_shift); + + BornCWCST.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + BornCWCST.estimate_gpu_overhead(); + return init_ok; +} + +void borncwcs_gpu_clear() { + BornCWCST.clear(); +} + +int** borncwcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return BornCWCST.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void borncwcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + BornCWCST.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double borncwcs_gpu_bytes() { + return BornCWCST.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_coul_long.h b/lib/gpu/lal_coul_long.h index d12198fccc48fe37e262d1dfa63cdfea0b7ae844..ae25b91dc77a9322449fbcc5c1f96d994710838c 100644 --- a/lib/gpu/lal_coul_long.h +++ b/lib/gpu/lal_coul_long.h @@ -72,7 +72,7 @@ class CoulLong : public BaseCharge { numtyp _cut_coulsq, _qqrd2e, _g_ewald; - private: + protected: bool _allocated; void loop(const bool _eflag, const bool _vflag); }; diff --git a/lib/gpu/lal_coul_long_cs.cpp b/lib/gpu/lal_coul_long_cs.cpp new file mode 100644 index 0000000000000000000000000000000000000000..7afa0ae5d21bfb95bbf5c18315907250e7155318 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.cpp @@ -0,0 +1,78 @@ +/*************************************************************************** + coul_long_cs.cpp + ------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the coul/long pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "coul_long_cs_cl.h" +#elif defined(USE_CUDART) +const char *coul_long_cs=0; +#else +#include "coul_long_cs_cubin.h" +#endif + +#include "lal_coul_long_cs.h" +#include +using namespace LAMMPS_AL; +#define CoulLongCST CoulLongCS + +extern Device pair_gpu_device; + +template +int CoulLongCST::init(const int ntypes, double **host_scale, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *_screen, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald) { + int success; + success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size, + gpu_split,_screen,coul_long_cs,"k_coul_long_cs"); + if (success!=0) + return success; + + int lj_types=ntypes; + this->shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + this->shared_types=true; + } + this->_lj_types=lj_types; + + // Allocate a host write buffer for data initialization + UCL_H_Vec host_write(lj_types*lj_types*32,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iscale.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack1(ntypes,lj_types,this->scale,host_write,host_scale); + + this->sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY); + for (int i=0; i<4; i++) { + host_write[i]=host_special_coul[i]; + } + ucl_copy(this->sp_cl,host_write,4,false); + + this->_cut_coulsq=host_cut_coulsq; + this->_qqrd2e=qqrd2e; + this->_g_ewald=g_ewald; + + this->_allocated=true; + this->_max_bytes=this->scale.row_bytes()+this->sp_cl.row_bytes(); + return 0; +} + +template class CoulLongCS; diff --git a/lib/gpu/lal_coul_long_cs.cu b/lib/gpu/lal_coul_long_cs.cu new file mode 100644 index 0000000000000000000000000000000000000000..3c34666131d2d363c03bc6f684bd9b573b54c043 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.cu @@ -0,0 +1,367 @@ +// ************************************************************************** +// coul_long_cs.cu +// ------------------- +// Trung Nguyen (Northwestern) +// +// Device code for acceleration of the coul/long/cs pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : June 2018 +// email : ndactrung@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL + +#include "lal_aux_fun1.h" +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture q_tex; +#else +texture pos_tex; +texture q_tex; +#endif + +#else +#define pos_tex x_ +#define q_tex q_ +#endif + +// Note: EWALD_P is different from that in lal_preprocessor.h +// acctyp is needed for these parameters +#define CS_EWALD_P (acctyp)9.95473818e-1 +#define B0 (acctyp)-0.1335096380159268 +#define B1 (acctyp)-2.57839507e-1 +#define B2 (acctyp)-1.37203639e-1 +#define B3 (acctyp)-8.88822059e-3 +#define B4 (acctyp)-5.80844129e-3 +#define B5 (acctyp)1.14652755e-1 + +#define EPSILON (acctyp)(1.0e-20) +#define EPS_EWALD (acctyp)(1.0e-6) +#define EPS_EWALD_SQR (acctyp)(1.0e-12) + +#if (ARCH < 300) + +#define store_answers_lq(f, e_coul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + __local acctyp red_acc[6][BLOCK_PAIR]; \ + \ + red_acc[0][tid]=f.x; \ + red_acc[1][tid]=f.y; \ + red_acc[2][tid]=f.z; \ + red_acc[3][tid]=e_coul; \ + \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<4; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + \ + f.x=red_acc[0][tid]; \ + f.y=red_acc[1][tid]; \ + f.z=red_acc[2][tid]; \ + e_coul=red_acc[3][tid]; \ + \ + if (vflag>0) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid]=virial[r]; \ + \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + \ + for (int r=0; r<6; r++) \ + virial[r]=red_acc[r][tid]; \ + } \ + } \ + \ + if (offset==0) { \ + __global acctyp *ap1=engv+ii; \ + if (eflag>0) { \ + *ap1=(acctyp)0; \ + ap1+=inum; \ + *ap1=e_coul*(acctyp)0.5; \ + ap1+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + *ap1=virial[i]*(acctyp)0.5; \ + ap1+=inum; \ + } \ + } \ + ans[ii]=f; \ + } + +#else + +#define store_answers_lq(f, e_coul, virial, ii, inum, tid, \ + t_per_atom, offset, eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + f.x += shfl_xor(f.x, s, t_per_atom); \ + f.y += shfl_xor(f.y, s, t_per_atom); \ + f.z += shfl_xor(f.z, s, t_per_atom); \ + e_coul += shfl_xor(e_coul, s, t_per_atom); \ + } \ + if (vflag>0) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + for (int r=0; r<6; r++) \ + virial[r] += shfl_xor(virial[r], s, t_per_atom); \ + } \ + } \ + } \ + if (offset==0) { \ + __global acctyp *ap1=engv+ii; \ + if (eflag>0) { \ + *ap1=(acctyp)0; \ + ap1+=inum; \ + *ap1=e_coul*(acctyp)0.5; \ + ap1+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + *ap1=virial[i]*(acctyp)0.5; \ + ap1+=inum; \ + } \ + } \ + ans[ii]=f; \ + } + +#endif + +__kernel void k_coul_long_cs(const __global numtyp4 *restrict x_, + const __global numtyp *restrict scale, + const int lj_types, + const __global numtyp *restrict sp_cl_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp sp_cl[4]; + sp_cl[0]=sp_cl_in[0]; + sp_cl[1]=sp_cl_in[1]; + sp_cl[2]=sp_cl_in[2]; + sp_cl[3]=sp_cl_in[3]; + + acctyp e_coul=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + if (ii0) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_lq(f,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + +__kernel void k_coul_long_cs_fast(const __global numtyp4 *restrict x_, + const __global numtyp *restrict scale_in, + const __global numtyp *restrict sp_cl_in, + const __global int *dev_nbor, + const __global int *dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, + const __global numtyp *restrict q_, + const numtyp cut_coulsq, const numtyp qqrd2e, + const numtyp g_ewald, const int t_per_atom) { + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + __local numtyp scale[MAX_SHARED_TYPES*MAX_SHARED_TYPES]; + __local numtyp sp_cl[4]; + if (tid<4) + sp_cl[tid]=sp_cl_in[tid]; + if (tid0) { + numtyp e = prefactor*_erfc; + if (factor_coul<(numtyp)1.0) e -= ((numtyp)1.0-factor_coul)*prefactor; + e_coul += e; + } + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + + } // for nbor + store_answers_lq(f,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag, + vflag,ans,engv); + } // if ii +} + diff --git a/lib/gpu/lal_coul_long_cs.h b/lib/gpu/lal_coul_long_cs.h new file mode 100644 index 0000000000000000000000000000000000000000..3cfcb80fc86c9ab3f3066e086533cad795a378be --- /dev/null +++ b/lib/gpu/lal_coul_long_cs.h @@ -0,0 +1,50 @@ +/*************************************************************************** + coul_long_cs.h + ------------------- + Trung Nguyen (Northwestern) + + Class for acceleration of the coul/long/cs pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#ifndef LAL_COUL_LONG_CS_H +#define LAL_COUL_LONG_CS_H + +#include "lal_coul_long.h" + +namespace LAMMPS_AL { + +template +class CoulLongCS : public CoulLong { + public: + CoulLongCS() {} + ~CoulLongCS() {} + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, double **scale, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + const double gpu_split, FILE *screen, + const double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +}; + +} + +#endif diff --git a/lib/gpu/lal_coul_long_cs_ext.cpp b/lib/gpu/lal_coul_long_cs_ext.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ae57eb20382a0e47e1d987921e521d84a169dfb3 --- /dev/null +++ b/lib/gpu/lal_coul_long_cs_ext.cpp @@ -0,0 +1,145 @@ +/*************************************************************************** + coul_long_cs_ext.cpp + ------------------- + Trung Nguyen (Northwestern) + + Functions for LAMMPS access to coul/long/cs acceleration routines. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : June 2018 + email : ndactrung@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_coul_long_cs.h" + +using namespace std; +using namespace LAMMPS_AL; + +static CoulLongCS CLCSMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int clcs_gpu_init(const int ntypes, double **host_scale, + const int inum, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, int &gpu_mode, + FILE *screen, double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald) { + CLCSMF.clear(); + gpu_mode=CLCSMF.device->gpu_mode(); + double gpu_split=CLCSMF.device->particle_split(); + int first_gpu=CLCSMF.device->first_device(); + int last_gpu=CLCSMF.device->last_device(); + int world_me=CLCSMF.device->world_me(); + int gpu_rank=CLCSMF.device->gpu_rank(); + int procs_per_gpu=CLCSMF.device->procs_per_gpu(); + + CLCSMF.device->init_message(screen,"coul/long/cs",first_gpu,last_gpu); + + bool message=false; + if (CLCSMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=CLCSMF.init(ntypes, host_scale, inum, nall, 300, maxspecial, + cell_size, gpu_split, screen, host_cut_coulsq, + host_special_coul, qqrd2e, g_ewald); + + CLCSMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + CLCSMF.estimate_gpu_overhead(); + return init_ok; +} + +// --------------------------------------------------------------------------- +// Copy updated coeffs from host to device +// --------------------------------------------------------------------------- +void clcs_gpu_reinit(const int ntypes, double **host_scale) { + int world_me=CLCSMF.device->world_me(); + int gpu_rank=CLCSMF.device->gpu_rank(); + int procs_per_gpu=CLCSMF.device->procs_per_gpu(); + + if (world_me==0) + CLCSMF.reinit(ntypes, host_scale); + + CLCSMF.device->world_barrier(); + + for (int i=0; igpu_barrier(); + } +} + +void clcs_gpu_clear() { + CLCSMF.clear(); +} + +int** clcs_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd) { + return CLCSMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success, + host_q, boxlo, prd); +} + +void clcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd) { + CLCSMF.compute(ago,inum_full,nall,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success, + host_q,nlocal,boxlo,prd); +} + +double clcs_gpu_bytes() { + return CLCSMF.host_memory_usage(); +} + + diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index 0ea128a5b38a0b5007052e14d23cc24019eab8d4..6b4d0ab2a504e404a72af7bf35d3bc436f9fdd8a 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -34,8 +34,8 @@ using namespace LAMMPS_AL; template DeviceT::Device() : _init_count(0), _device_init(false), - _gpu_mode(GPU_FORCE), _first_device(0), - _last_device(0), _compiled(false) { + _gpu_mode(GPU_FORCE), _first_device(0), + _last_device(0), _platform_id(-1), _compiled(false) { } template @@ -67,6 +67,17 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, _particle_split=p_split; _cell_size=cell_size; _block_pair=block_pair; + // support selecting platform though "package device" keyword. + // "0:generic" will select platform 0 and tune for generic device + // "1:fermi" will select platform 1 and tune for Nvidia Fermi gpu + if (ocl_vendor) { + char *sep = NULL; + if ((sep = strstr(ocl_vendor,":"))) { + *sep = '\0'; + _platform_id = atoi(ocl_vendor); + ocl_vendor = sep+1; + } + } // Get the rank/size within the world MPI_Comm_rank(_comm_world,&_world_me); @@ -119,8 +130,16 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, // Time on the device only if 1 proc per gpu _time_device=true; + +#if 0 + // XXX: the following setting triggers a memory leak with OpenCL and MPI + // setting _time_device=true for all processes doesn't seem to be a + // problem with either (no segfault, no (large) memory leak. + // thus keeping this disabled for now. may need to review later. + // 2018-07-23 if (_procs_per_gpu>1) _time_device=false; +#endif // Set up a per device communicator MPI_Comm_split(node_comm,my_gpu,0,&_comm_gpu); @@ -135,6 +154,9 @@ int DeviceT::init_device(MPI_Comm world, MPI_Comm replica, const int first_gpu, return -7; #endif + if (gpu->set_platform_accelerator(_platform_id)!=UCL_SUCCESS) + return -12; + if (gpu->set(my_gpu)!=UCL_SUCCESS) return -6; @@ -191,13 +213,15 @@ int DeviceT::set_ocl_params(char *ocl_vendor) { _ocl_vendor_string="-DUSE_OPENCL"; int token_count=0; std::string params[13]; - char *pch = strtok(ocl_vendor,"\" "); + char *pch = strtok(ocl_vendor,","); + pch = strtok(NULL,","); + if (pch == NULL) return -11; while (pch != NULL) { if (token_count==13) return -11; params[token_count]=pch; token_count++; - pch = strtok(NULL,"\" "); + pch = strtok(NULL,","); } _ocl_vendor_string+=" -DMEM_THREADS="+params[0]+ " -DTHREADS_PER_ATOM="+params[1]+ @@ -656,7 +680,7 @@ int DeviceT::compile_kernels() { dev_program=new UCL_Program(*gpu); int success=dev_program->load_string(device,compile_string().c_str()); if (success!=UCL_SUCCESS) - return -4; + return -6; k_zero.set_function(*dev_program,"kernel_zero"); k_info.set_function(*dev_program,"kernel_info"); _compiled=true; diff --git a/lib/gpu/lal_device.h b/lib/gpu/lal_device.h index 95e9f2a4309fa755bf10458f6c07ae12a8196191..695b0a62f9236f9f4e16119391ce05c6eafbf8e8 100644 --- a/lib/gpu/lal_device.h +++ b/lib/gpu/lal_device.h @@ -292,7 +292,7 @@ class Device { MPI_Comm _comm_world, _comm_replica, _comm_gpu; int _procs_per_gpu, _gpu_rank, _world_me, _world_size, _replica_me, _replica_size; - int _gpu_mode, _first_device, _last_device, _nthreads; + int _gpu_mode, _first_device, _last_device, _platform_id, _nthreads; double _particle_split; double _cpu_full; double _ptx_arch; diff --git a/lib/gpu/lal_lj_expand_coul_long.cpp b/lib/gpu/lal_lj_expand_coul_long.cpp index 6a3da9b68604ed9e6d4f5ddf936c141b14b90aae..32a4f8120e2e42d40ae6f67bcf960515182b3ca0 100644 --- a/lib/gpu/lal_lj_expand_coul_long.cpp +++ b/lib/gpu/lal_lj_expand_coul_long.cpp @@ -10,7 +10,7 @@ __________________________________________________________________________ begin : - email : trung.nguyen@northwestern.edu + email : ndactrung@gmail.com ***************************************************************************/ #if defined(USE_OPENCL) diff --git a/lib/gpu/lal_lj_expand_coul_long.cu b/lib/gpu/lal_lj_expand_coul_long.cu index eaea5b0e12aeada9e58288d3f33b08e61c150b46..aa8f02be8c521134f80201e873ad5636b33783e4 100644 --- a/lib/gpu/lal_lj_expand_coul_long.cu +++ b/lib/gpu/lal_lj_expand_coul_long.cu @@ -10,7 +10,7 @@ // __________________________________________________________________________ // // begin : -// email : trung.nguyen@northwestern.edu +// email : ndactrung@gmail.com // ***************************************************************************/ #ifdef NV_KERNEL @@ -94,17 +94,21 @@ __kernel void k_lj_expand_coul_long(const __global numtyp4 *restrict x_, int mtype=itype*lj_types+jtype; if (rsq0) - lj3[tid]=lj3_in[tid]; + lj3[tid]=lj3_in[tid]; } acctyp energy=(acctyp)0; @@ -212,17 +215,21 @@ __kernel void k_lj_expand_coul_long_fast(const __global numtyp4 *restrict x_, numtyp rsq = delx*delx+dely*dely+delz*delz; if (rsq diff --git a/lib/gpu/lal_neighbor.cpp b/lib/gpu/lal_neighbor.cpp index 04e08c3e9c25d07b7a637b100b1d9ed4c3c3a01a..3e128bcf57349d39399f5cf625e5f863186a3630 100644 --- a/lib/gpu/lal_neighbor.cpp +++ b/lib/gpu/lal_neighbor.cpp @@ -127,10 +127,10 @@ void Neighbor::alloc(bool &success) { dev_packed.clear(); success=success && (dev_packed.alloc((_max_nbors+2)*_max_atoms,*dev, _packed_permissions)==UCL_SUCCESS); - dev_acc.clear(); - success=success && (dev_acc.alloc(_max_atoms,*dev, + dev_ilist.clear(); + success=success && (dev_ilist.alloc(_max_atoms,*dev, UCL_READ_WRITE)==UCL_SUCCESS); - _c_bytes+=dev_packed.row_bytes()+dev_acc.row_bytes(); + _c_bytes+=dev_packed.row_bytes()+dev_ilist.row_bytes(); } if (_max_host>0) { nbor_host.clear(); @@ -197,7 +197,7 @@ void Neighbor::clear() { host_packed.clear(); host_acc.clear(); - dev_acc.clear(); + dev_ilist.clear(); dev_nbor.clear(); nbor_host.clear(); dev_packed.clear(); @@ -281,7 +281,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); UCL_H_Vec host_view; host_view.alloc(_max_atoms,*dev,UCL_READ_WRITE); @@ -289,7 +289,7 @@ void Neighbor::get_host(const int inum, int *ilist, int *numj, int i=ilist[ii]; host_view[i] = ii; } - ucl_copy(dev_acc,host_view,true); + ucl_copy(dev_ilist,host_view,true); time_nbor.stop(); @@ -364,7 +364,7 @@ void Neighbor::get_host3(const int inum, const int nlist, int *ilist, int *numj, } UCL_D_Vec acc_view; acc_view.view_offset(inum,dev_nbor,inum*2); - ucl_copy(acc_view,host_acc,true); + ucl_copy(acc_view,host_acc,inum*2,true); time_nbor.stop(); if (_use_packing==false) { diff --git a/lib/gpu/lal_neighbor.h b/lib/gpu/lal_neighbor.h index 05168834c6034a3cc336ef429242d441a63c9945..996deaff6d12bbbfa6789ac12dae0910b7f7f699 100644 --- a/lib/gpu/lal_neighbor.h +++ b/lib/gpu/lal_neighbor.h @@ -110,7 +110,7 @@ class Neighbor { } if (_time_device) { time_nbor.add_to_total(); - time_kernel.add_to_total(); + if (_use_packing==false) time_kernel.add_to_total(); if (_gpu_nbor==2) { time_hybrid1.add_to_total(); time_hybrid2.add_to_total(); @@ -200,7 +200,7 @@ class Neighbor { /// Host storage for nbor counts (row 1) & accumulated neighbor counts (row2) UCL_H_Vec host_acc; /// Device storage for accessing atom indices from the neighbor list (3-body) - UCL_D_Vec dev_acc; + UCL_D_Vec dev_ilist; // ----------------- Data for GPU Neighbor Calculation --------------- diff --git a/lib/gpu/lal_neighbor_gpu.cu b/lib/gpu/lal_neighbor_gpu.cu index b0b3cfb90c958c5c7e7f0c84816be3b03ba73d04..83692a24e4c04bfd9d1441c2a49b5da01fc9813e 100644 --- a/lib/gpu/lal_neighbor_gpu.cu +++ b/lib/gpu/lal_neighbor_gpu.cu @@ -118,24 +118,24 @@ __kernel void transpose(__global tagint *restrict out, const __global tagint *restrict in, int columns_in, int rows_in) { - __local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1]; + __local tagint block[BLOCK_CELL_2D][BLOCK_CELL_2D+1]; - unsigned ti=THREAD_ID_X; - unsigned tj=THREAD_ID_Y; - unsigned bi=BLOCK_ID_X; - unsigned bj=BLOCK_ID_Y; + unsigned ti=THREAD_ID_X; + unsigned tj=THREAD_ID_Y; + unsigned bi=BLOCK_ID_X; + unsigned bj=BLOCK_ID_Y; - unsigned i=bi*BLOCK_CELL_2D+ti; - unsigned j=bj*BLOCK_CELL_2D+tj; - if ((i 1e-5) { + if (r2 < cell_size*cell_size && pid_j != pid_i) { // && r2 > 1e-5 cnt++; if (cnt <= neigh_bin_size) { *neigh_list = pid_j; @@ -243,8 +243,8 @@ __kernel void calc_neigh_list_cell(const __global numtyp4 *restrict x_, } } } - __syncthreads(); - } // for (k) + __syncthreads(); + } // for (k) } } } diff --git a/lib/gpu/lal_sw.cpp b/lib/gpu/lal_sw.cpp index 24984e48785d665c63ad9cae54dc45812846a5f2..46b6382a6097aeaab518a2cc509b6eeb5d92e41b 100644 --- a/lib/gpu/lal_sw.cpp +++ b/lib/gpu/lal_sw.cpp @@ -243,7 +243,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -252,7 +252,7 @@ void SWT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &sw1, &sw2, &sw3, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); diff --git a/lib/gpu/lal_sw.cu b/lib/gpu/lal_sw.cu index 517de70691cd735cac9c9dab5cc849a257f5d373..3b6de5a683d603e74f53b8c2364942fd0f83f2cf 100644 --- a/lib/gpu/lal_sw.cu +++ b/lib/gpu/lal_sw.cu @@ -544,7 +544,7 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -614,13 +614,13 @@ __kernel void k_sw_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -698,7 +698,7 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -768,13 +768,13 @@ __kernel void k_sw_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_tersoff.cpp b/lib/gpu/lal_tersoff.cpp index a63d286d9c16a9120ee9e300f16d9fda4e5ecdfc..ef55b98a2dba21347cc9830858f9663f0ff21b31 100644 --- a/lib/gpu/lal_tersoff.cpp +++ b/lib/gpu/lal_tersoff.cpp @@ -272,7 +272,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff.cu b/lib/gpu/lal_tersoff.cu index cec0ccc44341c10f9678e57b8de628d169980262..836f05660d7b066dcaf7398ed11e10e96eec7b07 100644 --- a/lib/gpu/lal_tersoff.cu +++ b/lib/gpu/lal_tersoff.cu @@ -696,7 +696,7 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -777,13 +777,13 @@ __kernel void k_tersoff_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -941,7 +941,7 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, const __global acctyp4 *restrict zetaij, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -1022,13 +1022,13 @@ __kernel void k_tersoff_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/gpu/lal_tersoff_mod.cpp b/lib/gpu/lal_tersoff_mod.cpp index c37c07f1a1234d1945cfefdac45d42f9be446458..3cbb488cab878c497c0f0cf7eede5f9c5ce9663c 100644 --- a/lib/gpu/lal_tersoff_mod.cpp +++ b/lib/gpu/lal_tersoff_mod.cpp @@ -272,7 +272,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -311,7 +311,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -320,7 +320,7 @@ void TersoffMT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &ts5, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_mod.cu b/lib/gpu/lal_tersoff_mod.cu index 576359b5146246d74078b0deff98a700bbdcb533..dfb94c41451c4a553a244e14c2aa05710cf1ebe6 100644 --- a/lib/gpu/lal_tersoff_mod.cu +++ b/lib/gpu/lal_tersoff_mod.cu @@ -272,7 +272,7 @@ __kernel void k_tersoff_mod_zeta(const __global numtyp4 *restrict x_, if (iinbor->dev_nbor, &this->_nbor_data->begin(), &this->dev_short_nbor, - &_eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); + &eflag, &this->_ainum, &nbor_pitch, &this->_threads_per_atom); ainum=this->ans->inum(); nbor_pitch=this->nbor->nbor_pitch(); @@ -337,7 +337,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end_vatom.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); @@ -346,7 +346,7 @@ void TersoffZT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, &ts1, &ts2, &ts4, &cutsq, &map, &elem2param, &_nelements, &_nparams, &_zetaij, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_tersoff_zbl.cu b/lib/gpu/lal_tersoff_zbl.cu index e8bb017f5901a9184b80403d8814aab50794500c..73ff51c70404cfea89fa7c9195e26ac12b6fbbcd 100644 --- a/lib/gpu/lal_tersoff_zbl.cu +++ b/lib/gpu/lal_tersoff_zbl.cu @@ -278,7 +278,7 @@ __kernel void k_tersoff_zbl_zeta(const __global numtyp4 *restrict x_, if (iik_three_end_vatom.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } else { @@ -286,7 +286,7 @@ void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { this->k_three_end.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, &map, &elem2param, &_nelements, &this->nbor->dev_nbor, &this->_nbor_data->begin(), - &this->nbor->dev_acc, &this->dev_short_nbor, + &this->nbor->dev_ilist, &this->dev_short_nbor, &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); } diff --git a/lib/gpu/lal_vashishta.cu b/lib/gpu/lal_vashishta.cu index d2e8bb1496abfd7355f88730cbb0d69c1c22339d..0da46c3b534cc29cba600851db0dda05a2cf38da 100644 --- a/lib/gpu/lal_vashishta.cu +++ b/lib/gpu/lal_vashishta.cu @@ -554,7 +554,7 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -623,13 +623,13 @@ __kernel void k_vashishta_three_end(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; @@ -709,7 +709,7 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, const int nelements, const __global int * dev_nbor, const __global int * dev_packed, - const __global int * dev_acc, + const __global int * dev_ilist, const __global int * dev_short_nbor, __global acctyp4 *restrict ans, __global acctyp *restrict engv, @@ -778,13 +778,13 @@ __kernel void k_vashishta_three_end_vatom(const __global numtyp4 *restrict x_, int nbor_k,numk; if (dev_nbor==dev_packed) { if (gpu_nbor) nbor_k=j+nbor_pitch; - else nbor_k=dev_acc[j]+nbor_pitch; + else nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); nbor_k+=offset_k; } else { - nbor_k=dev_acc[j]+nbor_pitch; + nbor_k=dev_ilist[j]+nbor_pitch; numk=dev_nbor[nbor_k]; nbor_k+=nbor_pitch; nbor_k=dev_nbor[nbor_k]; diff --git a/lib/latte/Install.py b/lib/latte/Install.py index 4b94ac3cba4381e5cbabbff902ee837b5b053138..3b211858dd15b5336c0d962e7bf9bcbe88edcf08 100644 --- a/lib/latte/Install.py +++ b/lib/latte/Install.py @@ -4,7 +4,7 @@ # used to automate the steps described in the README file in this dir from __future__ import print_function -import sys,os,re,subprocess +import sys,os,re,subprocess,hashlib # help message @@ -12,19 +12,19 @@ help = """ Syntax from src dir: make lib-latte args="-b" or: make lib-latte args="-p /usr/local/latte" or: make lib-latte args="-m gfortran" - or: make lib-latte args="-b -v 1.1.1" + or: make lib-latte args="-b -v 1.2.1" Syntax from lib dir: python Install.py -b or: python Install.py -p /usr/local/latte or: python Install.py -m gfortran - or: python Install.py -v 1.1.1 -b + or: python Install.py -v 1.2.1 -b specify one or more options, order does not matter -b = download and build the LATTE library -p = specify folder of existing LATTE installation -m = copy Makefile.lammps.suffix to Makefile.lammps - -v = set version of LATTE library to download and set up (default = 1.1.1) + -v = set version of LATTE library to download and set up (default = 1.2.1) Example: @@ -34,7 +34,14 @@ make lib-latte args="-p $HOME/latte" # use existing LATTE installation # settings -version = '1.1.1' +version = '1.2.1' + +# known checksums for different LATTE versions. used to validate the download. +checksums = { \ + '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ + '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ + '1.2.1' : '85ac414fdada2d04619c8f936344df14', \ + } # print error message or help @@ -91,6 +98,17 @@ def geturl(url,fname): error("Failed to download source code with 'curl' or 'wget'") return +def checkmd5sum(md5sum,fname): + with open(fname,'rb') as fh: + m = hashlib.md5() + while True: + data = fh.read(81920) + if not data: + break + m.update(data) + fh.close() + return m.hexdigest() == md5sum + # parse args args = sys.argv[1:] @@ -144,7 +162,12 @@ if buildflag: print("Downloading LATTE ...") geturl(url,"LATTE.tar.gz") - print("Unpacking LATTE zipfile ...") + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version],'LATTE.tar.gz'): + error("Checksum for LATTE library does not match") + + print("Unpacking LATTE ...") if os.path.exists(lattedir): cmd = 'rm -rf "%s"' % lattedir subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) @@ -162,7 +185,7 @@ if buildflag: # create 3 links in lib/latte to LATTE dirs # do this -b or -p is set - + if buildflag or pathflag: print("Creating links to LATTE files") if os.path.isfile("includelink") or os.path.islink("includelink"): diff --git a/lib/linalg/Makefile.gfortran b/lib/linalg/Makefile.gfortran index 7e1d97a5bce8bc2982fba617541d9f48bee4e0dd..2a777099e98a2d92687fcaaa58154bdaf397bab7 100644 --- a/lib/linalg/Makefile.gfortran +++ b/lib/linalg/Makefile.gfortran @@ -7,13 +7,14 @@ SHELL = /bin/sh # ------ FILES ------ SRC = $(wildcard *.f) +SRC1 = $(wildcard *.F) -FILES = $(SRC) Makefile.* README +FILES = $(SRC) $(SRC1) Makefile.* README # ------ DEFINITIONS ------ LIB = liblinalg.a -OBJ = $(SRC:.f=.o) +OBJ = $(SRC:.f=.o) $(SRC1:.F=.o) # ------ SETTINGS ------ @@ -34,7 +35,7 @@ lib: $(OBJ) # ------ COMPILE RULES ------ %.o:%.F - $(F90) $(F90FLAGS) -c $< + $(FC) $(FFLAGS) -c $< %.o:%.f $(FC) $(FFLAGS) -c $< diff --git a/lib/linalg/Makefile.mpi b/lib/linalg/Makefile.mpi index dd22ff134caf02e6350304125af4a0420da1cf25..26bfab4c80857355a055c5322f27ea4fdac55b82 100644 --- a/lib/linalg/Makefile.mpi +++ b/lib/linalg/Makefile.mpi @@ -7,13 +7,14 @@ SHELL = /bin/sh # ------ FILES ------ SRC = $(wildcard *.f) +SRC1 = $(wildcard *.F) -FILES = $(SRC) Makefile.* README +FILES = $(SRC) $(SRC1) Makefile.* README # ------ DEFINITIONS ------ LIB = liblinalg.a -OBJ = $(SRC:.f=.o) +OBJ = $(SRC:.f=.o) $(SRC1:.F=.o) # ------ SETTINGS ------ @@ -34,7 +35,7 @@ lib: $(OBJ) # ------ COMPILE RULES ------ %.o:%.F - $(F90) $(F90FLAGS) -c $< + $(FC) $(FFLAGS) -c $< %.o:%.f $(FC) $(FFLAGS) -c $< diff --git a/lib/linalg/dasum.f b/lib/linalg/dasum.f index c1bd78ac815d18d79f8218011d74f780ce8f7073..cc5977f77044edc96caf5a94295ee834d4fe4025 100644 --- a/lib/linalg/dasum.f +++ b/lib/linalg/dasum.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DASUM(N,DX,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * .. * .. Array Arguments .. * DOUBLE PRECISION DX(*) * .. -* +* * *> \par Purpose: * ============= @@ -26,15 +26,35 @@ *> DASUM takes the sum of the absolute values. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -51,10 +71,10 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DASUM(N,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/daxpy.f b/lib/linalg/daxpy.f index 64a02d68bc8d1eefd1e8838606fc2abd9e5d0456..cb94fc1e0ab5e99df8d71893be0ecc0e88eefdeb 100644 --- a/lib/linalg/daxpy.f +++ b/lib/linalg/daxpy.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DAXPY(N,DA,DX,INCX,DY,INCY) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION DA * INTEGER INCX,INCY,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION DX(*),DY(*) * .. -* +* * *> \par Purpose: * ============= @@ -28,15 +28,52 @@ *> uses unrolled loops for increments equal to one. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DA +*> \verbatim +*> DA is DOUBLE PRECISION +*> On entry, DA specifies the scalar alpha. +*> \endverbatim +*> +*> \param[in] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +*> +*> \param[in,out] DY +*> \verbatim +*> DY is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of DY +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -52,10 +89,10 @@ * ===================================================================== SUBROUTINE DAXPY(N,DA,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA diff --git a/lib/linalg/dbdsqr.f b/lib/linalg/dbdsqr.f index 007e99779b8b836a407524c52f43993529103d2f..93db95e7a8604fbbd50d9878f47c74ad0972c39d 100644 --- a/lib/linalg/dbdsqr.f +++ b/lib/linalg/dbdsqr.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DBDSQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DBDSQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DBDSQR( UPLO, N, NCVT, NRU, NCC, D, E, VT, LDVT, U, * LDU, C, LDC, WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDC, LDU, LDVT, N, NCC, NCVT, NRU @@ -29,7 +29,7 @@ * DOUBLE PRECISION C( LDC, * ), D( * ), E( * ), U( LDU, * ), * $ VT( LDVT, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -40,9 +40,9 @@ *> left singular vectors from the singular value decomposition (SVD) of *> a real N-by-N (upper or lower) bidiagonal matrix B using the implicit *> zero-shift QR algorithm. The SVD of B has the form -*> +*> *> B = Q * S * P**T -*> +*> *> where S is the diagonal matrix of singular values, Q is an orthogonal *> matrix of left singular vectors, and P is an orthogonal matrix of *> right singular vectors. If left singular vectors are requested, this @@ -113,7 +113,7 @@ *> \verbatim *> E is DOUBLE PRECISION array, dimension (N-1) *> On entry, the N-1 offdiagonal elements of the bidiagonal -*> matrix B. +*> matrix B. *> On exit, if INFO = 0, E is destroyed; if INFO > 0, D and E *> will contain the diagonal and superdiagonal elements of a *> bidiagonal matrix orthogonally equivalent to the one given @@ -179,7 +179,7 @@ *> = 1, a split was marked by a positive value in E *> = 2, current block of Z not diagonalized after 30*N *> iterations (in inner while loop) -*> = 3, termination criterion of outer while loop not met +*> = 3, termination criterion of outer while loop not met *> (program created more than N unreduced blocks) *> else NCVT = NRU = NCC = 0, *> the algorithm did not converge; D and E contain the @@ -212,17 +212,28 @@ *> algorithm through its inner loop. The algorithms stops *> (and so fails to converge) if the number of passes *> through the inner loop exceeds MAXITR*N**2. +*> +*> \endverbatim +* +*> \par Note: +* =========== +*> +*> \verbatim +*> Bug report from Cezary Dendek. +*> On March 23rd 2017, the INTEGER variable MAXIT = MAXITR*N**2 is +*> removed since it can overflow pretty easily (for N larger or equal +*> than 18,919). We instead use MAXITDIVN = MAXITR*N. *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date June 2017 * *> \ingroup auxOTHERcomputational * @@ -230,10 +241,10 @@ SUBROUTINE DBDSQR( UPLO, N, NCVT, NRU, NCC, D, E, VT, LDVT, U, $ LDU, C, LDC, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* June 2017 * * .. Scalar Arguments .. CHARACTER UPLO @@ -266,8 +277,8 @@ * .. * .. Local Scalars .. LOGICAL LOWER, ROTATE - INTEGER I, IDIR, ISUB, ITER, J, LL, LLL, M, MAXIT, NM1, - $ NM12, NM13, OLDLL, OLDM + INTEGER I, IDIR, ISUB, ITER, ITERDIVN, J, LL, LLL, M, + $ MAXITDIVN, NM1, NM12, NM13, OLDLL, OLDM DOUBLE PRECISION ABSE, ABSS, COSL, COSR, CS, EPS, F, G, H, MU, $ OLDCS, OLDSN, R, SHIFT, SIGMN, SIGMX, SINL, $ SINR, SLL, SMAX, SMIN, SMINL, SMINOA, @@ -329,7 +340,7 @@ CALL DLASQ1( N, D, E, WORK, INFO ) * * If INFO equals 2, dqds didn't finish, try to finish -* +* IF( INFO .NE. 2 ) RETURN INFO = 0 END IF @@ -400,20 +411,21 @@ 40 CONTINUE 50 CONTINUE SMINOA = SMINOA / SQRT( DBLE( N ) ) - THRESH = MAX( TOL*SMINOA, MAXITR*N*N*UNFL ) + THRESH = MAX( TOL*SMINOA, MAXITR*(N*(N*UNFL)) ) ELSE * * Absolute accuracy desired * - THRESH = MAX( ABS( TOL )*SMAX, MAXITR*N*N*UNFL ) + THRESH = MAX( ABS( TOL )*SMAX, MAXITR*(N*(N*UNFL)) ) END IF * * Prepare for main iteration loop for the singular values * (MAXIT is the maximum number of passes through the inner * loop permitted before nonconvergence signalled.) * - MAXIT = MAXITR*N*N - ITER = 0 + MAXITDIVN = MAXITR*N + ITERDIVN = 0 + ITER = -1 OLDLL = -1 OLDM = -1 * @@ -429,8 +441,13 @@ * IF( M.LE.1 ) $ GO TO 160 - IF( ITER.GT.MAXIT ) - $ GO TO 200 +* + IF( ITER.GE.N ) THEN + ITER = ITER - N + ITERDIVN = ITERDIVN + 1 + IF( ITERDIVN.GE.MAXITDIVN ) + $ GO TO 200 + END IF * * Find diagonal block of matrix to work on * diff --git a/lib/linalg/dcabs1.f b/lib/linalg/dcabs1.f index f6debb9ac261ffd2987feec1ef8bad9b2ec964bf..d6d850ed0fcb993a561e97a407f08cdb35fb6fa3 100644 --- a/lib/linalg/dcabs1.f +++ b/lib/linalg/dcabs1.f @@ -2,47 +2,55 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DCABS1(Z) -* +* * .. Scalar Arguments .. * COMPLEX*16 Z * .. * .. -* +* * *> \par Purpose: * ============= *> *> \verbatim *> -*> DCABS1 computes absolute value of a double complex number +*> DCABS1 computes |Re(.)| + |Im(.)| of a double complex number +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] Z +*> \verbatim +*> Z is COMPLEX*16 *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * * ===================================================================== DOUBLE PRECISION FUNCTION DCABS1(Z) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 Z diff --git a/lib/linalg/dcopy.f b/lib/linalg/dcopy.f index d9d5ac7aa2823e2f1919f80b1f360ef06fc96dc1..27bc08582b39d179563931dd05564eae9e455b69 100644 --- a/lib/linalg/dcopy.f +++ b/lib/linalg/dcopy.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DCOPY(N,DX,INCX,DY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * DOUBLE PRECISION DX(*),DY(*) * .. -* +* * *> \par Purpose: * ============= @@ -24,18 +24,49 @@ *> \verbatim *> *> DCOPY copies a vector, x, to a vector, y. -*> uses unrolled loops for increments equal to one. +*> uses unrolled loops for increments equal to 1. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +*> +*> \param[out] DY +*> \verbatim +*> DY is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of DY *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -51,10 +82,10 @@ * ===================================================================== SUBROUTINE DCOPY(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -85,7 +116,7 @@ DY(I) = DX(I) END DO IF (N.LT.7) RETURN - END IF + END IF MP1 = M + 1 DO I = MP1,N,7 DY(I) = DX(I) @@ -96,7 +127,7 @@ DY(I+5) = DX(I+5) DY(I+6) = DX(I+6) END DO - ELSE + ELSE * * code for unequal increments or equal increments * not equal to 1 diff --git a/lib/linalg/ddot.f b/lib/linalg/ddot.f index cc0c1b7a43e0712322650c6856307d65cdfd13bb..3d18695aab0827181c83cb50ecf4aaca365f9ecd 100644 --- a/lib/linalg/ddot.f +++ b/lib/linalg/ddot.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DDOT(N,DX,INCX,DY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * DOUBLE PRECISION DX(*),DY(*) * .. -* +* * *> \par Purpose: * ============= @@ -27,15 +27,46 @@ *> uses unrolled loops for increments equal to one. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +*> +*> \param[in] DY +*> \verbatim +*> DY is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of DY +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -51,10 +82,10 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DDOT(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N diff --git a/lib/linalg/dgebd2.f b/lib/linalg/dgebd2.f index 4b4dcc964159ec8bd46a65b0944f9a135de3bd06..2bec4e29c718a9bf98657cecd669de82ccadffb5 100644 --- a/lib/linalg/dgebd2.f +++ b/lib/linalg/dgebd2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGEBD2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGEBD2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGEBD2( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, M, N * .. @@ -27,7 +27,7 @@ * DOUBLE PRECISION A( LDA, * ), D( * ), E( * ), TAUP( * ), * $ TAUQ( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -100,7 +100,7 @@ *> *> \param[out] TAUQ *> \verbatim -*> TAUQ is DOUBLE PRECISION array dimension (min(M,N)) +*> TAUQ is DOUBLE PRECISION array, dimension (min(M,N)) *> The scalar factors of the elementary reflectors which *> represent the orthogonal matrix Q. See Further Details. *> \endverbatim @@ -127,12 +127,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * *> \ingroup doubleGEcomputational * @@ -189,10 +189,10 @@ * ===================================================================== SUBROUTINE DGEBD2( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgebrd.f b/lib/linalg/dgebrd.f index 6cb61f002f5b9c0d9125b19cf7f9f1d04a490aa6..957cf2e53975afdca2e4d7c397ae8ee9f378d9d6 100644 --- a/lib/linalg/dgebrd.f +++ b/lib/linalg/dgebrd.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGEBRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGEBRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGEBRD( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, LWORK, * INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, LWORK, M, N * .. @@ -28,7 +28,7 @@ * DOUBLE PRECISION A( LDA, * ), D( * ), E( * ), TAUP( * ), * $ TAUQ( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -101,7 +101,7 @@ *> *> \param[out] TAUQ *> \verbatim -*> TAUQ is DOUBLE PRECISION array dimension (min(M,N)) +*> TAUQ is DOUBLE PRECISION array, dimension (min(M,N)) *> The scalar factors of the elementary reflectors which *> represent the orthogonal matrix Q. See Further Details. *> \endverbatim @@ -142,12 +142,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date June 2017 * *> \ingroup doubleGEcomputational * @@ -205,10 +205,10 @@ SUBROUTINE DGEBRD( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, LWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* June 2017 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N diff --git a/lib/linalg/dgecon.f b/lib/linalg/dgecon.f index df9d8e1c4030944c2d286c93b068c113ed8bbe13..be20bbcd2ad2b0651f188fb0cd1f9e5007c45e49 100644 --- a/lib/linalg/dgecon.f +++ b/lib/linalg/dgecon.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGECON + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGECON + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK, * INFO ) -* +* * .. Scalar Arguments .. * CHARACTER NORM * INTEGER INFO, LDA, N @@ -30,7 +30,7 @@ * INTEGER IWORK( * ) * DOUBLE PRECISION A( LDA, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -111,12 +111,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * @@ -124,10 +124,10 @@ SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dgelq2.f b/lib/linalg/dgelq2.f index 0d64ba52105f00f7bb7fc48830450bc656ea61ad..04aa57fc19324a4f018d1c1f791ac44a35606c7f 100644 --- a/lib/linalg/dgelq2.f +++ b/lib/linalg/dgelq2.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGELQ2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGELQ2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGELQ2( M, N, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -91,12 +91,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleGEcomputational * @@ -121,10 +121,10 @@ * ===================================================================== SUBROUTINE DGELQ2( M, N, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgelqf.f b/lib/linalg/dgelqf.f index d27b04ab1d0464cd371de931d249ca453987f73c..834c47168f1ce9f1e8d6bc9cb28ce19c13ccb04d 100644 --- a/lib/linalg/dgelqf.f +++ b/lib/linalg/dgelqf.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGELQF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGELQF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGELQF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, LWORK, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -105,12 +105,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * @@ -135,10 +135,10 @@ * ===================================================================== SUBROUTINE DGELQF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N diff --git a/lib/linalg/dgelsd.f b/lib/linalg/dgelsd.f new file mode 100644 index 0000000000000000000000000000000000000000..f2cfd633761a442a6c20b3d4c344706b00f19f1f --- /dev/null +++ b/lib/linalg/dgelsd.f @@ -0,0 +1,629 @@ +*> \brief DGELSD computes the minimum-norm solution to a linear least squares problem for GE matrices +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DGELSD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DGELSD( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, +* WORK, LWORK, IWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK +* DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. +* INTEGER IWORK( * ) +* DOUBLE PRECISION A( LDA, * ), B( LDB, * ), S( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DGELSD computes the minimum-norm solution to a real linear least +*> squares problem: +*> minimize 2-norm(| b - A*x |) +*> using the singular value decomposition (SVD) of A. A is an M-by-N +*> matrix which may be rank-deficient. +*> +*> Several right hand side vectors b and solution vectors x can be +*> handled in a single call; they are stored as the columns of the +*> M-by-NRHS right hand side matrix B and the N-by-NRHS solution +*> matrix X. +*> +*> The problem is solved in three steps: +*> (1) Reduce the coefficient matrix A to bidiagonal form with +*> Householder transformations, reducing the original problem +*> into a "bidiagonal least squares problem" (BLS) +*> (2) Solve the BLS using a divide and conquer approach. +*> (3) Apply back all the Householder transformations to solve +*> the original least squares problem. +*> +*> The effective rank of A is determined by treating as zero those +*> singular values which are less than RCOND times the largest singular +*> value. +*> +*> The divide and conquer algorithm makes very mild assumptions about +*> floating point arithmetic. It will work on machines with a guard +*> digit in add/subtract, or on those binary machines without guard +*> digits which subtract like the Cray X-MP, Cray Y-MP, Cray C-90, or +*> Cray-2. It could conceivably fail on hexadecimal or decimal machines +*> without guard digits, but we know of none. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of A. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of A. N >= 0. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of right hand sides, i.e., the number of columns +*> of the matrices B and X. NRHS >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> On entry, the M-by-N matrix A. +*> On exit, A has been destroyed. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,M). +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB,NRHS) +*> On entry, the M-by-NRHS right hand side matrix B. +*> On exit, B is overwritten by the N-by-NRHS solution +*> matrix X. If m >= n and RANK = n, the residual +*> sum-of-squares for the solution in the i-th column is given +*> by the sum of squares of elements n+1:m in that column. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >= max(1,max(M,N)). +*> \endverbatim +*> +*> \param[out] S +*> \verbatim +*> S is DOUBLE PRECISION array, dimension (min(M,N)) +*> The singular values of A in decreasing order. +*> The condition number of A in the 2-norm = S(1)/S(min(m,n)). +*> \endverbatim +*> +*> \param[in] RCOND +*> \verbatim +*> RCOND is DOUBLE PRECISION +*> RCOND is used to determine the effective rank of A. +*> Singular values S(i) <= RCOND*S(1) are treated as zero. +*> If RCOND < 0, machine precision is used instead. +*> \endverbatim +*> +*> \param[out] RANK +*> \verbatim +*> RANK is INTEGER +*> The effective rank of A, i.e., the number of singular values +*> which are greater than RCOND*S(1). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. LWORK must be at least 1. +*> The exact minimum amount of workspace needed depends on M, +*> N and NRHS. As long as LWORK is at least +*> 12*N + 2*N*SMLSIZ + 8*N*NLVL + N*NRHS + (SMLSIZ+1)**2, +*> if M is greater than or equal to N or +*> 12*M + 2*M*SMLSIZ + 8*M*NLVL + M*NRHS + (SMLSIZ+1)**2, +*> if M is less than N, the code will execute correctly. +*> SMLSIZ is returned by ILAENV and is equal to the maximum +*> size of the subproblems at the bottom of the computation +*> tree (usually about 25), and +*> NLVL = MAX( 0, INT( LOG_2( MIN( M,N )/(SMLSIZ+1) ) ) + 1 ) +*> For good performance, LWORK should generally be larger. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal size of the WORK array, returns +*> this value as the first entry of the WORK array, and no error +*> message related to LWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (MAX(1,LIWORK)) +*> LIWORK >= max(1, 3 * MINMN * NLVL + 11 * MINMN), +*> where MINMN = MIN( M,N ). +*> On exit, if INFO = 0, IWORK(1) returns the minimum LIWORK. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: the algorithm for computing the SVD failed to converge; +*> if INFO = i, i off-diagonal elements of an intermediate +*> bidiagonal form did not converge to zero. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2017 +* +*> \ingroup doubleGEsolve +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Ren-Cang Li, Computer Science Division, University of +*> California at Berkeley, USA \n +*> Osni Marques, LBNL/NERSC, USA \n +* +* ===================================================================== + SUBROUTINE DGELSD( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, + $ WORK, LWORK, IWORK, INFO ) +* +* -- LAPACK driver routine (version 3.7.1) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2017 +* +* .. Scalar Arguments .. + INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK + DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION A( LDA, * ), B( LDB, * ), S( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE, TWO + PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0, TWO = 2.0D0 ) +* .. +* .. Local Scalars .. + LOGICAL LQUERY + INTEGER IASCL, IBSCL, IE, IL, ITAU, ITAUP, ITAUQ, + $ LDWORK, LIWORK, MAXMN, MAXWRK, MINMN, MINWRK, + $ MM, MNTHR, NLVL, NWORK, SMLSIZ, WLALSD + DOUBLE PRECISION ANRM, BIGNUM, BNRM, EPS, SFMIN, SMLNUM +* .. +* .. External Subroutines .. + EXTERNAL DGEBRD, DGELQF, DGEQRF, DLABAD, DLACPY, DLALSD, + $ DLASCL, DLASET, DORMBR, DORMLQ, DORMQR, XERBLA +* .. +* .. External Functions .. + INTEGER ILAENV + DOUBLE PRECISION DLAMCH, DLANGE + EXTERNAL ILAENV, DLAMCH, DLANGE +* .. +* .. Intrinsic Functions .. + INTRINSIC DBLE, INT, LOG, MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input arguments. +* + INFO = 0 + MINMN = MIN( M, N ) + MAXMN = MAX( M, N ) + MNTHR = ILAENV( 6, 'DGELSD', ' ', M, N, NRHS, -1 ) + LQUERY = ( LWORK.EQ.-1 ) + IF( M.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, M ) ) THEN + INFO = -5 + ELSE IF( LDB.LT.MAX( 1, MAXMN ) ) THEN + INFO = -7 + END IF +* + SMLSIZ = ILAENV( 9, 'DGELSD', ' ', 0, 0, 0, 0 ) +* +* Compute workspace. +* (Note: Comments in the code beginning "Workspace:" describe the +* minimal amount of workspace needed at that point in the code, +* as well as the preferred amount for good performance. +* NB refers to the optimal block size for the immediately +* following subroutine, as returned by ILAENV.) +* + MINWRK = 1 + LIWORK = 1 + MINMN = MAX( 1, MINMN ) + NLVL = MAX( INT( LOG( DBLE( MINMN ) / DBLE( SMLSIZ+1 ) ) / + $ LOG( TWO ) ) + 1, 0 ) +* + IF( INFO.EQ.0 ) THEN + MAXWRK = 0 + LIWORK = 3*MINMN*NLVL + 11*MINMN + MM = M + IF( M.GE.N .AND. M.GE.MNTHR ) THEN +* +* Path 1a - overdetermined, with many more rows than columns. +* + MM = N + MAXWRK = MAX( MAXWRK, N+N*ILAENV( 1, 'DGEQRF', ' ', M, N, + $ -1, -1 ) ) + MAXWRK = MAX( MAXWRK, N+NRHS* + $ ILAENV( 1, 'DORMQR', 'LT', M, NRHS, N, -1 ) ) + END IF + IF( M.GE.N ) THEN +* +* Path 1 - overdetermined or exactly determined. +* + MAXWRK = MAX( MAXWRK, 3*N+( MM+N )* + $ ILAENV( 1, 'DGEBRD', ' ', MM, N, -1, -1 ) ) + MAXWRK = MAX( MAXWRK, 3*N+NRHS* + $ ILAENV( 1, 'DORMBR', 'QLT', MM, NRHS, N, -1 ) ) + MAXWRK = MAX( MAXWRK, 3*N+( N-1 )* + $ ILAENV( 1, 'DORMBR', 'PLN', N, NRHS, N, -1 ) ) + WLALSD = 9*N+2*N*SMLSIZ+8*N*NLVL+N*NRHS+(SMLSIZ+1)**2 + MAXWRK = MAX( MAXWRK, 3*N+WLALSD ) + MINWRK = MAX( 3*N+MM, 3*N+NRHS, 3*N+WLALSD ) + END IF + IF( N.GT.M ) THEN + WLALSD = 9*M+2*M*SMLSIZ+8*M*NLVL+M*NRHS+(SMLSIZ+1)**2 + IF( N.GE.MNTHR ) THEN +* +* Path 2a - underdetermined, with many more columns +* than rows. +* + MAXWRK = M + M*ILAENV( 1, 'DGELQF', ' ', M, N, -1, -1 ) + MAXWRK = MAX( MAXWRK, M*M+4*M+2*M* + $ ILAENV( 1, 'DGEBRD', ' ', M, M, -1, -1 ) ) + MAXWRK = MAX( MAXWRK, M*M+4*M+NRHS* + $ ILAENV( 1, 'DORMBR', 'QLT', M, NRHS, M, -1 ) ) + MAXWRK = MAX( MAXWRK, M*M+4*M+( M-1 )* + $ ILAENV( 1, 'DORMBR', 'PLN', M, NRHS, M, -1 ) ) + IF( NRHS.GT.1 ) THEN + MAXWRK = MAX( MAXWRK, M*M+M+M*NRHS ) + ELSE + MAXWRK = MAX( MAXWRK, M*M+2*M ) + END IF + MAXWRK = MAX( MAXWRK, M+NRHS* + $ ILAENV( 1, 'DORMLQ', 'LT', N, NRHS, M, -1 ) ) + MAXWRK = MAX( MAXWRK, M*M+4*M+WLALSD ) +! XXX: Ensure the Path 2a case below is triggered. The workspace +! calculation should use queries for all routines eventually. + MAXWRK = MAX( MAXWRK, + $ 4*M+M*M+MAX( M, 2*M-4, NRHS, N-3*M ) ) + ELSE +* +* Path 2 - remaining underdetermined cases. +* + MAXWRK = 3*M + ( N+M )*ILAENV( 1, 'DGEBRD', ' ', M, N, + $ -1, -1 ) + MAXWRK = MAX( MAXWRK, 3*M+NRHS* + $ ILAENV( 1, 'DORMBR', 'QLT', M, NRHS, N, -1 ) ) + MAXWRK = MAX( MAXWRK, 3*M+M* + $ ILAENV( 1, 'DORMBR', 'PLN', N, NRHS, M, -1 ) ) + MAXWRK = MAX( MAXWRK, 3*M+WLALSD ) + END IF + MINWRK = MAX( 3*M+NRHS, 3*M+M, 3*M+WLALSD ) + END IF + MINWRK = MIN( MINWRK, MAXWRK ) + WORK( 1 ) = MAXWRK + IWORK( 1 ) = LIWORK + + IF( LWORK.LT.MINWRK .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGELSD', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + GO TO 10 + END IF +* +* Quick return if possible. +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + RANK = 0 + RETURN + END IF +* +* Get machine parameters. +* + EPS = DLAMCH( 'P' ) + SFMIN = DLAMCH( 'S' ) + SMLNUM = SFMIN / EPS + BIGNUM = ONE / SMLNUM + CALL DLABAD( SMLNUM, BIGNUM ) +* +* Scale A if max entry outside range [SMLNUM,BIGNUM]. +* + ANRM = DLANGE( 'M', M, N, A, LDA, WORK ) + IASCL = 0 + IF( ANRM.GT.ZERO .AND. ANRM.LT.SMLNUM ) THEN +* +* Scale matrix norm up to SMLNUM. +* + CALL DLASCL( 'G', 0, 0, ANRM, SMLNUM, M, N, A, LDA, INFO ) + IASCL = 1 + ELSE IF( ANRM.GT.BIGNUM ) THEN +* +* Scale matrix norm down to BIGNUM. +* + CALL DLASCL( 'G', 0, 0, ANRM, BIGNUM, M, N, A, LDA, INFO ) + IASCL = 2 + ELSE IF( ANRM.EQ.ZERO ) THEN +* +* Matrix all zero. Return zero solution. +* + CALL DLASET( 'F', MAX( M, N ), NRHS, ZERO, ZERO, B, LDB ) + CALL DLASET( 'F', MINMN, 1, ZERO, ZERO, S, 1 ) + RANK = 0 + GO TO 10 + END IF +* +* Scale B if max entry outside range [SMLNUM,BIGNUM]. +* + BNRM = DLANGE( 'M', M, NRHS, B, LDB, WORK ) + IBSCL = 0 + IF( BNRM.GT.ZERO .AND. BNRM.LT.SMLNUM ) THEN +* +* Scale matrix norm up to SMLNUM. +* + CALL DLASCL( 'G', 0, 0, BNRM, SMLNUM, M, NRHS, B, LDB, INFO ) + IBSCL = 1 + ELSE IF( BNRM.GT.BIGNUM ) THEN +* +* Scale matrix norm down to BIGNUM. +* + CALL DLASCL( 'G', 0, 0, BNRM, BIGNUM, M, NRHS, B, LDB, INFO ) + IBSCL = 2 + END IF +* +* If M < N make sure certain entries of B are zero. +* + IF( M.LT.N ) + $ CALL DLASET( 'F', N-M, NRHS, ZERO, ZERO, B( M+1, 1 ), LDB ) +* +* Overdetermined case. +* + IF( M.GE.N ) THEN +* +* Path 1 - overdetermined or exactly determined. +* + MM = M + IF( M.GE.MNTHR ) THEN +* +* Path 1a - overdetermined, with many more rows than columns. +* + MM = N + ITAU = 1 + NWORK = ITAU + N +* +* Compute A=Q*R. +* (Workspace: need 2*N, prefer N+N*NB) +* + CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), WORK( NWORK ), + $ LWORK-NWORK+1, INFO ) +* +* Multiply B by transpose(Q). +* (Workspace: need N+NRHS, prefer N+NRHS*NB) +* + CALL DORMQR( 'L', 'T', M, NRHS, N, A, LDA, WORK( ITAU ), B, + $ LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* +* Zero out below R. +* + IF( N.GT.1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), LDA ) + END IF + END IF +* + IE = 1 + ITAUQ = IE + N + ITAUP = ITAUQ + N + NWORK = ITAUP + N +* +* Bidiagonalize R in A. +* (Workspace: need 3*N+MM, prefer 3*N+(MM+N)*NB) +* + CALL DGEBRD( MM, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), + $ WORK( ITAUP ), WORK( NWORK ), LWORK-NWORK+1, + $ INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors of R. +* (Workspace: need 3*N+NRHS, prefer 3*N+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', MM, NRHS, N, A, LDA, WORK( ITAUQ ), + $ B, LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* +* Solve the bidiagonal least squares problem. +* + CALL DLALSD( 'U', SMLSIZ, N, NRHS, S, WORK( IE ), B, LDB, + $ RCOND, RANK, WORK( NWORK ), IWORK, INFO ) + IF( INFO.NE.0 ) THEN + GO TO 10 + END IF +* +* Multiply B by right bidiagonalizing vectors of R. +* + CALL DORMBR( 'P', 'L', 'N', N, NRHS, N, A, LDA, WORK( ITAUP ), + $ B, LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* + ELSE IF( N.GE.MNTHR .AND. LWORK.GE.4*M+M*M+ + $ MAX( M, 2*M-4, NRHS, N-3*M, WLALSD ) ) THEN +* +* Path 2a - underdetermined, with many more columns than rows +* and sufficient workspace for an efficient algorithm. +* + LDWORK = M + IF( LWORK.GE.MAX( 4*M+M*LDA+MAX( M, 2*M-4, NRHS, N-3*M ), + $ M*LDA+M+M*NRHS, 4*M+M*LDA+WLALSD ) )LDWORK = LDA + ITAU = 1 + NWORK = M + 1 +* +* Compute A=L*Q. +* (Workspace: need 2*M, prefer M+M*NB) +* + CALL DGELQF( M, N, A, LDA, WORK( ITAU ), WORK( NWORK ), + $ LWORK-NWORK+1, INFO ) + IL = NWORK +* +* Copy L to WORK(IL), zeroing out above its diagonal. +* + CALL DLACPY( 'L', M, M, A, LDA, WORK( IL ), LDWORK ) + CALL DLASET( 'U', M-1, M-1, ZERO, ZERO, WORK( IL+LDWORK ), + $ LDWORK ) + IE = IL + LDWORK*M + ITAUQ = IE + M + ITAUP = ITAUQ + M + NWORK = ITAUP + M +* +* Bidiagonalize L in WORK(IL). +* (Workspace: need M*M+5*M, prefer M*M+4*M+2*M*NB) +* + CALL DGEBRD( M, M, WORK( IL ), LDWORK, S, WORK( IE ), + $ WORK( ITAUQ ), WORK( ITAUP ), WORK( NWORK ), + $ LWORK-NWORK+1, INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors of L. +* (Workspace: need M*M+4*M+NRHS, prefer M*M+4*M+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, M, WORK( IL ), LDWORK, + $ WORK( ITAUQ ), B, LDB, WORK( NWORK ), + $ LWORK-NWORK+1, INFO ) +* +* Solve the bidiagonal least squares problem. +* + CALL DLALSD( 'U', SMLSIZ, M, NRHS, S, WORK( IE ), B, LDB, + $ RCOND, RANK, WORK( NWORK ), IWORK, INFO ) + IF( INFO.NE.0 ) THEN + GO TO 10 + END IF +* +* Multiply B by right bidiagonalizing vectors of L. +* + CALL DORMBR( 'P', 'L', 'N', M, NRHS, M, WORK( IL ), LDWORK, + $ WORK( ITAUP ), B, LDB, WORK( NWORK ), + $ LWORK-NWORK+1, INFO ) +* +* Zero out below first M rows of B. +* + CALL DLASET( 'F', N-M, NRHS, ZERO, ZERO, B( M+1, 1 ), LDB ) + NWORK = ITAU + M +* +* Multiply transpose(Q) by B. +* (Workspace: need M+NRHS, prefer M+NRHS*NB) +* + CALL DORMLQ( 'L', 'T', N, NRHS, M, A, LDA, WORK( ITAU ), B, + $ LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* + ELSE +* +* Path 2 - remaining underdetermined cases. +* + IE = 1 + ITAUQ = IE + M + ITAUP = ITAUQ + M + NWORK = ITAUP + M +* +* Bidiagonalize A. +* (Workspace: need 3*M+N, prefer 3*M+(M+N)*NB) +* + CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), + $ WORK( ITAUP ), WORK( NWORK ), LWORK-NWORK+1, + $ INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors. +* (Workspace: need 3*M+NRHS, prefer 3*M+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, N, A, LDA, WORK( ITAUQ ), + $ B, LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* +* Solve the bidiagonal least squares problem. +* + CALL DLALSD( 'L', SMLSIZ, M, NRHS, S, WORK( IE ), B, LDB, + $ RCOND, RANK, WORK( NWORK ), IWORK, INFO ) + IF( INFO.NE.0 ) THEN + GO TO 10 + END IF +* +* Multiply B by right bidiagonalizing vectors of A. +* + CALL DORMBR( 'P', 'L', 'N', N, NRHS, M, A, LDA, WORK( ITAUP ), + $ B, LDB, WORK( NWORK ), LWORK-NWORK+1, INFO ) +* + END IF +* +* Undo scaling. +* + IF( IASCL.EQ.1 ) THEN + CALL DLASCL( 'G', 0, 0, ANRM, SMLNUM, N, NRHS, B, LDB, INFO ) + CALL DLASCL( 'G', 0, 0, SMLNUM, ANRM, MINMN, 1, S, MINMN, + $ INFO ) + ELSE IF( IASCL.EQ.2 ) THEN + CALL DLASCL( 'G', 0, 0, ANRM, BIGNUM, N, NRHS, B, LDB, INFO ) + CALL DLASCL( 'G', 0, 0, BIGNUM, ANRM, MINMN, 1, S, MINMN, + $ INFO ) + END IF + IF( IBSCL.EQ.1 ) THEN + CALL DLASCL( 'G', 0, 0, SMLNUM, BNRM, N, NRHS, B, LDB, INFO ) + ELSE IF( IBSCL.EQ.2 ) THEN + CALL DLASCL( 'G', 0, 0, BIGNUM, BNRM, N, NRHS, B, LDB, INFO ) + END IF +* + 10 CONTINUE + WORK( 1 ) = MAXWRK + IWORK( 1 ) = LIWORK + RETURN +* +* End of DGELSD +* + END diff --git a/lib/linalg/dgelss.f b/lib/linalg/dgelss.f new file mode 100644 index 0000000000000000000000000000000000000000..674a7ba78400b2f19e3f2370952bae8f8f59cea8 --- /dev/null +++ b/lib/linalg/dgelss.f @@ -0,0 +1,747 @@ +*> \brief DGELSS solves overdetermined or underdetermined systems for GE matrices +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DGELSS + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DGELSS( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, +* WORK, LWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK +* DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. +* DOUBLE PRECISION A( LDA, * ), B( LDB, * ), S( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DGELSS computes the minimum norm solution to a real linear least +*> squares problem: +*> +*> Minimize 2-norm(| b - A*x |). +*> +*> using the singular value decomposition (SVD) of A. A is an M-by-N +*> matrix which may be rank-deficient. +*> +*> Several right hand side vectors b and solution vectors x can be +*> handled in a single call; they are stored as the columns of the +*> M-by-NRHS right hand side matrix B and the N-by-NRHS solution matrix +*> X. +*> +*> The effective rank of A is determined by treating as zero those +*> singular values which are less than RCOND times the largest singular +*> value. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix A. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of right hand sides, i.e., the number of columns +*> of the matrices B and X. NRHS >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> On entry, the M-by-N matrix A. +*> On exit, the first min(m,n) rows of A are overwritten with +*> its right singular vectors, stored rowwise. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,M). +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB,NRHS) +*> On entry, the M-by-NRHS right hand side matrix B. +*> On exit, B is overwritten by the N-by-NRHS solution +*> matrix X. If m >= n and RANK = n, the residual +*> sum-of-squares for the solution in the i-th column is given +*> by the sum of squares of elements n+1:m in that column. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >= max(1,max(M,N)). +*> \endverbatim +*> +*> \param[out] S +*> \verbatim +*> S is DOUBLE PRECISION array, dimension (min(M,N)) +*> The singular values of A in decreasing order. +*> The condition number of A in the 2-norm = S(1)/S(min(m,n)). +*> \endverbatim +*> +*> \param[in] RCOND +*> \verbatim +*> RCOND is DOUBLE PRECISION +*> RCOND is used to determine the effective rank of A. +*> Singular values S(i) <= RCOND*S(1) are treated as zero. +*> If RCOND < 0, machine precision is used instead. +*> \endverbatim +*> +*> \param[out] RANK +*> \verbatim +*> RANK is INTEGER +*> The effective rank of A, i.e., the number of singular values +*> which are greater than RCOND*S(1). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. LWORK >= 1, and also: +*> LWORK >= 3*min(M,N) + max( 2*min(M,N), max(M,N), NRHS ) +*> For good performance, LWORK should generally be larger. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal size of the WORK array, returns +*> this value as the first entry of the WORK array, and no error +*> message related to LWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: the algorithm for computing the SVD failed to converge; +*> if INFO = i, i off-diagonal elements of an intermediate +*> bidiagonal form did not converge to zero. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup doubleGEsolve +* +* ===================================================================== + SUBROUTINE DGELSS( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, + $ WORK, LWORK, INFO ) +* +* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK + DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ), B( LDB, * ), S( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL LQUERY + INTEGER BDSPAC, BL, CHUNK, I, IASCL, IBSCL, IE, IL, + $ ITAU, ITAUP, ITAUQ, IWORK, LDWORK, MAXMN, + $ MAXWRK, MINMN, MINWRK, MM, MNTHR + INTEGER LWORK_DGEQRF, LWORK_DORMQR, LWORK_DGEBRD, + $ LWORK_DORMBR, LWORK_DORGBR, LWORK_DORMLQ, + $ LWORK_DGELQF + DOUBLE PRECISION ANRM, BIGNUM, BNRM, EPS, SFMIN, SMLNUM, THR +* .. +* .. Local Arrays .. + DOUBLE PRECISION DUM( 1 ) +* .. +* .. External Subroutines .. + EXTERNAL DBDSQR, DCOPY, DGEBRD, DGELQF, DGEMM, DGEMV, + $ DGEQRF, DLABAD, DLACPY, DLASCL, DLASET, DORGBR, + $ DORMBR, DORMLQ, DORMQR, DRSCL, XERBLA +* .. +* .. External Functions .. + INTEGER ILAENV + DOUBLE PRECISION DLAMCH, DLANGE + EXTERNAL ILAENV, DLAMCH, DLANGE +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + MINMN = MIN( M, N ) + MAXMN = MAX( M, N ) + LQUERY = ( LWORK.EQ.-1 ) + IF( M.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( NRHS.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, M ) ) THEN + INFO = -5 + ELSE IF( LDB.LT.MAX( 1, MAXMN ) ) THEN + INFO = -7 + END IF +* +* Compute workspace +* (Note: Comments in the code beginning "Workspace:" describe the +* minimal amount of workspace needed at that point in the code, +* as well as the preferred amount for good performance. +* NB refers to the optimal block size for the immediately +* following subroutine, as returned by ILAENV.) +* + IF( INFO.EQ.0 ) THEN + MINWRK = 1 + MAXWRK = 1 + IF( MINMN.GT.0 ) THEN + MM = M + MNTHR = ILAENV( 6, 'DGELSS', ' ', M, N, NRHS, -1 ) + IF( M.GE.N .AND. M.GE.MNTHR ) THEN +* +* Path 1a - overdetermined, with many more rows than +* columns +* +* Compute space needed for DGEQRF + CALL DGEQRF( M, N, A, LDA, DUM(1), DUM(1), -1, INFO ) + LWORK_DGEQRF=DUM(1) +* Compute space needed for DORMQR + CALL DORMQR( 'L', 'T', M, NRHS, N, A, LDA, DUM(1), B, + $ LDB, DUM(1), -1, INFO ) + LWORK_DORMQR=DUM(1) + MM = N + MAXWRK = MAX( MAXWRK, N + LWORK_DGEQRF ) + MAXWRK = MAX( MAXWRK, N + LWORK_DORMQR ) + END IF + IF( M.GE.N ) THEN +* +* Path 1 - overdetermined or exactly determined +* +* Compute workspace needed for DBDSQR +* + BDSPAC = MAX( 1, 5*N ) +* Compute space needed for DGEBRD + CALL DGEBRD( MM, N, A, LDA, S, DUM(1), DUM(1), + $ DUM(1), DUM(1), -1, INFO ) + LWORK_DGEBRD=DUM(1) +* Compute space needed for DORMBR + CALL DORMBR( 'Q', 'L', 'T', MM, NRHS, N, A, LDA, DUM(1), + $ B, LDB, DUM(1), -1, INFO ) + LWORK_DORMBR=DUM(1) +* Compute space needed for DORGBR + CALL DORGBR( 'P', N, N, N, A, LDA, DUM(1), + $ DUM(1), -1, INFO ) + LWORK_DORGBR=DUM(1) +* Compute total workspace needed + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DGEBRD ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORMBR ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORGBR ) + MAXWRK = MAX( MAXWRK, BDSPAC ) + MAXWRK = MAX( MAXWRK, N*NRHS ) + MINWRK = MAX( 3*N + MM, 3*N + NRHS, BDSPAC ) + MAXWRK = MAX( MINWRK, MAXWRK ) + END IF + IF( N.GT.M ) THEN +* +* Compute workspace needed for DBDSQR +* + BDSPAC = MAX( 1, 5*M ) + MINWRK = MAX( 3*M+NRHS, 3*M+N, BDSPAC ) + IF( N.GE.MNTHR ) THEN +* +* Path 2a - underdetermined, with many more columns +* than rows +* +* Compute space needed for DGELQF + CALL DGELQF( M, N, A, LDA, DUM(1), DUM(1), + $ -1, INFO ) + LWORK_DGELQF=DUM(1) +* Compute space needed for DGEBRD + CALL DGEBRD( M, M, A, LDA, S, DUM(1), DUM(1), + $ DUM(1), DUM(1), -1, INFO ) + LWORK_DGEBRD=DUM(1) +* Compute space needed for DORMBR + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, N, A, LDA, + $ DUM(1), B, LDB, DUM(1), -1, INFO ) + LWORK_DORMBR=DUM(1) +* Compute space needed for DORGBR + CALL DORGBR( 'P', M, M, M, A, LDA, DUM(1), + $ DUM(1), -1, INFO ) + LWORK_DORGBR=DUM(1) +* Compute space needed for DORMLQ + CALL DORMLQ( 'L', 'T', N, NRHS, M, A, LDA, DUM(1), + $ B, LDB, DUM(1), -1, INFO ) + LWORK_DORMLQ=DUM(1) +* Compute total workspace needed + MAXWRK = M + LWORK_DGELQF + MAXWRK = MAX( MAXWRK, M*M + 4*M + LWORK_DGEBRD ) + MAXWRK = MAX( MAXWRK, M*M + 4*M + LWORK_DORMBR ) + MAXWRK = MAX( MAXWRK, M*M + 4*M + LWORK_DORGBR ) + MAXWRK = MAX( MAXWRK, M*M + M + BDSPAC ) + IF( NRHS.GT.1 ) THEN + MAXWRK = MAX( MAXWRK, M*M + M + M*NRHS ) + ELSE + MAXWRK = MAX( MAXWRK, M*M + 2*M ) + END IF + MAXWRK = MAX( MAXWRK, M + LWORK_DORMLQ ) + ELSE +* +* Path 2 - underdetermined +* +* Compute space needed for DGEBRD + CALL DGEBRD( M, N, A, LDA, S, DUM(1), DUM(1), + $ DUM(1), DUM(1), -1, INFO ) + LWORK_DGEBRD=DUM(1) +* Compute space needed for DORMBR + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, M, A, LDA, + $ DUM(1), B, LDB, DUM(1), -1, INFO ) + LWORK_DORMBR=DUM(1) +* Compute space needed for DORGBR + CALL DORGBR( 'P', M, N, M, A, LDA, DUM(1), + $ DUM(1), -1, INFO ) + LWORK_DORGBR=DUM(1) + MAXWRK = 3*M + LWORK_DGEBRD + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORMBR ) + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR ) + MAXWRK = MAX( MAXWRK, BDSPAC ) + MAXWRK = MAX( MAXWRK, N*NRHS ) + END IF + END IF + MAXWRK = MAX( MINWRK, MAXWRK ) + END IF + WORK( 1 ) = MAXWRK +* + IF( LWORK.LT.MINWRK .AND. .NOT.LQUERY ) + $ INFO = -12 + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGELSS', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + RANK = 0 + RETURN + END IF +* +* Get machine parameters +* + EPS = DLAMCH( 'P' ) + SFMIN = DLAMCH( 'S' ) + SMLNUM = SFMIN / EPS + BIGNUM = ONE / SMLNUM + CALL DLABAD( SMLNUM, BIGNUM ) +* +* Scale A if max element outside range [SMLNUM,BIGNUM] +* + ANRM = DLANGE( 'M', M, N, A, LDA, WORK ) + IASCL = 0 + IF( ANRM.GT.ZERO .AND. ANRM.LT.SMLNUM ) THEN +* +* Scale matrix norm up to SMLNUM +* + CALL DLASCL( 'G', 0, 0, ANRM, SMLNUM, M, N, A, LDA, INFO ) + IASCL = 1 + ELSE IF( ANRM.GT.BIGNUM ) THEN +* +* Scale matrix norm down to BIGNUM +* + CALL DLASCL( 'G', 0, 0, ANRM, BIGNUM, M, N, A, LDA, INFO ) + IASCL = 2 + ELSE IF( ANRM.EQ.ZERO ) THEN +* +* Matrix all zero. Return zero solution. +* + CALL DLASET( 'F', MAX( M, N ), NRHS, ZERO, ZERO, B, LDB ) + CALL DLASET( 'F', MINMN, 1, ZERO, ZERO, S, MINMN ) + RANK = 0 + GO TO 70 + END IF +* +* Scale B if max element outside range [SMLNUM,BIGNUM] +* + BNRM = DLANGE( 'M', M, NRHS, B, LDB, WORK ) + IBSCL = 0 + IF( BNRM.GT.ZERO .AND. BNRM.LT.SMLNUM ) THEN +* +* Scale matrix norm up to SMLNUM +* + CALL DLASCL( 'G', 0, 0, BNRM, SMLNUM, M, NRHS, B, LDB, INFO ) + IBSCL = 1 + ELSE IF( BNRM.GT.BIGNUM ) THEN +* +* Scale matrix norm down to BIGNUM +* + CALL DLASCL( 'G', 0, 0, BNRM, BIGNUM, M, NRHS, B, LDB, INFO ) + IBSCL = 2 + END IF +* +* Overdetermined case +* + IF( M.GE.N ) THEN +* +* Path 1 - overdetermined or exactly determined +* + MM = M + IF( M.GE.MNTHR ) THEN +* +* Path 1a - overdetermined, with many more rows than columns +* + MM = N + ITAU = 1 + IWORK = ITAU + N +* +* Compute A=Q*R +* (Workspace: need 2*N, prefer N+N*NB) +* + CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), WORK( IWORK ), + $ LWORK-IWORK+1, INFO ) +* +* Multiply B by transpose(Q) +* (Workspace: need N+NRHS, prefer N+NRHS*NB) +* + CALL DORMQR( 'L', 'T', M, NRHS, N, A, LDA, WORK( ITAU ), B, + $ LDB, WORK( IWORK ), LWORK-IWORK+1, INFO ) +* +* Zero out below R +* + IF( N.GT.1 ) + $ CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), LDA ) + END IF +* + IE = 1 + ITAUQ = IE + N + ITAUP = ITAUQ + N + IWORK = ITAUP + N +* +* Bidiagonalize R in A +* (Workspace: need 3*N+MM, prefer 3*N+(MM+N)*NB) +* + CALL DGEBRD( MM, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), + $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, + $ INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors of R +* (Workspace: need 3*N+NRHS, prefer 3*N+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', MM, NRHS, N, A, LDA, WORK( ITAUQ ), + $ B, LDB, WORK( IWORK ), LWORK-IWORK+1, INFO ) +* +* Generate right bidiagonalizing vectors of R in A +* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* + CALL DORGBR( 'P', N, N, N, A, LDA, WORK( ITAUP ), + $ WORK( IWORK ), LWORK-IWORK+1, INFO ) + IWORK = IE + N +* +* Perform bidiagonal QR iteration +* multiply B by transpose of left singular vectors +* compute right singular vectors in A +* (Workspace: need BDSPAC) +* + CALL DBDSQR( 'U', N, N, 0, NRHS, S, WORK( IE ), A, LDA, DUM, + $ 1, B, LDB, WORK( IWORK ), INFO ) + IF( INFO.NE.0 ) + $ GO TO 70 +* +* Multiply B by reciprocals of singular values +* + THR = MAX( RCOND*S( 1 ), SFMIN ) + IF( RCOND.LT.ZERO ) + $ THR = MAX( EPS*S( 1 ), SFMIN ) + RANK = 0 + DO 10 I = 1, N + IF( S( I ).GT.THR ) THEN + CALL DRSCL( NRHS, S( I ), B( I, 1 ), LDB ) + RANK = RANK + 1 + ELSE + CALL DLASET( 'F', 1, NRHS, ZERO, ZERO, B( I, 1 ), LDB ) + END IF + 10 CONTINUE +* +* Multiply B by right singular vectors +* (Workspace: need N, prefer N*NRHS) +* + IF( LWORK.GE.LDB*NRHS .AND. NRHS.GT.1 ) THEN + CALL DGEMM( 'T', 'N', N, NRHS, N, ONE, A, LDA, B, LDB, ZERO, + $ WORK, LDB ) + CALL DLACPY( 'G', N, NRHS, WORK, LDB, B, LDB ) + ELSE IF( NRHS.GT.1 ) THEN + CHUNK = LWORK / N + DO 20 I = 1, NRHS, CHUNK + BL = MIN( NRHS-I+1, CHUNK ) + CALL DGEMM( 'T', 'N', N, BL, N, ONE, A, LDA, B( 1, I ), + $ LDB, ZERO, WORK, N ) + CALL DLACPY( 'G', N, BL, WORK, N, B( 1, I ), LDB ) + 20 CONTINUE + ELSE + CALL DGEMV( 'T', N, N, ONE, A, LDA, B, 1, ZERO, WORK, 1 ) + CALL DCOPY( N, WORK, 1, B, 1 ) + END IF +* + ELSE IF( N.GE.MNTHR .AND. LWORK.GE.4*M+M*M+ + $ MAX( M, 2*M-4, NRHS, N-3*M ) ) THEN +* +* Path 2a - underdetermined, with many more columns than rows +* and sufficient workspace for an efficient algorithm +* + LDWORK = M + IF( LWORK.GE.MAX( 4*M+M*LDA+MAX( M, 2*M-4, NRHS, N-3*M ), + $ M*LDA+M+M*NRHS ) )LDWORK = LDA + ITAU = 1 + IWORK = M + 1 +* +* Compute A=L*Q +* (Workspace: need 2*M, prefer M+M*NB) +* + CALL DGELQF( M, N, A, LDA, WORK( ITAU ), WORK( IWORK ), + $ LWORK-IWORK+1, INFO ) + IL = IWORK +* +* Copy L to WORK(IL), zeroing out above it +* + CALL DLACPY( 'L', M, M, A, LDA, WORK( IL ), LDWORK ) + CALL DLASET( 'U', M-1, M-1, ZERO, ZERO, WORK( IL+LDWORK ), + $ LDWORK ) + IE = IL + LDWORK*M + ITAUQ = IE + M + ITAUP = ITAUQ + M + IWORK = ITAUP + M +* +* Bidiagonalize L in WORK(IL) +* (Workspace: need M*M+5*M, prefer M*M+4*M+2*M*NB) +* + CALL DGEBRD( M, M, WORK( IL ), LDWORK, S, WORK( IE ), + $ WORK( ITAUQ ), WORK( ITAUP ), WORK( IWORK ), + $ LWORK-IWORK+1, INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors of L +* (Workspace: need M*M+4*M+NRHS, prefer M*M+4*M+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, M, WORK( IL ), LDWORK, + $ WORK( ITAUQ ), B, LDB, WORK( IWORK ), + $ LWORK-IWORK+1, INFO ) +* +* Generate right bidiagonalizing vectors of R in WORK(IL) +* (Workspace: need M*M+5*M-1, prefer M*M+4*M+(M-1)*NB) +* + CALL DORGBR( 'P', M, M, M, WORK( IL ), LDWORK, WORK( ITAUP ), + $ WORK( IWORK ), LWORK-IWORK+1, INFO ) + IWORK = IE + M +* +* Perform bidiagonal QR iteration, +* computing right singular vectors of L in WORK(IL) and +* multiplying B by transpose of left singular vectors +* (Workspace: need M*M+M+BDSPAC) +* + CALL DBDSQR( 'U', M, M, 0, NRHS, S, WORK( IE ), WORK( IL ), + $ LDWORK, A, LDA, B, LDB, WORK( IWORK ), INFO ) + IF( INFO.NE.0 ) + $ GO TO 70 +* +* Multiply B by reciprocals of singular values +* + THR = MAX( RCOND*S( 1 ), SFMIN ) + IF( RCOND.LT.ZERO ) + $ THR = MAX( EPS*S( 1 ), SFMIN ) + RANK = 0 + DO 30 I = 1, M + IF( S( I ).GT.THR ) THEN + CALL DRSCL( NRHS, S( I ), B( I, 1 ), LDB ) + RANK = RANK + 1 + ELSE + CALL DLASET( 'F', 1, NRHS, ZERO, ZERO, B( I, 1 ), LDB ) + END IF + 30 CONTINUE + IWORK = IE +* +* Multiply B by right singular vectors of L in WORK(IL) +* (Workspace: need M*M+2*M, prefer M*M+M+M*NRHS) +* + IF( LWORK.GE.LDB*NRHS+IWORK-1 .AND. NRHS.GT.1 ) THEN + CALL DGEMM( 'T', 'N', M, NRHS, M, ONE, WORK( IL ), LDWORK, + $ B, LDB, ZERO, WORK( IWORK ), LDB ) + CALL DLACPY( 'G', M, NRHS, WORK( IWORK ), LDB, B, LDB ) + ELSE IF( NRHS.GT.1 ) THEN + CHUNK = ( LWORK-IWORK+1 ) / M + DO 40 I = 1, NRHS, CHUNK + BL = MIN( NRHS-I+1, CHUNK ) + CALL DGEMM( 'T', 'N', M, BL, M, ONE, WORK( IL ), LDWORK, + $ B( 1, I ), LDB, ZERO, WORK( IWORK ), M ) + CALL DLACPY( 'G', M, BL, WORK( IWORK ), M, B( 1, I ), + $ LDB ) + 40 CONTINUE + ELSE + CALL DGEMV( 'T', M, M, ONE, WORK( IL ), LDWORK, B( 1, 1 ), + $ 1, ZERO, WORK( IWORK ), 1 ) + CALL DCOPY( M, WORK( IWORK ), 1, B( 1, 1 ), 1 ) + END IF +* +* Zero out below first M rows of B +* + CALL DLASET( 'F', N-M, NRHS, ZERO, ZERO, B( M+1, 1 ), LDB ) + IWORK = ITAU + M +* +* Multiply transpose(Q) by B +* (Workspace: need M+NRHS, prefer M+NRHS*NB) +* + CALL DORMLQ( 'L', 'T', N, NRHS, M, A, LDA, WORK( ITAU ), B, + $ LDB, WORK( IWORK ), LWORK-IWORK+1, INFO ) +* + ELSE +* +* Path 2 - remaining underdetermined cases +* + IE = 1 + ITAUQ = IE + M + ITAUP = ITAUQ + M + IWORK = ITAUP + M +* +* Bidiagonalize A +* (Workspace: need 3*M+N, prefer 3*M+(M+N)*NB) +* + CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), + $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, + $ INFO ) +* +* Multiply B by transpose of left bidiagonalizing vectors +* (Workspace: need 3*M+NRHS, prefer 3*M+NRHS*NB) +* + CALL DORMBR( 'Q', 'L', 'T', M, NRHS, N, A, LDA, WORK( ITAUQ ), + $ B, LDB, WORK( IWORK ), LWORK-IWORK+1, INFO ) +* +* Generate right bidiagonalizing vectors in A +* (Workspace: need 4*M, prefer 3*M+M*NB) +* + CALL DORGBR( 'P', M, N, M, A, LDA, WORK( ITAUP ), + $ WORK( IWORK ), LWORK-IWORK+1, INFO ) + IWORK = IE + M +* +* Perform bidiagonal QR iteration, +* computing right singular vectors of A in A and +* multiplying B by transpose of left singular vectors +* (Workspace: need BDSPAC) +* + CALL DBDSQR( 'L', M, N, 0, NRHS, S, WORK( IE ), A, LDA, DUM, + $ 1, B, LDB, WORK( IWORK ), INFO ) + IF( INFO.NE.0 ) + $ GO TO 70 +* +* Multiply B by reciprocals of singular values +* + THR = MAX( RCOND*S( 1 ), SFMIN ) + IF( RCOND.LT.ZERO ) + $ THR = MAX( EPS*S( 1 ), SFMIN ) + RANK = 0 + DO 50 I = 1, M + IF( S( I ).GT.THR ) THEN + CALL DRSCL( NRHS, S( I ), B( I, 1 ), LDB ) + RANK = RANK + 1 + ELSE + CALL DLASET( 'F', 1, NRHS, ZERO, ZERO, B( I, 1 ), LDB ) + END IF + 50 CONTINUE +* +* Multiply B by right singular vectors of A +* (Workspace: need N, prefer N*NRHS) +* + IF( LWORK.GE.LDB*NRHS .AND. NRHS.GT.1 ) THEN + CALL DGEMM( 'T', 'N', N, NRHS, M, ONE, A, LDA, B, LDB, ZERO, + $ WORK, LDB ) + CALL DLACPY( 'F', N, NRHS, WORK, LDB, B, LDB ) + ELSE IF( NRHS.GT.1 ) THEN + CHUNK = LWORK / N + DO 60 I = 1, NRHS, CHUNK + BL = MIN( NRHS-I+1, CHUNK ) + CALL DGEMM( 'T', 'N', N, BL, M, ONE, A, LDA, B( 1, I ), + $ LDB, ZERO, WORK, N ) + CALL DLACPY( 'F', N, BL, WORK, N, B( 1, I ), LDB ) + 60 CONTINUE + ELSE + CALL DGEMV( 'T', M, N, ONE, A, LDA, B, 1, ZERO, WORK, 1 ) + CALL DCOPY( N, WORK, 1, B, 1 ) + END IF + END IF +* +* Undo scaling +* + IF( IASCL.EQ.1 ) THEN + CALL DLASCL( 'G', 0, 0, ANRM, SMLNUM, N, NRHS, B, LDB, INFO ) + CALL DLASCL( 'G', 0, 0, SMLNUM, ANRM, MINMN, 1, S, MINMN, + $ INFO ) + ELSE IF( IASCL.EQ.2 ) THEN + CALL DLASCL( 'G', 0, 0, ANRM, BIGNUM, N, NRHS, B, LDB, INFO ) + CALL DLASCL( 'G', 0, 0, BIGNUM, ANRM, MINMN, 1, S, MINMN, + $ INFO ) + END IF + IF( IBSCL.EQ.1 ) THEN + CALL DLASCL( 'G', 0, 0, SMLNUM, BNRM, N, NRHS, B, LDB, INFO ) + ELSE IF( IBSCL.EQ.2 ) THEN + CALL DLASCL( 'G', 0, 0, BIGNUM, BNRM, N, NRHS, B, LDB, INFO ) + END IF +* + 70 CONTINUE + WORK( 1 ) = MAXWRK + RETURN +* +* End of DGELSS +* + END diff --git a/lib/linalg/dgemm.f b/lib/linalg/dgemm.f index 45d001b7ab935a7938324794fd91ed8bd7312432..3a60ca4e730b55d6361a963dc71f72bac9ce18b6 100644 --- a/lib/linalg/dgemm.f +++ b/lib/linalg/dgemm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER K,LDA,LDB,LDC,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),B(LDB,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -97,7 +97,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, ka ), where ka is +*> A is DOUBLE PRECISION array, dimension ( LDA, ka ), where ka is *> k when TRANSA = 'N' or 'n', and is m otherwise. *> Before entry with TRANSA = 'N' or 'n', the leading m by k *> part of the array A must contain the matrix A, otherwise @@ -116,7 +116,7 @@ *> *> \param[in] B *> \verbatim -*> B is DOUBLE PRECISION array of DIMENSION ( LDB, kb ), where kb is +*> B is DOUBLE PRECISION array, dimension ( LDB, kb ), where kb is *> n when TRANSB = 'N' or 'n', and is k otherwise. *> Before entry with TRANSB = 'N' or 'n', the leading k by n *> part of the array B must contain the matrix B, otherwise @@ -142,7 +142,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is DOUBLE PRECISION array of DIMENSION ( LDC, n ). +*> C is DOUBLE PRECISION array, dimension ( LDC, N ) *> Before entry, the leading m by n part of the array C must *> contain the matrix C, except when beta is zero, in which *> case C need not be set on entry. @@ -161,12 +161,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -187,10 +187,10 @@ * ===================================================================== SUBROUTINE DGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -311,12 +311,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE @@ -353,12 +351,10 @@ 140 CONTINUE END IF DO 160 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 150 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 150 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 150 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 150 CONTINUE 160 CONTINUE 170 CONTINUE ELSE diff --git a/lib/linalg/dgemv.f b/lib/linalg/dgemv.f index 675257fac7e8f7438d5aa304b083ea6e765ceced..08e395b1cd2f13ef4291d0161e428475a59d6ace 100644 --- a/lib/linalg/dgemv.f +++ b/lib/linalg/dgemv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER INCX,INCY,LDA,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -71,7 +71,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry, the leading m by n part of the array A must *> contain the matrix of coefficients. *> \endverbatim @@ -86,7 +86,7 @@ *> *> \param[in] X *> \verbatim -*> X is DOUBLE PRECISION array of DIMENSION at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ) when TRANS = 'N' or 'n' *> and at least *> ( 1 + ( m - 1 )*abs( INCX ) ) otherwise. @@ -110,7 +110,7 @@ *> *> \param[in,out] Y *> \verbatim -*> Y is DOUBLE PRECISION array of DIMENSION at least +*> Y is DOUBLE PRECISION array, dimension at least *> ( 1 + ( m - 1 )*abs( INCY ) ) when TRANS = 'N' or 'n' *> and at least *> ( 1 + ( n - 1 )*abs( INCY ) ) otherwise. @@ -129,12 +129,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level2 * @@ -156,10 +156,10 @@ * ===================================================================== SUBROUTINE DGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -278,24 +278,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF diff --git a/lib/linalg/dgeqr2.f b/lib/linalg/dgeqr2.f index 8e63db886668c2dfd73fef5938c5b6a251a38117..c1e91e9bdeb3ce1807d8c1b5d25672b09b4c94b3 100644 --- a/lib/linalg/dgeqr2.f +++ b/lib/linalg/dgeqr2.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGEQR2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGEQR2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGEQR2( M, N, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -91,12 +91,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleGEcomputational * @@ -121,10 +121,10 @@ * ===================================================================== SUBROUTINE DGEQR2( M, N, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgeqrf.f b/lib/linalg/dgeqrf.f index 299025758173b562e8e4a96fce309f024a5cf87e..83d7d8dd713d469708945721db395e11c916bc72 100644 --- a/lib/linalg/dgeqrf.f +++ b/lib/linalg/dgeqrf.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGEQRF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGEQRF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGEQRF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, LWORK, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -106,12 +106,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * @@ -136,10 +136,10 @@ * ===================================================================== SUBROUTINE DGEQRF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N diff --git a/lib/linalg/dger.f b/lib/linalg/dger.f index a042483703bb5a4c7d13a325e088621da59ae91a..bdc8ef4349d740e0d39a8c2aa2942165c37e9980 100644 --- a/lib/linalg/dger.f +++ b/lib/linalg/dger.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DGER(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA * INTEGER INCX,INCY,LDA,M,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -57,7 +57,7 @@ *> *> \param[in] X *> \verbatim -*> X is DOUBLE PRECISION array of dimension at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( m - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the m *> element vector x. @@ -72,7 +72,7 @@ *> *> \param[in] Y *> \verbatim -*> Y is DOUBLE PRECISION array of dimension at least +*> Y is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. @@ -87,7 +87,7 @@ *> *> \param[in,out] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry, the leading m by n part of the array A must *> contain the matrix of coefficients. On exit, A is *> overwritten by the updated matrix. @@ -104,12 +104,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level2 * @@ -130,10 +130,10 @@ * ===================================================================== SUBROUTINE DGER(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA diff --git a/lib/linalg/dgesv.f b/lib/linalg/dgesv.f index 8d47f839dce221867a940cdad64ec390f789c755..23999e167f4681c72ccd8f8227ef79dab41f52be 100644 --- a/lib/linalg/dgesv.f +++ b/lib/linalg/dgesv.f @@ -2,16 +2,16 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGESV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGESV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] *> \endhtmlonly * @@ -19,7 +19,7 @@ * =========== * * SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, LDB, N, NRHS * .. @@ -27,7 +27,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ), B( LDB, * ) * .. -* +* * *> \par Purpose: * ============= @@ -110,22 +110,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEsolve * * ===================================================================== SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO ) * -* -- LAPACK driver routine (version 3.4.0) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LDB, N, NRHS diff --git a/lib/linalg/dgesvd.f b/lib/linalg/dgesvd.f index 898570b66932e7dcfe0b6fc5f7b58259fb54dd33..ddf0bd5c2d92a79c0db93fb59a43ba53455e9fbf 100644 --- a/lib/linalg/dgesvd.f +++ b/lib/linalg/dgesvd.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGESVD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGESVD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGESVD( JOBU, JOBVT, M, N, A, LDA, S, U, LDU, VT, LDVT, * WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBU, JOBVT * INTEGER INFO, LDA, LDU, LDVT, LWORK, M, N @@ -29,7 +29,7 @@ * DOUBLE PRECISION A( LDA, * ), S( * ), U( LDU, * ), * $ VT( LDVT, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -173,9 +173,9 @@ *> LWORK is INTEGER *> The dimension of the array WORK. *> LWORK >= MAX(1,5*MIN(M,N)) for the paths (see comments inside code): -*> - PATH 1 (M much larger than N, JOBU='N') +*> - PATH 1 (M much larger than N, JOBU='N') *> - PATH 1t (N much larger than M, JOBVT='N') -*> LWORK >= MAX(1,3*MIN(M,N)+MAX(M,N),5*MIN(M,N)) for the other paths +*> LWORK >= MAX(1,3*MIN(M,N) + MAX(M,N),5*MIN(M,N)) for the other paths *> For good performance, LWORK should generally be larger. *> *> If LWORK = -1, then a workspace query is assumed; the routine @@ -198,10 +198,10 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * *> \date April 2012 * @@ -211,7 +211,7 @@ SUBROUTINE DGESVD( JOBU, JOBVT, M, N, A, LDA, S, U, LDU, $ VT, LDVT, WORK, LWORK, INFO ) * -* -- LAPACK driver routine (version 3.4.1) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- * April 2012 @@ -314,24 +314,24 @@ BDSPAC = 5*N * Compute space needed for DGEQRF CALL DGEQRF( M, N, A, LDA, DUM(1), DUM(1), -1, IERR ) - LWORK_DGEQRF=DUM(1) + LWORK_DGEQRF = INT( DUM(1) ) * Compute space needed for DORGQR CALL DORGQR( M, N, N, A, LDA, DUM(1), DUM(1), -1, IERR ) - LWORK_DORGQR_N=DUM(1) + LWORK_DORGQR_N = INT( DUM(1) ) CALL DORGQR( M, M, N, A, LDA, DUM(1), DUM(1), -1, IERR ) - LWORK_DORGQR_M=DUM(1) + LWORK_DORGQR_M = INT( DUM(1) ) * Compute space needed for DGEBRD CALL DGEBRD( N, N, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, IERR ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) * Compute space needed for DORGBR P CALL DORGBR( 'P', N, N, N, A, LDA, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_P=DUM(1) + LWORK_DORGBR_P = INT( DUM(1) ) * Compute space needed for DORGBR Q CALL DORGBR( 'Q', N, N, N, A, LDA, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_Q=DUM(1) + LWORK_DORGBR_Q = INT( DUM(1) ) * IF( M.GE.MNTHR ) THEN IF( WNTUN ) THEN @@ -339,9 +339,9 @@ * Path 1 (M much larger than N, JOBU='N') * MAXWRK = N + LWORK_DGEQRF - MAXWRK = MAX( MAXWRK, 3*N+LWORK_DGEBRD ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DGEBRD ) IF( WNTVO .OR. WNTVAS ) - $ MAXWRK = MAX( MAXWRK, 3*N+LWORK_DORGBR_P ) + $ MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORGBR_P ) MAXWRK = MAX( MAXWRK, BDSPAC ) MINWRK = MAX( 4*N, BDSPAC ) ELSE IF( WNTUO .AND. WNTVN ) THEN @@ -349,97 +349,97 @@ * Path 2 (M much larger than N, JOBU='O', JOBVT='N') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_N ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_N ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) - MAXWRK = MAX( N*N+WRKBL, N*N+M*N+N ) - MINWRK = MAX( 3*N+M, BDSPAC ) + MAXWRK = MAX( N*N + WRKBL, N*N + M*N + N ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUO .AND. WNTVAS ) THEN * * Path 3 (M much larger than N, JOBU='O', JOBVT='S' or * 'A') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_N ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_N ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) - MAXWRK = MAX( N*N+WRKBL, N*N+M*N+N ) - MINWRK = MAX( 3*N+M, BDSPAC ) + MAXWRK = MAX( N*N + WRKBL, N*N + M*N + N ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUS .AND. WNTVN ) THEN * * Path 4 (M much larger than N, JOBU='S', JOBVT='N') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_N ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_N ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUS .AND. WNTVO ) THEN * * Path 5 (M much larger than N, JOBU='S', JOBVT='O') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_N ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_N ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = 2*N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUS .AND. WNTVAS ) THEN * * Path 6 (M much larger than N, JOBU='S', JOBVT='S' or * 'A') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_N ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_N ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUA .AND. WNTVN ) THEN * * Path 7 (M much larger than N, JOBU='A', JOBVT='N') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_M ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_M ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUA .AND. WNTVO ) THEN * * Path 8 (M much larger than N, JOBU='A', JOBVT='O') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_M ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_M ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = 2*N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) ELSE IF( WNTUA .AND. WNTVAS ) THEN * * Path 9 (M much larger than N, JOBU='A', JOBVT='S' or * 'A') * WRKBL = N + LWORK_DGEQRF - WRKBL = MAX( WRKBL, N+LWORK_DORGQR_M ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_Q ) - WRKBL = MAX( WRKBL, 3*N+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, N + LWORK_DORGQR_M ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, 3*N + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = N*N + WRKBL - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) END IF ELSE * @@ -447,25 +447,25 @@ * CALL DGEBRD( M, N, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, IERR ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) MAXWRK = 3*N + LWORK_DGEBRD IF( WNTUS .OR. WNTUO ) THEN CALL DORGBR( 'Q', M, N, N, A, LDA, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_Q=DUM(1) - MAXWRK = MAX( MAXWRK, 3*N+LWORK_DORGBR_Q ) + LWORK_DORGBR_Q = INT( DUM(1) ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORGBR_Q ) END IF IF( WNTUA ) THEN CALL DORGBR( 'Q', M, M, N, A, LDA, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_Q=DUM(1) - MAXWRK = MAX( MAXWRK, 3*N+LWORK_DORGBR_Q ) + LWORK_DORGBR_Q = INT( DUM(1) ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORGBR_Q ) END IF IF( .NOT.WNTVN ) THEN - MAXWRK = MAX( MAXWRK, 3*N+LWORK_DORGBR_P ) + MAXWRK = MAX( MAXWRK, 3*N + LWORK_DORGBR_P ) END IF MAXWRK = MAX( MAXWRK, BDSPAC ) - MINWRK = MAX( 3*N+M, BDSPAC ) + MINWRK = MAX( 3*N + M, BDSPAC ) END IF ELSE IF( MINMN.GT.0 ) THEN * @@ -475,33 +475,33 @@ BDSPAC = 5*M * Compute space needed for DGELQF CALL DGELQF( M, N, A, LDA, DUM(1), DUM(1), -1, IERR ) - LWORK_DGELQF=DUM(1) + LWORK_DGELQF = INT( DUM(1) ) * Compute space needed for DORGLQ CALL DORGLQ( N, N, M, DUM(1), N, DUM(1), DUM(1), -1, IERR ) - LWORK_DORGLQ_N=DUM(1) + LWORK_DORGLQ_N = INT( DUM(1) ) CALL DORGLQ( M, N, M, A, LDA, DUM(1), DUM(1), -1, IERR ) - LWORK_DORGLQ_M=DUM(1) + LWORK_DORGLQ_M = INT( DUM(1) ) * Compute space needed for DGEBRD CALL DGEBRD( M, M, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, IERR ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) * Compute space needed for DORGBR P CALL DORGBR( 'P', M, M, M, A, N, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_P=DUM(1) + LWORK_DORGBR_P = INT( DUM(1) ) * Compute space needed for DORGBR Q CALL DORGBR( 'Q', M, M, M, A, N, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_Q=DUM(1) + LWORK_DORGBR_Q = INT( DUM(1) ) IF( N.GE.MNTHR ) THEN IF( WNTVN ) THEN * * Path 1t(N much larger than M, JOBVT='N') * MAXWRK = M + LWORK_DGELQF - MAXWRK = MAX( MAXWRK, 3*M+LWORK_DGEBRD ) + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DGEBRD ) IF( WNTUO .OR. WNTUAS ) - $ MAXWRK = MAX( MAXWRK, 3*M+LWORK_DORGBR_Q ) + $ MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR_Q ) MAXWRK = MAX( MAXWRK, BDSPAC ) MINWRK = MAX( 4*M, BDSPAC ) ELSE IF( WNTVO .AND. WNTUN ) THEN @@ -509,97 +509,97 @@ * Path 2t(N much larger than M, JOBU='N', JOBVT='O') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_M ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_M ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) - MAXWRK = MAX( M*M+WRKBL, M*M+M*N+M ) - MINWRK = MAX( 3*M+N, BDSPAC ) + MAXWRK = MAX( M*M + WRKBL, M*M + M*N + M ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVO .AND. WNTUAS ) THEN * * Path 3t(N much larger than M, JOBU='S' or 'A', * JOBVT='O') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_M ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_M ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) - MAXWRK = MAX( M*M+WRKBL, M*M+M*N+M ) - MINWRK = MAX( 3*M+N, BDSPAC ) + MAXWRK = MAX( M*M + WRKBL, M*M + M*N + M ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVS .AND. WNTUN ) THEN * * Path 4t(N much larger than M, JOBU='N', JOBVT='S') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_M ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_M ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVS .AND. WNTUO ) THEN * * Path 5t(N much larger than M, JOBU='O', JOBVT='S') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_M ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_M ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = 2*M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVS .AND. WNTUAS ) THEN * * Path 6t(N much larger than M, JOBU='S' or 'A', * JOBVT='S') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_M ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_M ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVA .AND. WNTUN ) THEN * * Path 7t(N much larger than M, JOBU='N', JOBVT='A') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_N ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_N ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVA .AND. WNTUO ) THEN * * Path 8t(N much larger than M, JOBU='O', JOBVT='A') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_N ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_N ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = 2*M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) ELSE IF( WNTVA .AND. WNTUAS ) THEN * * Path 9t(N much larger than M, JOBU='S' or 'A', * JOBVT='A') * WRKBL = M + LWORK_DGELQF - WRKBL = MAX( WRKBL, M+LWORK_DORGLQ_N ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DGEBRD ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_P ) - WRKBL = MAX( WRKBL, 3*M+LWORK_DORGBR_Q ) + WRKBL = MAX( WRKBL, M + LWORK_DORGLQ_N ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DGEBRD ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_P ) + WRKBL = MAX( WRKBL, 3*M + LWORK_DORGBR_Q ) WRKBL = MAX( WRKBL, BDSPAC ) MAXWRK = M*M + WRKBL - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) END IF ELSE * @@ -607,26 +607,26 @@ * CALL DGEBRD( M, N, A, LDA, S, DUM(1), DUM(1), $ DUM(1), DUM(1), -1, IERR ) - LWORK_DGEBRD=DUM(1) + LWORK_DGEBRD = INT( DUM(1) ) MAXWRK = 3*M + LWORK_DGEBRD IF( WNTVS .OR. WNTVO ) THEN * Compute space needed for DORGBR P CALL DORGBR( 'P', M, N, M, A, N, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_P=DUM(1) - MAXWRK = MAX( MAXWRK, 3*M+LWORK_DORGBR_P ) + LWORK_DORGBR_P = INT( DUM(1) ) + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR_P ) END IF IF( WNTVA ) THEN CALL DORGBR( 'P', N, N, M, A, N, DUM(1), $ DUM(1), -1, IERR ) - LWORK_DORGBR_P=DUM(1) - MAXWRK = MAX( MAXWRK, 3*M+LWORK_DORGBR_P ) + LWORK_DORGBR_P = INT( DUM(1) ) + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR_P ) END IF IF( .NOT.WNTUN ) THEN - MAXWRK = MAX( MAXWRK, 3*M+LWORK_DORGBR_Q ) + MAXWRK = MAX( MAXWRK, 3*M + LWORK_DORGBR_Q ) END IF MAXWRK = MAX( MAXWRK, BDSPAC ) - MINWRK = MAX( 3*M+N, BDSPAC ) + MINWRK = MAX( 3*M + N, BDSPAC ) END IF END IF MAXWRK = MAX( MAXWRK, MINWRK ) @@ -685,21 +685,24 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Zero out below R * - CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), LDA ) + IF( N .GT. 1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), + $ LDA ) + END IF IE = 1 ITAUQ = IE + N ITAUP = ITAUQ + N IWORK = ITAUP + N * * Bidiagonalize R in A -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, @@ -708,7 +711,7 @@ IF( WNTVO .OR. WNTVAS ) THEN * * If right singular vectors desired, generate P'. -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -739,13 +742,13 @@ * Sufficient workspace for a fast algorithm * IR = 1 - IF( LWORK.GE.MAX( WRKBL, LDA*N+N )+LDA*N ) THEN + IF( LWORK.GE.MAX( WRKBL, LDA*N + N ) + LDA*N ) THEN * * WORK(IU) is LDA by N, WORK(IR) is LDA by N * LDWRKU = LDA LDWRKR = LDA - ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N+N )+N*N ) THEN + ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N + N ) + N*N ) THEN * * WORK(IU) is LDA by N, WORK(IR) is N by N * @@ -762,7 +765,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -774,7 +777,7 @@ $ LDWRKR ) * * Generate Q in A -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -784,14 +787,14 @@ IWORK = ITAUP + N * * Bidiagonalize R in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, WORK( IR ), LDWRKR, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left vectors bidiagonalizing R -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), @@ -800,7 +803,7 @@ * * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IR) -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, 0, N, 0, S, WORK( IE ), DUM, 1, $ WORK( IR ), LDWRKR, DUM, 1, @@ -809,7 +812,7 @@ * * Multiply Q in A by left singular vectors of R in * WORK(IR), storing result in WORK(IU) and copying to A -* (Workspace: need N*N+2*N, prefer N*N+M*N+N) +* (Workspace: need N*N + 2*N, prefer N*N + M*N + N) * DO 10 I = 1, M, LDWRKU CHUNK = MIN( M-I+1, LDWRKU ) @@ -830,14 +833,14 @@ IWORK = ITAUP + N * * Bidiagonalize A -* (Workspace: need 3*N+M, prefer 3*N+(M+N)*NB) +* (Workspace: need 3*N + M, prefer 3*N + (M + N)*NB) * CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left vectors bidiagonalizing A -* (Workspace: need 4*N, prefer 3*N+N*NB) +* (Workspace: need 4*N, prefer 3*N + N*NB) * CALL DORGBR( 'Q', M, N, N, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -863,13 +866,13 @@ * Sufficient workspace for a fast algorithm * IR = 1 - IF( LWORK.GE.MAX( WRKBL, LDA*N+N )+LDA*N ) THEN + IF( LWORK.GE.MAX( WRKBL, LDA*N + N ) + LDA*N ) THEN * * WORK(IU) is LDA by N and WORK(IR) is LDA by N * LDWRKU = LDA LDWRKR = LDA - ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N+N )+N*N ) THEN + ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N + N ) + N*N ) THEN * * WORK(IU) is LDA by N and WORK(IR) is N by N * @@ -886,7 +889,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -899,7 +902,7 @@ $ VT( 2, 1 ), LDVT ) * * Generate Q in A -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -909,7 +912,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in VT, copying result to WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, VT, LDVT, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -917,14 +920,14 @@ CALL DLACPY( 'L', N, N, VT, LDVT, WORK( IR ), LDWRKR ) * * Generate left vectors bidiagonalizing R in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right vectors bidiagonalizing R in VT -* (Workspace: need N*N+4*N-1, prefer N*N+3*N+(N-1)*NB) +* (Workspace: need N*N + 4*N-1, prefer N*N + 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -933,7 +936,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IR) and computing right * singular vectors of R in VT -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, N, N, 0, S, WORK( IE ), VT, LDVT, $ WORK( IR ), LDWRKR, DUM, 1, @@ -942,7 +945,7 @@ * * Multiply Q in A by left singular vectors of R in * WORK(IR), storing result in WORK(IU) and copying to A -* (Workspace: need N*N+2*N, prefer N*N+M*N+N) +* (Workspace: need N*N + 2*N, prefer N*N + M*N + N) * DO 20 I = 1, M, LDWRKU CHUNK = MIN( M-I+1, LDWRKU ) @@ -961,7 +964,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -974,7 +977,7 @@ $ VT( 2, 1 ), LDVT ) * * Generate Q in A -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -984,21 +987,21 @@ IWORK = ITAUP + N * * Bidiagonalize R in VT -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, VT, LDVT, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply Q in A by left vectors bidiagonalizing R -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, VT, LDVT, $ WORK( ITAUQ ), A, LDA, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right vectors bidiagonalizing R in VT -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1042,7 +1045,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1055,7 +1058,7 @@ $ WORK( IR+1 ), LDWRKR ) * * Generate Q in A -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1065,7 +1068,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, WORK( IR ), LDWRKR, S, $ WORK( IE ), WORK( ITAUQ ), @@ -1073,7 +1076,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate left vectors bidiagonalizing R in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), @@ -1082,7 +1085,7 @@ * * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IR) -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, 0, N, 0, S, WORK( IE ), DUM, $ 1, WORK( IR ), LDWRKR, DUM, 1, @@ -1103,14 +1106,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DORGQR( M, N, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1121,18 +1124,20 @@ * * Zero out below R in A * - CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), - $ LDA ) + IF( N .GT. 1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, + $ A( 2, 1 ), LDA ) + END IF * * Bidiagonalize R in A -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply Q in U by left vectors bidiagonalizing R -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, A, LDA, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), @@ -1167,7 +1172,7 @@ LDWRKU = LDA IR = IU + LDWRKU*N LDWRKR = LDA - ELSE IF( LWORK.GE.WRKBL+( LDA+N )*N ) THEN + ELSE IF( LWORK.GE.WRKBL+( LDA + N )*N ) THEN * * WORK(IU) is LDA by N and WORK(IR) is N by N * @@ -1186,7 +1191,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need 2*N*N+2*N, prefer 2*N*N+N+N*NB) +* (Workspace: need 2*N*N + 2*N, prefer 2*N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1199,7 +1204,7 @@ $ WORK( IU+1 ), LDWRKU ) * * Generate Q in A -* (Workspace: need 2*N*N+2*N, prefer 2*N*N+N+N*NB) +* (Workspace: need 2*N*N + 2*N, prefer 2*N*N + N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1210,7 +1215,7 @@ * * Bidiagonalize R in WORK(IU), copying result to * WORK(IR) -* (Workspace: need 2*N*N+4*N, +* (Workspace: need 2*N*N + 4*N, * prefer 2*N*N+3*N+2*N*NB) * CALL DGEBRD( N, N, WORK( IU ), LDWRKU, S, @@ -1221,14 +1226,14 @@ $ WORK( IR ), LDWRKR ) * * Generate left bidiagonalizing vectors in WORK(IU) -* (Workspace: need 2*N*N+4*N, prefer 2*N*N+3*N+N*NB) +* (Workspace: need 2*N*N + 4*N, prefer 2*N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IU ), LDWRKU, $ WORK( ITAUQ ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in WORK(IR) -* (Workspace: need 2*N*N+4*N-1, +* (Workspace: need 2*N*N + 4*N-1, * prefer 2*N*N+3*N+(N-1)*NB) * CALL DORGBR( 'P', N, N, N, WORK( IR ), LDWRKR, @@ -1239,7 +1244,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IU) and computing * right singular vectors of R in WORK(IR) -* (Workspace: need 2*N*N+BDSPAC) +* (Workspace: need 2*N*N + BDSPAC) * CALL DBDSQR( 'U', N, N, N, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, WORK( IU ), @@ -1266,14 +1271,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DORGQR( M, N, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1284,25 +1289,27 @@ * * Zero out below R in A * - CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), - $ LDA ) + IF( N .GT. 1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, + $ A( 2, 1 ), LDA ) + END IF * * Bidiagonalize R in A -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply Q in U by left vectors bidiagonalizing R -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, A, LDA, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right vectors bidiagonalizing R in A -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1346,7 +1353,7 @@ IWORK = ITAU + N * * Compute A=Q*R -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1359,7 +1366,7 @@ $ WORK( IU+1 ), LDWRKU ) * * Generate Q in A -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DORGQR( M, N, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1369,7 +1376,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in WORK(IU), copying result to VT -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, WORK( IU ), LDWRKU, S, $ WORK( IE ), WORK( ITAUQ ), @@ -1379,14 +1386,14 @@ $ LDVT ) * * Generate left bidiagonalizing vectors in WORK(IU) -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IU ), LDWRKU, $ WORK( ITAUQ ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in VT -* (Workspace: need N*N+4*N-1, +* (Workspace: need N*N + 4*N-1, * prefer N*N+3*N+(N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), @@ -1396,7 +1403,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IU) and computing * right singular vectors of R in VT -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, N, N, 0, S, WORK( IE ), VT, $ LDVT, WORK( IU ), LDWRKU, DUM, 1, @@ -1417,14 +1424,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DORGQR( M, N, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1441,7 +1448,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in VT -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, VT, LDVT, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -1449,14 +1456,14 @@ * * Multiply Q in U by left bidiagonalizing vectors * in VT -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, VT, LDVT, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in VT -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1503,7 +1510,7 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1517,7 +1524,7 @@ $ WORK( IR+1 ), LDWRKR ) * * Generate Q in U -* (Workspace: need N*N+N+M, prefer N*N+N+M*NB) +* (Workspace: need N*N + N + M, prefer N*N + N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1527,7 +1534,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, WORK( IR ), LDWRKR, S, $ WORK( IE ), WORK( ITAUQ ), @@ -1535,7 +1542,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in WORK(IR) -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), @@ -1544,7 +1551,7 @@ * * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IR) -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, 0, N, 0, S, WORK( IE ), DUM, $ 1, WORK( IR ), LDWRKR, DUM, 1, @@ -1569,14 +1576,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need N+M, prefer N+M*NB) +* (Workspace: need N + M, prefer N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1587,11 +1594,13 @@ * * Zero out below R in A * - CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), - $ LDA ) + IF( N .GT. 1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, + $ A( 2, 1 ), LDA ) + END IF * * Bidiagonalize R in A -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -1599,7 +1608,7 @@ * * Multiply Q in U by left bidiagonalizing vectors * in A -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, A, LDA, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), @@ -1634,7 +1643,7 @@ LDWRKU = LDA IR = IU + LDWRKU*N LDWRKR = LDA - ELSE IF( LWORK.GE.WRKBL+( LDA+N )*N ) THEN + ELSE IF( LWORK.GE.WRKBL+( LDA + N )*N ) THEN * * WORK(IU) is LDA by N and WORK(IR) is N by N * @@ -1653,14 +1662,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N*N+2*N, prefer 2*N*N+N+N*NB) +* (Workspace: need 2*N*N + 2*N, prefer 2*N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need 2*N*N+N+M, prefer 2*N*N+N+M*NB) +* (Workspace: need 2*N*N + N + M, prefer 2*N*N + N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1678,7 +1687,7 @@ * * Bidiagonalize R in WORK(IU), copying result to * WORK(IR) -* (Workspace: need 2*N*N+4*N, +* (Workspace: need 2*N*N + 4*N, * prefer 2*N*N+3*N+2*N*NB) * CALL DGEBRD( N, N, WORK( IU ), LDWRKU, S, @@ -1689,14 +1698,14 @@ $ WORK( IR ), LDWRKR ) * * Generate left bidiagonalizing vectors in WORK(IU) -* (Workspace: need 2*N*N+4*N, prefer 2*N*N+3*N+N*NB) +* (Workspace: need 2*N*N + 4*N, prefer 2*N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IU ), LDWRKU, $ WORK( ITAUQ ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in WORK(IR) -* (Workspace: need 2*N*N+4*N-1, +* (Workspace: need 2*N*N + 4*N-1, * prefer 2*N*N+3*N+(N-1)*NB) * CALL DORGBR( 'P', N, N, N, WORK( IR ), LDWRKR, @@ -1707,7 +1716,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IU) and computing * right singular vectors of R in WORK(IR) -* (Workspace: need 2*N*N+BDSPAC) +* (Workspace: need 2*N*N + BDSPAC) * CALL DBDSQR( 'U', N, N, N, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, WORK( IU ), @@ -1737,14 +1746,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need N+M, prefer N+M*NB) +* (Workspace: need N + M, prefer N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1755,11 +1764,13 @@ * * Zero out below R in A * - CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, A( 2, 1 ), - $ LDA ) + IF( N .GT. 1 ) THEN + CALL DLASET( 'L', N-1, N-1, ZERO, ZERO, + $ A( 2, 1 ), LDA ) + END IF * * Bidiagonalize R in A -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -1767,14 +1778,14 @@ * * Multiply Q in U by left bidiagonalizing vectors * in A -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, A, LDA, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in A -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1818,14 +1829,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need N*N+2*N, prefer N*N+N+N*NB) +* (Workspace: need N*N + 2*N, prefer N*N + N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need N*N+N+M, prefer N*N+N+M*NB) +* (Workspace: need N*N + N + M, prefer N*N + N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1842,7 +1853,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in WORK(IU), copying result to VT -* (Workspace: need N*N+4*N, prefer N*N+3*N+2*N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + 2*N*NB) * CALL DGEBRD( N, N, WORK( IU ), LDWRKU, S, $ WORK( IE ), WORK( ITAUQ ), @@ -1852,14 +1863,14 @@ $ LDVT ) * * Generate left bidiagonalizing vectors in WORK(IU) -* (Workspace: need N*N+4*N, prefer N*N+3*N+N*NB) +* (Workspace: need N*N + 4*N, prefer N*N + 3*N + N*NB) * CALL DORGBR( 'Q', N, N, N, WORK( IU ), LDWRKU, $ WORK( ITAUQ ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in VT -* (Workspace: need N*N+4*N-1, +* (Workspace: need N*N + 4*N-1, * prefer N*N+3*N+(N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), @@ -1869,7 +1880,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of R in WORK(IU) and computing * right singular vectors of R in VT -* (Workspace: need N*N+BDSPAC) +* (Workspace: need N*N + BDSPAC) * CALL DBDSQR( 'U', N, N, N, 0, S, WORK( IE ), VT, $ LDVT, WORK( IU ), LDWRKU, DUM, 1, @@ -1894,14 +1905,14 @@ IWORK = ITAU + N * * Compute A=Q*R, copying result to U -* (Workspace: need 2*N, prefer N+N*NB) +* (Workspace: need 2*N, prefer N + N*NB) * CALL DGEQRF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) * * Generate Q in U -* (Workspace: need N+M, prefer N+M*NB) +* (Workspace: need N + M, prefer N + M*NB) * CALL DORGQR( M, M, N, U, LDU, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1918,7 +1929,7 @@ IWORK = ITAUP + N * * Bidiagonalize R in VT -* (Workspace: need 4*N, prefer 3*N+2*N*NB) +* (Workspace: need 4*N, prefer 3*N + 2*N*NB) * CALL DGEBRD( N, N, VT, LDVT, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -1926,14 +1937,14 @@ * * Multiply Q in U by left bidiagonalizing vectors * in VT -* (Workspace: need 3*N+M, prefer 3*N+M*NB) +* (Workspace: need 3*N + M, prefer 3*N + M*NB) * CALL DORMBR( 'Q', 'R', 'N', M, N, N, VT, LDVT, $ WORK( ITAUQ ), U, LDU, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in VT -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -1967,7 +1978,7 @@ IWORK = ITAUP + N * * Bidiagonalize A -* (Workspace: need 3*N+M, prefer 3*N+(M+N)*NB) +* (Workspace: need 3*N + M, prefer 3*N + (M + N)*NB) * CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, @@ -1976,7 +1987,7 @@ * * If left singular vectors desired in U, copy result to U * and generate left bidiagonalizing vectors in U -* (Workspace: need 3*N+NCU, prefer 3*N+NCU*NB) +* (Workspace: need 3*N + NCU, prefer 3*N + NCU*NB) * CALL DLACPY( 'L', M, N, A, LDA, U, LDU ) IF( WNTUS ) @@ -1990,7 +2001,7 @@ * * If right singular vectors desired in VT, copy result to * VT and generate right bidiagonalizing vectors in VT -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DLACPY( 'U', N, N, A, LDA, VT, LDVT ) CALL DORGBR( 'P', N, N, N, VT, LDVT, WORK( ITAUP ), @@ -2000,7 +2011,7 @@ * * If left singular vectors desired in A, generate left * bidiagonalizing vectors in A -* (Workspace: need 4*N, prefer 3*N+N*NB) +* (Workspace: need 4*N, prefer 3*N + N*NB) * CALL DORGBR( 'Q', M, N, N, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2009,7 +2020,7 @@ * * If right singular vectors desired in A, generate right * bidiagonalizing vectors in A -* (Workspace: need 4*N-1, prefer 3*N+(N-1)*NB) +* (Workspace: need 4*N-1, prefer 3*N + (N-1)*NB) * CALL DORGBR( 'P', N, N, N, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2071,7 +2082,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) @@ -2085,7 +2096,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in A -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, A, LDA, S, WORK( IE ), WORK( ITAUQ ), $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, @@ -2093,7 +2104,7 @@ IF( WNTUO .OR. WNTUAS ) THEN * * If left singular vectors desired, generate Q -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2126,14 +2137,14 @@ * Sufficient workspace for a fast algorithm * IR = 1 - IF( LWORK.GE.MAX( WRKBL, LDA*N+M )+LDA*M ) THEN + IF( LWORK.GE.MAX( WRKBL, LDA*N + M ) + LDA*M ) THEN * * WORK(IU) is LDA by N and WORK(IR) is LDA by M * LDWRKU = LDA CHUNK = N LDWRKR = LDA - ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N+M )+M*M ) THEN + ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N + M ) + M*M ) THEN * * WORK(IU) is LDA by N and WORK(IR) is M by M * @@ -2152,7 +2163,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2164,7 +2175,7 @@ $ WORK( IR+LDWRKR ), LDWRKR ) * * Generate Q in A -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2174,14 +2185,14 @@ IWORK = ITAUP + M * * Bidiagonalize L in WORK(IR) -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, WORK( IR ), LDWRKR, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate right vectors bidiagonalizing L -* (Workspace: need M*M+4*M-1, prefer M*M+3*M+(M-1)*NB) +* (Workspace: need M*M + 4*M-1, prefer M*M + 3*M + (M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IR ), LDWRKR, $ WORK( ITAUP ), WORK( IWORK ), @@ -2190,7 +2201,7 @@ * * Perform bidiagonal QR iteration, computing right * singular vectors of L in WORK(IR) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, 0, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, DUM, 1, DUM, 1, @@ -2199,7 +2210,7 @@ * * Multiply right singular vectors of L in WORK(IR) by Q * in A, storing result in WORK(IU) and copying to A -* (Workspace: need M*M+2*M, prefer M*M+M*N+M) +* (Workspace: need M*M + 2*M, prefer M*M + M*N + M) * DO 30 I = 1, N, CHUNK BLK = MIN( N-I+1, CHUNK ) @@ -2220,14 +2231,14 @@ IWORK = ITAUP + M * * Bidiagonalize A -* (Workspace: need 3*M+N, prefer 3*M+(M+N)*NB) +* (Workspace: need 3*M + N, prefer 3*M + (M + N)*NB) * CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate right vectors bidiagonalizing A -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'P', M, N, M, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2253,14 +2264,14 @@ * Sufficient workspace for a fast algorithm * IR = 1 - IF( LWORK.GE.MAX( WRKBL, LDA*N+M )+LDA*M ) THEN + IF( LWORK.GE.MAX( WRKBL, LDA*N + M ) + LDA*M ) THEN * * WORK(IU) is LDA by N and WORK(IR) is LDA by M * LDWRKU = LDA CHUNK = N LDWRKR = LDA - ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N+M )+M*M ) THEN + ELSE IF( LWORK.GE.MAX( WRKBL, LDA*N + M ) + M*M ) THEN * * WORK(IU) is LDA by N and WORK(IR) is M by M * @@ -2279,7 +2290,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2291,7 +2302,7 @@ $ LDU ) * * Generate Q in A -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2301,7 +2312,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in U, copying result to WORK(IR) -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, U, LDU, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -2309,14 +2320,14 @@ CALL DLACPY( 'U', M, M, U, LDU, WORK( IR ), LDWRKR ) * * Generate right vectors bidiagonalizing L in WORK(IR) -* (Workspace: need M*M+4*M-1, prefer M*M+3*M+(M-1)*NB) +* (Workspace: need M*M + 4*M-1, prefer M*M + 3*M + (M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IR ), LDWRKR, $ WORK( ITAUP ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate left vectors bidiagonalizing L in U -* (Workspace: need M*M+4*M, prefer M*M+3*M+M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2325,7 +2336,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of L in U, and computing right * singular vectors of L in WORK(IR) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, M, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, U, LDU, DUM, 1, @@ -2334,7 +2345,7 @@ * * Multiply right singular vectors of L in WORK(IR) by Q * in A, storing result in WORK(IU) and copying to A -* (Workspace: need M*M+2*M, prefer M*M+M*N+M)) +* (Workspace: need M*M + 2*M, prefer M*M + M*N + M)) * DO 40 I = 1, N, CHUNK BLK = MIN( N-I+1, CHUNK ) @@ -2353,7 +2364,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2365,7 +2376,7 @@ $ LDU ) * * Generate Q in A -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2375,21 +2386,21 @@ IWORK = ITAUP + M * * Bidiagonalize L in U -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, U, LDU, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply right vectors bidiagonalizing L by Q in A -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, U, LDU, $ WORK( ITAUP ), A, LDA, WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate left vectors bidiagonalizing L in U -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2433,7 +2444,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2446,7 +2457,7 @@ $ WORK( IR+LDWRKR ), LDWRKR ) * * Generate Q in A -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2456,7 +2467,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in WORK(IR) -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, WORK( IR ), LDWRKR, S, $ WORK( IE ), WORK( ITAUQ ), @@ -2465,7 +2476,7 @@ * * Generate right vectors bidiagonalizing L in * WORK(IR) -* (Workspace: need M*M+4*M, prefer M*M+3*M+(M-1)*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + (M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IR ), LDWRKR, $ WORK( ITAUP ), WORK( IWORK ), @@ -2474,7 +2485,7 @@ * * Perform bidiagonal QR iteration, computing right * singular vectors of L in WORK(IR) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, 0, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, DUM, 1, DUM, 1, @@ -2495,7 +2506,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2505,7 +2516,7 @@ CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DORGLQ( M, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2520,14 +2531,14 @@ $ LDA ) * * Bidiagonalize L in A -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply right vectors bidiagonalizing L by Q in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, A, LDA, $ WORK( ITAUP ), VT, LDVT, @@ -2562,7 +2573,7 @@ LDWRKU = LDA IR = IU + LDWRKU*M LDWRKR = LDA - ELSE IF( LWORK.GE.WRKBL+( LDA+M )*M ) THEN + ELSE IF( LWORK.GE.WRKBL+( LDA + M )*M ) THEN * * WORK(IU) is LDA by M and WORK(IR) is M by M * @@ -2581,7 +2592,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need 2*M*M+2*M, prefer 2*M*M+M+M*NB) +* (Workspace: need 2*M*M + 2*M, prefer 2*M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2594,7 +2605,7 @@ $ WORK( IU+LDWRKU ), LDWRKU ) * * Generate Q in A -* (Workspace: need 2*M*M+2*M, prefer 2*M*M+M+M*NB) +* (Workspace: need 2*M*M + 2*M, prefer 2*M*M + M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2605,7 +2616,7 @@ * * Bidiagonalize L in WORK(IU), copying result to * WORK(IR) -* (Workspace: need 2*M*M+4*M, +* (Workspace: need 2*M*M + 4*M, * prefer 2*M*M+3*M+2*M*NB) * CALL DGEBRD( M, M, WORK( IU ), LDWRKU, S, @@ -2616,7 +2627,7 @@ $ WORK( IR ), LDWRKR ) * * Generate right bidiagonalizing vectors in WORK(IU) -* (Workspace: need 2*M*M+4*M-1, +* (Workspace: need 2*M*M + 4*M-1, * prefer 2*M*M+3*M+(M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IU ), LDWRKU, @@ -2624,7 +2635,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in WORK(IR) -* (Workspace: need 2*M*M+4*M, prefer 2*M*M+3*M+M*NB) +* (Workspace: need 2*M*M + 4*M, prefer 2*M*M + 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), @@ -2634,7 +2645,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of L in WORK(IR) and computing * right singular vectors of L in WORK(IU) -* (Workspace: need 2*M*M+BDSPAC) +* (Workspace: need 2*M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, M, 0, S, WORK( IE ), $ WORK( IU ), LDWRKU, WORK( IR ), @@ -2661,14 +2672,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DORGLQ( M, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2683,21 +2694,21 @@ $ LDA ) * * Bidiagonalize L in A -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Multiply right vectors bidiagonalizing L by Q in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, A, LDA, $ WORK( ITAUP ), VT, LDVT, $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors of L in A -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2741,7 +2752,7 @@ IWORK = ITAU + M * * Compute A=L*Q -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2754,7 +2765,7 @@ $ WORK( IU+LDWRKU ), LDWRKU ) * * Generate Q in A -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DORGLQ( M, N, M, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2764,7 +2775,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in WORK(IU), copying result to U -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, WORK( IU ), LDWRKU, S, $ WORK( IE ), WORK( ITAUQ ), @@ -2774,7 +2785,7 @@ $ LDU ) * * Generate right bidiagonalizing vectors in WORK(IU) -* (Workspace: need M*M+4*M-1, +* (Workspace: need M*M + 4*M-1, * prefer M*M+3*M+(M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IU ), LDWRKU, @@ -2782,7 +2793,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in U -* (Workspace: need M*M+4*M, prefer M*M+3*M+M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2791,7 +2802,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of L in U and computing right * singular vectors of L in WORK(IU) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, M, 0, S, WORK( IE ), $ WORK( IU ), LDWRKU, U, LDU, DUM, 1, @@ -2812,14 +2823,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DORGLQ( M, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2835,7 +2846,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in U -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, U, LDU, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -2843,14 +2854,14 @@ * * Multiply right bidiagonalizing vectors in U by Q * in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, U, LDU, $ WORK( ITAUP ), VT, LDVT, $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in U -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2877,7 +2888,7 @@ * N right singular vectors to be computed in VT and * no left singular vectors to be computed * - IF( LWORK.GE.M*M+MAX( N+M, 4*M, BDSPAC ) ) THEN + IF( LWORK.GE.M*M+MAX( N + M, 4*M, BDSPAC ) ) THEN * * Sufficient workspace for a fast algorithm * @@ -2897,7 +2908,7 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2911,7 +2922,7 @@ $ WORK( IR+LDWRKR ), LDWRKR ) * * Generate Q in VT -* (Workspace: need M*M+M+N, prefer M*M+M+N*NB) +* (Workspace: need M*M + M + N, prefer M*M + M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2921,7 +2932,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in WORK(IR) -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, WORK( IR ), LDWRKR, S, $ WORK( IE ), WORK( ITAUQ ), @@ -2929,7 +2940,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate right bidiagonalizing vectors in WORK(IR) -* (Workspace: need M*M+4*M-1, +* (Workspace: need M*M + 4*M-1, * prefer M*M+3*M+(M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IR ), LDWRKR, @@ -2939,7 +2950,7 @@ * * Perform bidiagonal QR iteration, computing right * singular vectors of L in WORK(IR) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, 0, 0, S, WORK( IE ), $ WORK( IR ), LDWRKR, DUM, 1, DUM, 1, @@ -2964,14 +2975,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need M+N, prefer M+N*NB) +* (Workspace: need M + N, prefer M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -2986,7 +2997,7 @@ $ LDA ) * * Bidiagonalize L in A -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -2994,7 +3005,7 @@ * * Multiply right bidiagonalizing vectors in A by Q * in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, A, LDA, $ WORK( ITAUP ), VT, LDVT, @@ -3017,7 +3028,7 @@ * N right singular vectors to be computed in VT and * M left singular vectors to be overwritten on A * - IF( LWORK.GE.2*M*M+MAX( N+M, 4*M, BDSPAC ) ) THEN + IF( LWORK.GE.2*M*M+MAX( N + M, 4*M, BDSPAC ) ) THEN * * Sufficient workspace for a fast algorithm * @@ -3029,7 +3040,7 @@ LDWRKU = LDA IR = IU + LDWRKU*M LDWRKR = LDA - ELSE IF( LWORK.GE.WRKBL+( LDA+M )*M ) THEN + ELSE IF( LWORK.GE.WRKBL+( LDA + M )*M ) THEN * * WORK(IU) is LDA by M and WORK(IR) is M by M * @@ -3048,14 +3059,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M*M+2*M, prefer 2*M*M+M+M*NB) +* (Workspace: need 2*M*M + 2*M, prefer 2*M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need 2*M*M+M+N, prefer 2*M*M+M+N*NB) +* (Workspace: need 2*M*M + M + N, prefer 2*M*M + M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3073,7 +3084,7 @@ * * Bidiagonalize L in WORK(IU), copying result to * WORK(IR) -* (Workspace: need 2*M*M+4*M, +* (Workspace: need 2*M*M + 4*M, * prefer 2*M*M+3*M+2*M*NB) * CALL DGEBRD( M, M, WORK( IU ), LDWRKU, S, @@ -3084,7 +3095,7 @@ $ WORK( IR ), LDWRKR ) * * Generate right bidiagonalizing vectors in WORK(IU) -* (Workspace: need 2*M*M+4*M-1, +* (Workspace: need 2*M*M + 4*M-1, * prefer 2*M*M+3*M+(M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IU ), LDWRKU, @@ -3092,7 +3103,7 @@ $ LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in WORK(IR) -* (Workspace: need 2*M*M+4*M, prefer 2*M*M+3*M+M*NB) +* (Workspace: need 2*M*M + 4*M, prefer 2*M*M + 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, WORK( IR ), LDWRKR, $ WORK( ITAUQ ), WORK( IWORK ), @@ -3102,7 +3113,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of L in WORK(IR) and computing * right singular vectors of L in WORK(IU) -* (Workspace: need 2*M*M+BDSPAC) +* (Workspace: need 2*M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, M, 0, S, WORK( IE ), $ WORK( IU ), LDWRKU, WORK( IR ), @@ -3132,14 +3143,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need M+N, prefer M+N*NB) +* (Workspace: need M + N, prefer M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3154,7 +3165,7 @@ $ LDA ) * * Bidiagonalize L in A -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, A, LDA, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -3162,14 +3173,14 @@ * * Multiply right bidiagonalizing vectors in A by Q * in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, A, LDA, $ WORK( ITAUP ), VT, LDVT, $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in A -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3193,7 +3204,7 @@ * N right singular vectors to be computed in VT and * M left singular vectors to be computed in U * - IF( LWORK.GE.M*M+MAX( N+M, 4*M, BDSPAC ) ) THEN + IF( LWORK.GE.M*M+MAX( N + M, 4*M, BDSPAC ) ) THEN * * Sufficient workspace for a fast algorithm * @@ -3213,14 +3224,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need M*M+2*M, prefer M*M+M+M*NB) +* (Workspace: need M*M + 2*M, prefer M*M + M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need M*M+M+N, prefer M*M+M+N*NB) +* (Workspace: need M*M + M + N, prefer M*M + M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3237,7 +3248,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in WORK(IU), copying result to U -* (Workspace: need M*M+4*M, prefer M*M+3*M+2*M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + 2*M*NB) * CALL DGEBRD( M, M, WORK( IU ), LDWRKU, S, $ WORK( IE ), WORK( ITAUQ ), @@ -3247,14 +3258,14 @@ $ LDU ) * * Generate right bidiagonalizing vectors in WORK(IU) -* (Workspace: need M*M+4*M, prefer M*M+3*M+(M-1)*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + (M-1)*NB) * CALL DORGBR( 'P', M, M, M, WORK( IU ), LDWRKU, $ WORK( ITAUP ), WORK( IWORK ), $ LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in U -* (Workspace: need M*M+4*M, prefer M*M+3*M+M*NB) +* (Workspace: need M*M + 4*M, prefer M*M + 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3263,7 +3274,7 @@ * Perform bidiagonal QR iteration, computing left * singular vectors of L in U and computing right * singular vectors of L in WORK(IU) -* (Workspace: need M*M+BDSPAC) +* (Workspace: need M*M + BDSPAC) * CALL DBDSQR( 'U', M, M, M, 0, S, WORK( IE ), $ WORK( IU ), LDWRKU, U, LDU, DUM, 1, @@ -3288,14 +3299,14 @@ IWORK = ITAU + M * * Compute A=L*Q, copying result to VT -* (Workspace: need 2*M, prefer M+M*NB) +* (Workspace: need 2*M, prefer M + M*NB) * CALL DGELQF( M, N, A, LDA, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) * * Generate Q in VT -* (Workspace: need M+N, prefer M+N*NB) +* (Workspace: need M + N, prefer M + N*NB) * CALL DORGLQ( N, N, M, VT, LDVT, WORK( ITAU ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3311,7 +3322,7 @@ IWORK = ITAUP + M * * Bidiagonalize L in U -* (Workspace: need 4*M, prefer 3*M+2*M*NB) +* (Workspace: need 4*M, prefer 3*M + 2*M*NB) * CALL DGEBRD( M, M, U, LDU, S, WORK( IE ), $ WORK( ITAUQ ), WORK( ITAUP ), @@ -3319,14 +3330,14 @@ * * Multiply right bidiagonalizing vectors in U by Q * in VT -* (Workspace: need 3*M+N, prefer 3*M+N*NB) +* (Workspace: need 3*M + N, prefer 3*M + N*NB) * CALL DORMBR( 'P', 'L', 'T', M, N, M, U, LDU, $ WORK( ITAUP ), VT, LDVT, $ WORK( IWORK ), LWORK-IWORK+1, IERR ) * * Generate left bidiagonalizing vectors in U -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'Q', M, M, M, U, LDU, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3360,7 +3371,7 @@ IWORK = ITAUP + M * * Bidiagonalize A -* (Workspace: need 3*M+N, prefer 3*M+(M+N)*NB) +* (Workspace: need 3*M + N, prefer 3*M + (M + N)*NB) * CALL DGEBRD( M, N, A, LDA, S, WORK( IE ), WORK( ITAUQ ), $ WORK( ITAUP ), WORK( IWORK ), LWORK-IWORK+1, @@ -3369,7 +3380,7 @@ * * If left singular vectors desired in U, copy result to U * and generate left bidiagonalizing vectors in U -* (Workspace: need 4*M-1, prefer 3*M+(M-1)*NB) +* (Workspace: need 4*M-1, prefer 3*M + (M-1)*NB) * CALL DLACPY( 'L', M, M, A, LDA, U, LDU ) CALL DORGBR( 'Q', M, M, N, U, LDU, WORK( ITAUQ ), @@ -3379,7 +3390,7 @@ * * If right singular vectors desired in VT, copy result to * VT and generate right bidiagonalizing vectors in VT -* (Workspace: need 3*M+NRVT, prefer 3*M+NRVT*NB) +* (Workspace: need 3*M + NRVT, prefer 3*M + NRVT*NB) * CALL DLACPY( 'U', M, N, A, LDA, VT, LDVT ) IF( WNTVA ) @@ -3393,7 +3404,7 @@ * * If left singular vectors desired in A, generate left * bidiagonalizing vectors in A -* (Workspace: need 4*M-1, prefer 3*M+(M-1)*NB) +* (Workspace: need 4*M-1, prefer 3*M + (M-1)*NB) * CALL DORGBR( 'Q', M, M, N, A, LDA, WORK( ITAUQ ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) @@ -3402,7 +3413,7 @@ * * If right singular vectors desired in A, generate right * bidiagonalizing vectors in A -* (Workspace: need 4*M, prefer 3*M+M*NB) +* (Workspace: need 4*M, prefer 3*M + M*NB) * CALL DORGBR( 'P', M, N, M, A, LDA, WORK( ITAUP ), $ WORK( IWORK ), LWORK-IWORK+1, IERR ) diff --git a/lib/linalg/dgetf2.f b/lib/linalg/dgetf2.f index 649d0671deb88d3ee5f84f2e9b87e1e7e82c3e17..5458a5f3eb0e5099519539205cf0218fdf5b6862 100644 --- a/lib/linalg/dgetf2.f +++ b/lib/linalg/dgetf2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGETF2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGETF2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGETF2( M, N, A, LDA, IPIV, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, M, N * .. @@ -27,7 +27,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -96,22 +96,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETF2( M, N, A, LDA, IPIV, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N @@ -128,11 +128,11 @@ PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) * .. * .. Local Scalars .. - DOUBLE PRECISION SFMIN + DOUBLE PRECISION SFMIN INTEGER I, J, JP * .. * .. External Functions .. - DOUBLE PRECISION DLAMCH + DOUBLE PRECISION DLAMCH INTEGER IDAMAX EXTERNAL DLAMCH, IDAMAX * .. @@ -164,9 +164,9 @@ IF( M.EQ.0 .OR. N.EQ.0 ) $ RETURN * -* Compute machine safe minimum -* - SFMIN = DLAMCH('S') +* Compute machine safe minimum +* + SFMIN = DLAMCH('S') * DO 10 J = 1, MIN( M, N ) * @@ -183,15 +183,15 @@ * * Compute elements J+1:M of J-th column. * - IF( J.LT.M ) THEN - IF( ABS(A( J, J )) .GE. SFMIN ) THEN - CALL DSCAL( M-J, ONE / A( J, J ), A( J+1, J ), 1 ) - ELSE - DO 20 I = 1, M-J - A( J+I, J ) = A( J+I, J ) / A( J, J ) - 20 CONTINUE - END IF - END IF + IF( J.LT.M ) THEN + IF( ABS(A( J, J )) .GE. SFMIN ) THEN + CALL DSCAL( M-J, ONE / A( J, J ), A( J+1, J ), 1 ) + ELSE + DO 20 I = 1, M-J + A( J+I, J ) = A( J+I, J ) / A( J, J ) + 20 CONTINUE + END IF + END IF * ELSE IF( INFO.EQ.0 ) THEN * diff --git a/lib/linalg/dgetrf.f b/lib/linalg/dgetrf.f index 45bb97f30c511f86e6fdd1b76510fe71192529a8..9a340b60f32733552cfa8e18421a53aa9a99cefc 100644 --- a/lib/linalg/dgetrf.f +++ b/lib/linalg/dgetrf.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGETRF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGETRF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, M, N * .. @@ -27,7 +27,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -96,22 +96,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N @@ -131,7 +131,7 @@ INTEGER I, IINFO, J, JB, NB * .. * .. External Subroutines .. - EXTERNAL DGEMM, DGETF2, DLASWP, DTRSM, XERBLA + EXTERNAL DGEMM, DGETRF2, DLASWP, DTRSM, XERBLA * .. * .. External Functions .. INTEGER ILAENV @@ -169,7 +169,7 @@ * * Use unblocked code. * - CALL DGETF2( M, N, A, LDA, IPIV, INFO ) + CALL DGETRF2( M, N, A, LDA, IPIV, INFO ) ELSE * * Use blocked code. @@ -180,7 +180,7 @@ * Factor diagonal and subdiagonal blocks and test for exact * singularity. * - CALL DGETF2( M-J+1, JB, A( J, J ), LDA, IPIV( J ), IINFO ) + CALL DGETRF2( M-J+1, JB, A( J, J ), LDA, IPIV( J ), IINFO ) * * Adjust INFO and the pivot indices. * diff --git a/lib/linalg/dgetrf2.f b/lib/linalg/dgetrf2.f new file mode 100644 index 0000000000000000000000000000000000000000..77948d23056828acbfb921ea2383987daefd9ed5 --- /dev/null +++ b/lib/linalg/dgetrf2.f @@ -0,0 +1,272 @@ +*> \brief \b DGETRF2 +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +* Definition: +* =========== +* +* RECURSIVE SUBROUTINE DGETRF2( M, N, A, LDA, IPIV, INFO ) +* +* .. Scalar Arguments .. +* INTEGER INFO, LDA, M, N +* .. +* .. Array Arguments .. +* INTEGER IPIV( * ) +* DOUBLE PRECISION A( LDA, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DGETRF2 computes an LU factorization of a general M-by-N matrix A +*> using partial pivoting with row interchanges. +*> +*> The factorization has the form +*> A = P * L * U +*> where P is a permutation matrix, L is lower triangular with unit +*> diagonal elements (lower trapezoidal if m > n), and U is upper +*> triangular (upper trapezoidal if m < n). +*> +*> This is the recursive version of the algorithm. It divides +*> the matrix into four submatrices: +*> +*> [ A11 | A12 ] where A11 is n1 by n1 and A22 is n2 by n2 +*> A = [ -----|----- ] with n1 = min(m,n)/2 +*> [ A21 | A22 ] n2 = n-n1 +*> +*> [ A11 ] +*> The subroutine calls itself to factor [ --- ], +*> [ A12 ] +*> [ A12 ] +*> do the swaps on [ --- ], solve A12, update A22, +*> [ A22 ] +*> +*> then calls itself to factor A22 and do the swaps on A21. +*> +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix A. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> On entry, the M-by-N matrix to be factored. +*> On exit, the factors L and U from the factorization +*> A = P*L*U; the unit diagonal elements of L are not stored. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,M). +*> \endverbatim +*> +*> \param[out] IPIV +*> \verbatim +*> IPIV is INTEGER array, dimension (min(M,N)) +*> The pivot indices; for 1 <= i <= min(M,N), row i of the +*> matrix was interchanged with row IPIV(i). +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> > 0: if INFO = i, U(i,i) is exactly zero. The factorization +*> has been completed, but the factor U is exactly +*> singular, and division by zero will occur if it is used +*> to solve a system of equations. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2016 +* +*> \ingroup doubleGEcomputational +* +* ===================================================================== + RECURSIVE SUBROUTINE DGETRF2( M, N, A, LDA, IPIV, INFO ) +* +* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2016 +* +* .. Scalar Arguments .. + INTEGER INFO, LDA, M, N +* .. +* .. Array Arguments .. + INTEGER IPIV( * ) + DOUBLE PRECISION A( LDA, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + DOUBLE PRECISION SFMIN, TEMP + INTEGER I, IINFO, N1, N2 +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH + INTEGER IDAMAX + EXTERNAL DLAMCH, IDAMAX +* .. +* .. External Subroutines .. + EXTERNAL DGEMM, DSCAL, DLASWP, DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters +* + INFO = 0 + IF( M.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, M ) ) THEN + INFO = -4 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DGETRF2', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 ) + $ RETURN + + IF ( M.EQ.1 ) THEN +* +* Use unblocked code for one row case +* Just need to handle IPIV and INFO +* + IPIV( 1 ) = 1 + IF ( A(1,1).EQ.ZERO ) + $ INFO = 1 +* + ELSE IF( N.EQ.1 ) THEN +* +* Use unblocked code for one column case +* +* +* Compute machine safe minimum +* + SFMIN = DLAMCH('S') +* +* Find pivot and test for singularity +* + I = IDAMAX( M, A( 1, 1 ), 1 ) + IPIV( 1 ) = I + IF( A( I, 1 ).NE.ZERO ) THEN +* +* Apply the interchange +* + IF( I.NE.1 ) THEN + TEMP = A( 1, 1 ) + A( 1, 1 ) = A( I, 1 ) + A( I, 1 ) = TEMP + END IF +* +* Compute elements 2:M of the column +* + IF( ABS(A( 1, 1 )) .GE. SFMIN ) THEN + CALL DSCAL( M-1, ONE / A( 1, 1 ), A( 2, 1 ), 1 ) + ELSE + DO 10 I = 1, M-1 + A( 1+I, 1 ) = A( 1+I, 1 ) / A( 1, 1 ) + 10 CONTINUE + END IF +* + ELSE + INFO = 1 + END IF +* + ELSE +* +* Use recursive code +* + N1 = MIN( M, N ) / 2 + N2 = N-N1 +* +* [ A11 ] +* Factor [ --- ] +* [ A21 ] +* + CALL DGETRF2( M, N1, A, LDA, IPIV, IINFO ) + + IF ( INFO.EQ.0 .AND. IINFO.GT.0 ) + $ INFO = IINFO +* +* [ A12 ] +* Apply interchanges to [ --- ] +* [ A22 ] +* + CALL DLASWP( N2, A( 1, N1+1 ), LDA, 1, N1, IPIV, 1 ) +* +* Solve A12 +* + CALL DTRSM( 'L', 'L', 'N', 'U', N1, N2, ONE, A, LDA, + $ A( 1, N1+1 ), LDA ) +* +* Update A22 +* + CALL DGEMM( 'N', 'N', M-N1, N2, N1, -ONE, A( N1+1, 1 ), LDA, + $ A( 1, N1+1 ), LDA, ONE, A( N1+1, N1+1 ), LDA ) +* +* Factor A22 +* + CALL DGETRF2( M-N1, N2, A( N1+1, N1+1 ), LDA, IPIV( N1+1 ), + $ IINFO ) +* +* Adjust INFO and the pivot indices +* + IF ( INFO.EQ.0 .AND. IINFO.GT.0 ) + $ INFO = IINFO + N1 + DO 20 I = N1+1, MIN( M, N ) + IPIV( I ) = IPIV( I ) + N1 + 20 CONTINUE +* +* Apply interchanges to A21 +* + CALL DLASWP( N1, A( 1, 1 ), LDA, N1+1, MIN( M, N), IPIV, 1 ) +* + END IF + RETURN +* +* End of DGETRF2 +* + END diff --git a/lib/linalg/dgetri.f b/lib/linalg/dgetri.f index ad5324c07ef779da7104da25ee4aac395ca1da72..9d8cf2ad3e58c0976b78facb2595a06bb6040938 100644 --- a/lib/linalg/dgetri.f +++ b/lib/linalg/dgetri.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGETRI + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGETRI + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGETRI( N, A, LDA, IPIV, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, LDA, LWORK, N * .. @@ -27,7 +27,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRI( N, A, LDA, IPIV, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, N diff --git a/lib/linalg/dgetrs.f b/lib/linalg/dgetrs.f index 02e9832af79bbb45e570db2fe226a5324ea64d39..7ac727776e565b0aabc8a91cfda2ea0af64c8303 100644 --- a/lib/linalg/dgetrs.f +++ b/lib/linalg/dgetrs.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DGETRS + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DGETRS + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DGETRS( TRANS, N, NRHS, A, LDA, IPIV, B, LDB, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER TRANS * INTEGER INFO, LDA, LDB, N, NRHS @@ -28,7 +28,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ), B( LDB, * ) * .. -* +* * *> \par Purpose: * ============= @@ -109,22 +109,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRS( TRANS, N, NRHS, A, LDA, IPIV, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER TRANS diff --git a/lib/linalg/disnan.f b/lib/linalg/disnan.f index 355b82795565e5f9e54305258861f0a61a6f036b..a565ed36d48312d56c6e8b2304259a7971c34645 100644 --- a/lib/linalg/disnan.f +++ b/lib/linalg/disnan.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DISNAN + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DISNAN + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * LOGICAL FUNCTION DISNAN( DIN ) -* +* * .. Scalar Arguments .. -* DOUBLE PRECISION DIN +* DOUBLE PRECISION, INTENT(IN) :: DIN * .. -* +* * *> \par Purpose: * ============= @@ -47,25 +47,25 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== LOGICAL FUNCTION DISNAN( DIN ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. - DOUBLE PRECISION DIN + DOUBLE PRECISION, INTENT(IN) :: DIN * .. * * ===================================================================== diff --git a/lib/linalg/dlabad.f b/lib/linalg/dlabad.f index 9eda3c91db792aa8ff3b9c1e9ac8257c84fe0359..01b8158f663ed049fa08241db067d8cc6c50988a 100644 --- a/lib/linalg/dlabad.f +++ b/lib/linalg/dlabad.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLABAD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLABAD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLABAD( SMALL, LARGE ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION LARGE, SMALL * .. -* +* * *> \par Purpose: * ============= @@ -62,22 +62,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLABAD( SMALL, LARGE ) * -* -- LAPACK auxiliary routine (version 3.4.0) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION LARGE, SMALL diff --git a/lib/linalg/dlabrd.f b/lib/linalg/dlabrd.f index 72d148119a159dedcf1b83fc48c477407060387c..b5e734dc7c1166c7de38f4fd85979b1ba6dc8220 100644 --- a/lib/linalg/dlabrd.f +++ b/lib/linalg/dlabrd.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLABRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLABRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLABRD( M, N, NB, A, LDA, D, E, TAUQ, TAUP, X, LDX, Y, * LDY ) -* +* * .. Scalar Arguments .. * INTEGER LDA, LDX, LDY, M, N, NB * .. @@ -28,7 +28,7 @@ * DOUBLE PRECISION A( LDA, * ), D( * ), E( * ), TAUP( * ), * $ TAUQ( * ), X( LDX, * ), Y( LDY, * ) * .. -* +* * *> \par Purpose: * ============= @@ -110,7 +110,7 @@ *> *> \param[out] TAUQ *> \verbatim -*> TAUQ is DOUBLE PRECISION array dimension (NB) +*> TAUQ is DOUBLE PRECISION array, dimension (NB) *> The scalar factors of the elementary reflectors which *> represent the orthogonal matrix Q. See Further Details. *> \endverbatim @@ -151,12 +151,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * *> \ingroup doubleOTHERauxiliary * @@ -210,10 +210,10 @@ SUBROUTINE DLABRD( M, N, NB, A, LDA, D, E, TAUQ, TAUP, X, LDX, Y, $ LDY ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. INTEGER LDA, LDX, LDY, M, N, NB diff --git a/lib/linalg/dlacn2.f b/lib/linalg/dlacn2.f index 9dd3c85ea2a506e74e9415840776658bb9cb4952..952854043afc05418587f2e19d454dceb06c6b9b 100644 --- a/lib/linalg/dlacn2.f +++ b/lib/linalg/dlacn2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLACN2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLACN2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLACN2( N, V, X, ISGN, EST, KASE, ISAVE ) -* +* * .. Scalar Arguments .. * INTEGER KASE, N * DOUBLE PRECISION EST @@ -28,7 +28,7 @@ * INTEGER ISGN( * ), ISAVE( 3 ) * DOUBLE PRECISION V( * ), X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -75,7 +75,7 @@ *> EST is DOUBLE PRECISION *> On entry with KASE = 1 or 2 and ISAVE(1) = 3, EST should be *> unchanged from the previous call to DLACN2. -*> On exit, EST is an estimate (a lower bound) for norm(A). +*> On exit, EST is an estimate (a lower bound) for norm(A). *> \endverbatim *> *> \param[in,out] KASE @@ -96,12 +96,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * @@ -136,10 +136,10 @@ * ===================================================================== SUBROUTINE DLACN2( N, V, X, ISGN, EST, KASE, ISAVE ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER KASE, N diff --git a/lib/linalg/dlacpy.f b/lib/linalg/dlacpy.f index a9a23c9454eb8483aac927b9a59c88e29fade96c..d1c396724a5b5e473bb57bcf2479a881326e0724 100644 --- a/lib/linalg/dlacpy.f +++ b/lib/linalg/dlacpy.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLACPY + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLACPY + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLACPY( UPLO, M, N, A, LDA, B, LDB ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER LDA, LDB, M, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), B( LDB, * ) * .. -* +* * *> \par Purpose: * ============= @@ -91,22 +91,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLACPY( UPLO, M, N, A, LDA, B, LDB ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dladiv.f b/lib/linalg/dladiv.f index 306a6b0020e39a5dd94b0045cc85ba15b33a678e..dd8110adf2f8005a05bccfd97fc34adca1fc84e2 100644 --- a/lib/linalg/dladiv.f +++ b/lib/linalg/dladiv.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLADIV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLADIV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLADIV( A, B, C, D, P, Q ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION A, B, C, D, P, Q * .. -* +* * *> \par Purpose: * ============= @@ -36,8 +36,9 @@ *> p + i*q = --------- *> c + i*d *> -*> The algorithm is due to Robert L. Smith and can be found -*> in D. Knuth, The art of Computer Programming, Vol.2, p.195 +*> The algorithm is due to Michael Baudin and Robert L. Smith +*> and can be found in the paper +*> "A Robust Complex Division in Scilab" *> \endverbatim * * Arguments: @@ -78,22 +79,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date January 2013 * -*> \ingroup auxOTHERauxiliary +*> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLADIV( A, B, C, D, P, Q ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* January 2013 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, D, P, Q @@ -101,28 +102,155 @@ * * ===================================================================== * +* .. Parameters .. + DOUBLE PRECISION BS + PARAMETER ( BS = 2.0D0 ) + DOUBLE PRECISION HALF + PARAMETER ( HALF = 0.5D0 ) + DOUBLE PRECISION TWO + PARAMETER ( TWO = 2.0D0 ) +* * .. Local Scalars .. - DOUBLE PRECISION E, F + DOUBLE PRECISION AA, BB, CC, DD, AB, CD, S, OV, UN, BE, EPS +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH + EXTERNAL DLAMCH +* .. +* .. External Subroutines .. + EXTERNAL DLADIV1 * .. * .. Intrinsic Functions .. - INTRINSIC ABS + INTRINSIC ABS, MAX * .. * .. Executable Statements .. * - IF( ABS( D ).LT.ABS( C ) ) THEN - E = D / C - F = C + D*E - P = ( A+B*E ) / F - Q = ( B-A*E ) / F + AA = A + BB = B + CC = C + DD = D + AB = MAX( ABS(A), ABS(B) ) + CD = MAX( ABS(C), ABS(D) ) + S = 1.0D0 + + OV = DLAMCH( 'Overflow threshold' ) + UN = DLAMCH( 'Safe minimum' ) + EPS = DLAMCH( 'Epsilon' ) + BE = BS / (EPS*EPS) + + IF( AB >= HALF*OV ) THEN + AA = HALF * AA + BB = HALF * BB + S = TWO * S + END IF + IF( CD >= HALF*OV ) THEN + CC = HALF * CC + DD = HALF * DD + S = HALF * S + END IF + IF( AB <= UN*BS/EPS ) THEN + AA = AA * BE + BB = BB * BE + S = S / BE + END IF + IF( CD <= UN*BS/EPS ) THEN + CC = CC * BE + DD = DD * BE + S = S * BE + END IF + IF( ABS( D ).LE.ABS( C ) ) THEN + CALL DLADIV1(AA, BB, CC, DD, P, Q) ELSE - E = C / D - F = D + C*E - P = ( B+A*E ) / F - Q = ( -A+B*E ) / F + CALL DLADIV1(BB, AA, DD, CC, P, Q) + Q = -Q END IF + P = P * S + Q = Q * S * RETURN * * End of DLADIV * END + +*> \ingroup doubleOTHERauxiliary + + + SUBROUTINE DLADIV1( A, B, C, D, P, Q ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* January 2013 +* +* .. Scalar Arguments .. + DOUBLE PRECISION A, B, C, D, P, Q +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D0 ) +* +* .. Local Scalars .. + DOUBLE PRECISION R, T +* .. +* .. External Functions .. + DOUBLE PRECISION DLADIV2 + EXTERNAL DLADIV2 +* .. +* .. Executable Statements .. +* + R = D / C + T = ONE / (C + D * R) + P = DLADIV2(A, B, C, D, R, T) + A = -A + Q = DLADIV2(B, A, C, D, R, T) +* + RETURN +* +* End of DLADIV1 +* + END + +*> \ingroup doubleOTHERauxiliary + + DOUBLE PRECISION FUNCTION DLADIV2( A, B, C, D, R, T ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* January 2013 +* +* .. Scalar Arguments .. + DOUBLE PRECISION A, B, C, D, R, T +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO + PARAMETER ( ZERO = 0.0D0 ) +* +* .. Local Scalars .. + DOUBLE PRECISION BR +* .. +* .. Executable Statements .. +* + IF( R.NE.ZERO ) THEN + BR = B * R + IF( BR.NE.ZERO ) THEN + DLADIV2 = (A + BR) * T + ELSE + DLADIV2 = A * T + (B * T) * R + END IF + ELSE + DLADIV2 = (A + D * (B / C)) * T + END IF +* + RETURN +* +* End of DLADIV12 +* + END diff --git a/lib/linalg/dlae2.f b/lib/linalg/dlae2.f index 302eeaa1f7561f760bd539e2ee7a9f4623914ad0..ed77ff6dfe67864d60573202409b695153da48d0 100644 --- a/lib/linalg/dlae2.f +++ b/lib/linalg/dlae2.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAE2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAE2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAE2( A, B, C, RT1, RT2 ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION A, B, C, RT1, RT2 * .. -* +* * *> \par Purpose: * ============= @@ -73,14 +73,14 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -102,10 +102,10 @@ * ===================================================================== SUBROUTINE DLAE2( A, B, C, RT1, RT2 ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, RT1, RT2 diff --git a/lib/linalg/dlaed0.f b/lib/linalg/dlaed0.f index d8d7f53e1d0fb2887556fb212ce3b0c106399fbc..4e92da98ea93d66689f3f9e0ba3aec4766ba5c85 100644 --- a/lib/linalg/dlaed0.f +++ b/lib/linalg/dlaed0.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED0 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED0 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED0( ICOMPQ, QSIZ, N, D, E, Q, LDQ, QSTORE, LDQS, * WORK, IWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER ICOMPQ, INFO, LDQ, LDQS, N, QSIZ * .. @@ -29,7 +29,7 @@ * DOUBLE PRECISION D( * ), E( * ), Q( LDQ, * ), QSTORE( LDQS, * ), * $ WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -153,12 +153,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -172,10 +172,10 @@ SUBROUTINE DLAED0( ICOMPQ, QSIZ, N, D, E, Q, LDQ, QSTORE, LDQS, $ WORK, IWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER ICOMPQ, INFO, LDQ, LDQS, N, QSIZ diff --git a/lib/linalg/dlaed1.f b/lib/linalg/dlaed1.f index c37c1d2100c3fe533705cd2319ecaf88ea19ca9c..30e71fa241c71893659ce9e4a1d434ada04b2947 100644 --- a/lib/linalg/dlaed1.f +++ b/lib/linalg/dlaed1.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED1 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED1 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED1( N, D, Q, LDQ, INDXQ, RHO, CUTPNT, WORK, IWORK, * INFO ) -* +* * .. Scalar Arguments .. * INTEGER CUTPNT, INFO, LDQ, N * DOUBLE PRECISION RHO @@ -29,7 +29,7 @@ * INTEGER INDXQ( * ), IWORK( * ) * DOUBLE PRECISION D( * ), Q( LDQ, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -54,7 +54,7 @@ *> *> The first stage consists of deflating the size of the problem *> when there are multiple eigenvalues or if there is a zero in -*> the Z vector. For each such occurence the dimension of the +*> the Z vector. For each such occurrence the dimension of the *> secular equation problem is reduced by one. This stage is *> performed by the routine DLAED2. *> @@ -143,12 +143,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * @@ -163,10 +163,10 @@ SUBROUTINE DLAED1( N, D, Q, LDQ, INDXQ, RHO, CUTPNT, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. INTEGER CUTPNT, INFO, LDQ, N diff --git a/lib/linalg/dlaed2.f b/lib/linalg/dlaed2.f index a75d72a737a05680235b920ac24d825961c20a32..fbcc87a8803980a043537495c96f1a7f58157625 100644 --- a/lib/linalg/dlaed2.f +++ b/lib/linalg/dlaed2.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED2( K, N, N1, D, Q, LDQ, INDXQ, RHO, Z, DLAMDA, W, * Q2, INDX, INDXC, INDXP, COLTYP, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDQ, N, N1 * DOUBLE PRECISION RHO @@ -31,7 +31,7 @@ * DOUBLE PRECISION D( * ), DLAMDA( * ), Q( LDQ, * ), Q2( * ), * $ W( * ), Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -192,12 +192,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -212,10 +212,10 @@ SUBROUTINE DLAED2( K, N, N1, D, Q, LDQ, INDXQ, RHO, Z, DLAMDA, W, $ Q2, INDX, INDXC, INDXP, COLTYP, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDQ, N, N1 @@ -520,10 +520,10 @@ * into the last N - K slots of D and Q respectively. * IF( K.LT.N ) THEN - CALL DLACPY( 'A', N, CTOT( 4 ), Q2( IQ1 ), N, + CALL DLACPY( 'A', N, CTOT( 4 ), Q2( IQ1 ), N, $ Q( 1, K+1 ), LDQ ) CALL DCOPY( N-K, Z( K+1 ), 1, D( K+1 ), 1 ) - END IF + END IF * * Copy CTOT into COLTYP for referencing in DLAED3. * diff --git a/lib/linalg/dlaed3.f b/lib/linalg/dlaed3.f index 411d0f890f32e0a37f17c29a856494b0788dbd6d..d200fc0a2202922354aba22e6758c7b4b62a690f 100644 --- a/lib/linalg/dlaed3.f +++ b/lib/linalg/dlaed3.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED3 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED3 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED3( K, N, N1, D, Q, LDQ, RHO, DLAMDA, Q2, INDX, * CTOT, W, S, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDQ, N, N1 * DOUBLE PRECISION RHO @@ -30,7 +30,7 @@ * DOUBLE PRECISION D( * ), DLAMDA( * ), Q( LDQ, * ), Q2( * ), * $ S( * ), W( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,7 +116,7 @@ *> *> \param[in] Q2 *> \verbatim -*> Q2 is DOUBLE PRECISION array, dimension (LDQ2, N) +*> Q2 is DOUBLE PRECISION array, dimension (LDQ2*N) *> The first K columns of this matrix contain the non-deflated *> eigenvectors for the split problem. *> \endverbatim @@ -165,12 +165,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * *> \ingroup auxOTHERcomputational * @@ -185,10 +185,10 @@ SUBROUTINE DLAED3( K, N, N1, D, Q, LDQ, RHO, DLAMDA, Q2, INDX, $ CTOT, W, S, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. INTEGER INFO, K, LDQ, N, N1 diff --git a/lib/linalg/dlaed4.f b/lib/linalg/dlaed4.f index c898b5b6187ad49168132d5b110214a9aa0c35e3..e7dc839df5a57ca9f094785286553c45db564452 100644 --- a/lib/linalg/dlaed4.f +++ b/lib/linalg/dlaed4.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED4 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED4 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED4( N, I, D, Z, DELTA, RHO, DLAM, INFO ) -* +* * .. Scalar Arguments .. * INTEGER I, INFO, N * DOUBLE PRECISION DLAM, RHO @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( * ), DELTA( * ), Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -127,12 +127,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -145,10 +145,10 @@ * ===================================================================== SUBROUTINE DLAED4( N, I, D, Z, DELTA, RHO, DLAM, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER I, INFO, N diff --git a/lib/linalg/dlaed5.f b/lib/linalg/dlaed5.f index 3ac9aa19a8a044b02876f507592dc47570024b84..3ea9e401cfbc2849e58344c4bd2e2b58c3d817c7 100644 --- a/lib/linalg/dlaed5.f +++ b/lib/linalg/dlaed5.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED5 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED5 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED5( I, D, Z, DELTA, RHO, DLAM ) -* +* * .. Scalar Arguments .. * INTEGER I * DOUBLE PRECISION DLAM, RHO @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( 2 ), DELTA( 2 ), Z( 2 ) * .. -* +* * *> \par Purpose: * ============= @@ -90,12 +90,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -108,10 +108,10 @@ * ===================================================================== SUBROUTINE DLAED5( I, D, Z, DELTA, RHO, DLAM ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER I diff --git a/lib/linalg/dlaed6.f b/lib/linalg/dlaed6.f index 1ce4932b8e7e97650db1bbe5f47e5c00d3414ce9..daa8db39e4ce4a5f6a26c70017b3a3224b4027ab 100644 --- a/lib/linalg/dlaed6.f +++ b/lib/linalg/dlaed6.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED6 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED6 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED6( KNITER, ORGATI, RHO, D, Z, FINIT, TAU, INFO ) -* +* * .. Scalar Arguments .. * LOGICAL ORGATI * INTEGER INFO, KNITER @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( 3 ), Z( 3 ) * .. -* +* * *> \par Purpose: * ============= @@ -110,12 +110,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -140,10 +140,10 @@ * ===================================================================== SUBROUTINE DLAED6( KNITER, ORGATI, RHO, D, Z, FINIT, TAU, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. LOGICAL ORGATI @@ -175,7 +175,7 @@ INTEGER I, ITER, NITER DOUBLE PRECISION A, B, BASE, C, DDF, DF, EPS, ERRETM, ETA, F, $ FC, SCLFAC, SCLINV, SMALL1, SMALL2, SMINV1, - $ SMINV2, TEMP, TEMP1, TEMP2, TEMP3, TEMP4, + $ SMINV2, TEMP, TEMP1, TEMP2, TEMP3, TEMP4, $ LBD, UBD * .. * .. Intrinsic Functions .. @@ -195,7 +195,7 @@ IF( FINIT .LT. ZERO )THEN LBD = ZERO ELSE - UBD = ZERO + UBD = ZERO END IF * NITER = 1 @@ -363,7 +363,7 @@ * TAU = TAU + ETA IF( TAU .LT. LBD .OR. TAU .GT. UBD ) - $ TAU = ( LBD + UBD )/TWO + $ TAU = ( LBD + UBD )/TWO * FC = ZERO ERRETM = ZERO @@ -381,13 +381,14 @@ DF = DF + TEMP2 DDF = DDF + TEMP3 ELSE - GO TO 60 + GO TO 60 END IF 40 CONTINUE F = FINIT + TAU*FC ERRETM = EIGHT*( ABS( FINIT )+ABS( TAU )*ERRETM ) + $ ABS( TAU )*DF - IF( ABS( F ).LE.EPS*ERRETM ) + IF( ( ABS( F ).LE.FOUR*EPS*ERRETM ) .OR. + $ ( (UBD-LBD).LE.FOUR*EPS*ABS(TAU) ) ) $ GO TO 60 IF( F .LE. ZERO )THEN LBD = TAU diff --git a/lib/linalg/dlaed7.f b/lib/linalg/dlaed7.f index 972c1bc5902428506aea55575f3c36f0e10e560e..9c528addedf2af22a69c20cd91c5423ce8ecc098 100644 --- a/lib/linalg/dlaed7.f +++ b/lib/linalg/dlaed7.f @@ -2,18 +2,18 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED7 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED7 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== @@ -22,7 +22,7 @@ * LDQ, INDXQ, RHO, CUTPNT, QSTORE, QPTR, PRMPTR, * PERM, GIVPTR, GIVCOL, GIVNUM, WORK, IWORK, * INFO ) -* +* * .. Scalar Arguments .. * INTEGER CURLVL, CURPBM, CUTPNT, ICOMPQ, INFO, LDQ, N, * $ QSIZ, TLVLS @@ -34,7 +34,7 @@ * DOUBLE PRECISION D( * ), GIVNUM( 2, * ), Q( LDQ, * ), * $ QSTORE( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -59,7 +59,7 @@ *> *> The first stage consists of deflating the size of the problem *> when there are multiple eigenvalues or if there is a zero in -*> the Z vector. For each such occurence the dimension of the +*> the Z vector. For each such occurrence the dimension of the *> secular equation problem is reduced by one. This stage is *> performed by the routine DLAED8. *> @@ -239,12 +239,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * @@ -260,10 +260,10 @@ $ PERM, GIVPTR, GIVCOL, GIVNUM, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. INTEGER CURLVL, CURPBM, CUTPNT, ICOMPQ, INFO, LDQ, N, @@ -304,7 +304,7 @@ ELSE IF( N.LT.0 ) THEN INFO = -2 ELSE IF( ICOMPQ.EQ.1 .AND. QSIZ.LT.N ) THEN - INFO = -4 + INFO = -3 ELSE IF( LDQ.LT.MAX( 1, N ) ) THEN INFO = -9 ELSE IF( MIN( 1, N ).GT.CUTPNT .OR. N.LT.CUTPNT ) THEN diff --git a/lib/linalg/dlaed8.f b/lib/linalg/dlaed8.f index 42b4ea15775f8784d4a502905d43d09c0d77b217..c053347b10d77c0c1acddc6dc2c9823a3c08f4c0 100644 --- a/lib/linalg/dlaed8.f +++ b/lib/linalg/dlaed8.f @@ -2,18 +2,18 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED8 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED8 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== @@ -21,7 +21,7 @@ * SUBROUTINE DLAED8( ICOMPQ, K, N, QSIZ, D, Q, LDQ, INDXQ, RHO, * CUTPNT, Z, DLAMDA, Q2, LDQ2, W, PERM, GIVPTR, * GIVCOL, GIVNUM, INDXP, INDX, INFO ) -* +* * .. Scalar Arguments .. * INTEGER CUTPNT, GIVPTR, ICOMPQ, INFO, K, LDQ, LDQ2, N, * $ QSIZ @@ -33,7 +33,7 @@ * DOUBLE PRECISION D( * ), DLAMDA( * ), GIVNUM( 2, * ), * $ Q( LDQ, * ), Q2( LDQ2, * ), W( * ), Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -223,12 +223,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -243,10 +243,10 @@ $ CUTPNT, Z, DLAMDA, Q2, LDQ2, W, PERM, GIVPTR, $ GIVCOL, GIVNUM, INDXP, INDX, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER CUTPNT, GIVPTR, ICOMPQ, INFO, K, LDQ, LDQ2, N, @@ -308,8 +308,8 @@ END IF * * Need to initialize GIVPTR to O here in case of quick exit -* to prevent an unspecified code behavior (usually sigfault) -* when IWORK array on entry to *stedc is not zeroed +* to prevent an unspecified code behavior (usually sigfault) +* when IWORK array on entry to *stedc is not zeroed * (or at least some IWORK entries which used in *laed7 for GIVPTR). * GIVPTR = 0 diff --git a/lib/linalg/dlaed9.f b/lib/linalg/dlaed9.f index 8aa0687573af1f84699d85b89cafb38bb48273cd..d3be22502a1a9d5079299014c18f7054e9fda332 100644 --- a/lib/linalg/dlaed9.f +++ b/lib/linalg/dlaed9.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAED9 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAED9 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAED9( K, KSTART, KSTOP, N, D, Q, LDQ, RHO, DLAMDA, W, * S, LDS, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, KSTART, KSTOP, LDQ, LDS, N * DOUBLE PRECISION RHO @@ -29,7 +29,7 @@ * DOUBLE PRECISION D( * ), DLAMDA( * ), Q( LDQ, * ), S( LDS, * ), * $ W( * ) * .. -* +* * *> \par Purpose: * ============= @@ -137,12 +137,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -156,10 +156,10 @@ SUBROUTINE DLAED9( K, KSTART, KSTOP, N, D, Q, LDQ, RHO, DLAMDA, W, $ S, LDS, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, KSTART, KSTOP, LDQ, LDS, N diff --git a/lib/linalg/dlaeda.f b/lib/linalg/dlaeda.f index 749a7c365ac80a37bad29bab82b8a2ba63e2ff35..4ca08a087920eb185f26831e0df5b0dbc3a9e48c 100644 --- a/lib/linalg/dlaeda.f +++ b/lib/linalg/dlaeda.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAEDA + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAEDA + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAEDA( N, TLVLS, CURLVL, CURPBM, PRMPTR, PERM, GIVPTR, * GIVCOL, GIVNUM, Q, QPTR, Z, ZTEMP, INFO ) -* +* * .. Scalar Arguments .. * INTEGER CURLVL, CURPBM, INFO, N, TLVLS * .. @@ -29,7 +29,7 @@ * $ PRMPTR( * ), QPTR( * ) * DOUBLE PRECISION GIVNUM( 2, * ), Q( * ), Z( * ), ZTEMP( * ) * .. -* +* * *> \par Purpose: * ============= @@ -147,12 +147,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -166,10 +166,10 @@ SUBROUTINE DLAEDA( N, TLVLS, CURLVL, CURPBM, PRMPTR, PERM, GIVPTR, $ GIVCOL, GIVNUM, Q, QPTR, Z, ZTEMP, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER CURLVL, CURPBM, INFO, N, TLVLS diff --git a/lib/linalg/dlaev2.f b/lib/linalg/dlaev2.f index 2e333ddf2c7ddafd26f667bb096c0fabbfaaacf8..4906f1a20c7c038dedbc98f39ef1925260e4b114 100644 --- a/lib/linalg/dlaev2.f +++ b/lib/linalg/dlaev2.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAEV2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAEV2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAEV2( A, B, C, RT1, RT2, CS1, SN1 ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION A, B, C, CS1, RT1, RT2, SN1 * .. -* +* * *> \par Purpose: * ============= @@ -89,14 +89,14 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -120,10 +120,10 @@ * ===================================================================== SUBROUTINE DLAEV2( A, B, C, RT1, RT2, CS1, SN1 ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, CS1, RT1, RT2, SN1 diff --git a/lib/linalg/dlaisnan.f b/lib/linalg/dlaisnan.f index 58595c5c33097e97a0fe8037eeaf1b5071393570..c2e87d88a005bc78c9f25a80a06afc46be6921fb 100644 --- a/lib/linalg/dlaisnan.f +++ b/lib/linalg/dlaisnan.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAISNAN + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAISNAN + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * LOGICAL FUNCTION DLAISNAN( DIN1, DIN2 ) -* +* * .. Scalar Arguments .. -* DOUBLE PRECISION DIN1, DIN2 +* DOUBLE PRECISION, INTENT(IN) :: DIN1, DIN2 * .. -* +* * *> \par Purpose: * ============= @@ -62,25 +62,25 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== LOGICAL FUNCTION DLAISNAN( DIN1, DIN2 ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. - DOUBLE PRECISION DIN1, DIN2 + DOUBLE PRECISION, INTENT(IN) :: DIN1, DIN2 * .. * * ===================================================================== diff --git a/lib/linalg/dlals0.f b/lib/linalg/dlals0.f new file mode 100644 index 0000000000000000000000000000000000000000..d4cff166d6ab717bf26b5573357731cdce5bf985 --- /dev/null +++ b/lib/linalg/dlals0.f @@ -0,0 +1,499 @@ +*> \brief \b DLALS0 applies back multiplying factors in solving the least squares problem using divide and conquer SVD approach. Used by sgelsd. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLALS0 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLALS0( ICOMPQ, NL, NR, SQRE, NRHS, B, LDB, BX, LDBX, +* PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, +* POLES, DIFL, DIFR, Z, K, C, S, WORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER GIVPTR, ICOMPQ, INFO, K, LDB, LDBX, LDGCOL, +* $ LDGNUM, NL, NR, NRHS, SQRE +* DOUBLE PRECISION C, S +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( LDGCOL, * ), PERM( * ) +* DOUBLE PRECISION B( LDB, * ), BX( LDBX, * ), DIFL( * ), +* $ DIFR( LDGNUM, * ), GIVNUM( LDGNUM, * ), +* $ POLES( LDGNUM, * ), WORK( * ), Z( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLALS0 applies back the multiplying factors of either the left or the +*> right singular vector matrix of a diagonal matrix appended by a row +*> to the right hand side matrix B in solving the least squares problem +*> using the divide-and-conquer SVD approach. +*> +*> For the left singular vector matrix, three types of orthogonal +*> matrices are involved: +*> +*> (1L) Givens rotations: the number of such rotations is GIVPTR; the +*> pairs of columns/rows they were applied to are stored in GIVCOL; +*> and the C- and S-values of these rotations are stored in GIVNUM. +*> +*> (2L) Permutation. The (NL+1)-st row of B is to be moved to the first +*> row, and for J=2:N, PERM(J)-th row of B is to be moved to the +*> J-th row. +*> +*> (3L) The left singular vector matrix of the remaining matrix. +*> +*> For the right singular vector matrix, four types of orthogonal +*> matrices are involved: +*> +*> (1R) The right singular vector matrix of the remaining matrix. +*> +*> (2R) If SQRE = 1, one extra Givens rotation to generate the right +*> null space. +*> +*> (3R) The inverse transformation of (2L). +*> +*> (4R) The inverse transformation of (1L). +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether singular vectors are to be computed in +*> factored form: +*> = 0: Left singular vector matrix. +*> = 1: Right singular vector matrix. +*> \endverbatim +*> +*> \param[in] NL +*> \verbatim +*> NL is INTEGER +*> The row dimension of the upper block. NL >= 1. +*> \endverbatim +*> +*> \param[in] NR +*> \verbatim +*> NR is INTEGER +*> The row dimension of the lower block. NR >= 1. +*> \endverbatim +*> +*> \param[in] SQRE +*> \verbatim +*> SQRE is INTEGER +*> = 0: the lower block is an NR-by-NR square matrix. +*> = 1: the lower block is an NR-by-(NR+1) rectangular matrix. +*> +*> The bidiagonal matrix has row dimension N = NL + NR + 1, +*> and column dimension M = N + SQRE. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of columns of B and BX. NRHS must be at least 1. +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension ( LDB, NRHS ) +*> On input, B contains the right hand sides of the least +*> squares problem in rows 1 through M. On output, B contains +*> the solution X in rows 1 through N. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of B. LDB must be at least +*> max(1,MAX( M, N ) ). +*> \endverbatim +*> +*> \param[out] BX +*> \verbatim +*> BX is DOUBLE PRECISION array, dimension ( LDBX, NRHS ) +*> \endverbatim +*> +*> \param[in] LDBX +*> \verbatim +*> LDBX is INTEGER +*> The leading dimension of BX. +*> \endverbatim +*> +*> \param[in] PERM +*> \verbatim +*> PERM is INTEGER array, dimension ( N ) +*> The permutations (from deflation and sorting) applied +*> to the two blocks. +*> \endverbatim +*> +*> \param[in] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER +*> The number of Givens rotations which took place in this +*> subproblem. +*> \endverbatim +*> +*> \param[in] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension ( LDGCOL, 2 ) +*> Each pair of numbers indicates a pair of rows/columns +*> involved in a Givens rotation. +*> \endverbatim +*> +*> \param[in] LDGCOL +*> \verbatim +*> LDGCOL is INTEGER +*> The leading dimension of GIVCOL, must be at least N. +*> \endverbatim +*> +*> \param[in] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ) +*> Each number indicates the C or S value used in the +*> corresponding Givens rotation. +*> \endverbatim +*> +*> \param[in] LDGNUM +*> \verbatim +*> LDGNUM is INTEGER +*> The leading dimension of arrays DIFR, POLES and +*> GIVNUM, must be at least K. +*> \endverbatim +*> +*> \param[in] POLES +*> \verbatim +*> POLES is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ) +*> On entry, POLES(1:K, 1) contains the new singular +*> values obtained from solving the secular equation, and +*> POLES(1:K, 2) is an array containing the poles in the secular +*> equation. +*> \endverbatim +*> +*> \param[in] DIFL +*> \verbatim +*> DIFL is DOUBLE PRECISION array, dimension ( K ). +*> On entry, DIFL(I) is the distance between I-th updated +*> (undeflated) singular value and the I-th (undeflated) old +*> singular value. +*> \endverbatim +*> +*> \param[in] DIFR +*> \verbatim +*> DIFR is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ). +*> On entry, DIFR(I, 1) contains the distances between I-th +*> updated (undeflated) singular value and the I+1-th +*> (undeflated) old singular value. And DIFR(I, 2) is the +*> normalizing factor for the I-th right singular vector. +*> \endverbatim +*> +*> \param[in] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( K ) +*> Contain the components of the deflation-adjusted updating row +*> vector. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> Contains the dimension of the non-deflated matrix, +*> This is the order of the related secular equation. 1 <= K <=N. +*> \endverbatim +*> +*> \param[in] C +*> \verbatim +*> C is DOUBLE PRECISION +*> C contains garbage if SQRE =0 and the C-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[in] S +*> \verbatim +*> S is DOUBLE PRECISION +*> S contains garbage if SQRE =0 and the S-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension ( K ) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup doubleOTHERcomputational +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Ren-Cang Li, Computer Science Division, University of +*> California at Berkeley, USA \n +*> Osni Marques, LBNL/NERSC, USA \n +* +* ===================================================================== + SUBROUTINE DLALS0( ICOMPQ, NL, NR, SQRE, NRHS, B, LDB, BX, LDBX, + $ PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, + $ POLES, DIFL, DIFR, Z, K, C, S, WORK, INFO ) +* +* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER GIVPTR, ICOMPQ, INFO, K, LDB, LDBX, LDGCOL, + $ LDGNUM, NL, NR, NRHS, SQRE + DOUBLE PRECISION C, S +* .. +* .. Array Arguments .. + INTEGER GIVCOL( LDGCOL, * ), PERM( * ) + DOUBLE PRECISION B( LDB, * ), BX( LDBX, * ), DIFL( * ), + $ DIFR( LDGNUM, * ), GIVNUM( LDGNUM, * ), + $ POLES( LDGNUM, * ), WORK( * ), Z( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO, NEGONE + PARAMETER ( ONE = 1.0D0, ZERO = 0.0D0, NEGONE = -1.0D0 ) +* .. +* .. Local Scalars .. + INTEGER I, J, M, N, NLP1 + DOUBLE PRECISION DIFLJ, DIFRJ, DJ, DSIGJ, DSIGJP, TEMP +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DGEMV, DLACPY, DLASCL, DROT, DSCAL, + $ XERBLA +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMC3, DNRM2 + EXTERNAL DLAMC3, DNRM2 +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + N = NL + NR + 1 +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( NL.LT.1 ) THEN + INFO = -2 + ELSE IF( NR.LT.1 ) THEN + INFO = -3 + ELSE IF( ( SQRE.LT.0 ) .OR. ( SQRE.GT.1 ) ) THEN + INFO = -4 + ELSE IF( NRHS.LT.1 ) THEN + INFO = -5 + ELSE IF( LDB.LT.N ) THEN + INFO = -7 + ELSE IF( LDBX.LT.N ) THEN + INFO = -9 + ELSE IF( GIVPTR.LT.0 ) THEN + INFO = -11 + ELSE IF( LDGCOL.LT.N ) THEN + INFO = -13 + ELSE IF( LDGNUM.LT.N ) THEN + INFO = -15 + ELSE IF( K.LT.1 ) THEN + INFO = -20 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLALS0', -INFO ) + RETURN + END IF +* + M = N + SQRE + NLP1 = NL + 1 +* + IF( ICOMPQ.EQ.0 ) THEN +* +* Apply back orthogonal transformations from the left. +* +* Step (1L): apply back the Givens rotations performed. +* + DO 10 I = 1, GIVPTR + CALL DROT( NRHS, B( GIVCOL( I, 2 ), 1 ), LDB, + $ B( GIVCOL( I, 1 ), 1 ), LDB, GIVNUM( I, 2 ), + $ GIVNUM( I, 1 ) ) + 10 CONTINUE +* +* Step (2L): permute rows of B. +* + CALL DCOPY( NRHS, B( NLP1, 1 ), LDB, BX( 1, 1 ), LDBX ) + DO 20 I = 2, N + CALL DCOPY( NRHS, B( PERM( I ), 1 ), LDB, BX( I, 1 ), LDBX ) + 20 CONTINUE +* +* Step (3L): apply the inverse of the left singular vector +* matrix to BX. +* + IF( K.EQ.1 ) THEN + CALL DCOPY( NRHS, BX, LDBX, B, LDB ) + IF( Z( 1 ).LT.ZERO ) THEN + CALL DSCAL( NRHS, NEGONE, B, LDB ) + END IF + ELSE + DO 50 J = 1, K + DIFLJ = DIFL( J ) + DJ = POLES( J, 1 ) + DSIGJ = -POLES( J, 2 ) + IF( J.LT.K ) THEN + DIFRJ = -DIFR( J, 1 ) + DSIGJP = -POLES( J+1, 2 ) + END IF + IF( ( Z( J ).EQ.ZERO ) .OR. ( POLES( J, 2 ).EQ.ZERO ) ) + $ THEN + WORK( J ) = ZERO + ELSE + WORK( J ) = -POLES( J, 2 )*Z( J ) / DIFLJ / + $ ( POLES( J, 2 )+DJ ) + END IF + DO 30 I = 1, J - 1 + IF( ( Z( I ).EQ.ZERO ) .OR. + $ ( POLES( I, 2 ).EQ.ZERO ) ) THEN + WORK( I ) = ZERO + ELSE + WORK( I ) = POLES( I, 2 )*Z( I ) / + $ ( DLAMC3( POLES( I, 2 ), DSIGJ )- + $ DIFLJ ) / ( POLES( I, 2 )+DJ ) + END IF + 30 CONTINUE + DO 40 I = J + 1, K + IF( ( Z( I ).EQ.ZERO ) .OR. + $ ( POLES( I, 2 ).EQ.ZERO ) ) THEN + WORK( I ) = ZERO + ELSE + WORK( I ) = POLES( I, 2 )*Z( I ) / + $ ( DLAMC3( POLES( I, 2 ), DSIGJP )+ + $ DIFRJ ) / ( POLES( I, 2 )+DJ ) + END IF + 40 CONTINUE + WORK( 1 ) = NEGONE + TEMP = DNRM2( K, WORK, 1 ) + CALL DGEMV( 'T', K, NRHS, ONE, BX, LDBX, WORK, 1, ZERO, + $ B( J, 1 ), LDB ) + CALL DLASCL( 'G', 0, 0, TEMP, ONE, 1, NRHS, B( J, 1 ), + $ LDB, INFO ) + 50 CONTINUE + END IF +* +* Move the deflated rows of BX to B also. +* + IF( K.LT.MAX( M, N ) ) + $ CALL DLACPY( 'A', N-K, NRHS, BX( K+1, 1 ), LDBX, + $ B( K+1, 1 ), LDB ) + ELSE +* +* Apply back the right orthogonal transformations. +* +* Step (1R): apply back the new right singular vector matrix +* to B. +* + IF( K.EQ.1 ) THEN + CALL DCOPY( NRHS, B, LDB, BX, LDBX ) + ELSE + DO 80 J = 1, K + DSIGJ = POLES( J, 2 ) + IF( Z( J ).EQ.ZERO ) THEN + WORK( J ) = ZERO + ELSE + WORK( J ) = -Z( J ) / DIFL( J ) / + $ ( DSIGJ+POLES( J, 1 ) ) / DIFR( J, 2 ) + END IF + DO 60 I = 1, J - 1 + IF( Z( J ).EQ.ZERO ) THEN + WORK( I ) = ZERO + ELSE + WORK( I ) = Z( J ) / ( DLAMC3( DSIGJ, -POLES( I+1, + $ 2 ) )-DIFR( I, 1 ) ) / + $ ( DSIGJ+POLES( I, 1 ) ) / DIFR( I, 2 ) + END IF + 60 CONTINUE + DO 70 I = J + 1, K + IF( Z( J ).EQ.ZERO ) THEN + WORK( I ) = ZERO + ELSE + WORK( I ) = Z( J ) / ( DLAMC3( DSIGJ, -POLES( I, + $ 2 ) )-DIFL( I ) ) / + $ ( DSIGJ+POLES( I, 1 ) ) / DIFR( I, 2 ) + END IF + 70 CONTINUE + CALL DGEMV( 'T', K, NRHS, ONE, B, LDB, WORK, 1, ZERO, + $ BX( J, 1 ), LDBX ) + 80 CONTINUE + END IF +* +* Step (2R): if SQRE = 1, apply back the rotation that is +* related to the right null space of the subproblem. +* + IF( SQRE.EQ.1 ) THEN + CALL DCOPY( NRHS, B( M, 1 ), LDB, BX( M, 1 ), LDBX ) + CALL DROT( NRHS, BX( 1, 1 ), LDBX, BX( M, 1 ), LDBX, C, S ) + END IF + IF( K.LT.MAX( M, N ) ) + $ CALL DLACPY( 'A', N-K, NRHS, B( K+1, 1 ), LDB, BX( K+1, 1 ), + $ LDBX ) +* +* Step (3R): permute rows of B. +* + CALL DCOPY( NRHS, BX( 1, 1 ), LDBX, B( NLP1, 1 ), LDB ) + IF( SQRE.EQ.1 ) THEN + CALL DCOPY( NRHS, BX( M, 1 ), LDBX, B( M, 1 ), LDB ) + END IF + DO 90 I = 2, N + CALL DCOPY( NRHS, BX( I, 1 ), LDBX, B( PERM( I ), 1 ), LDB ) + 90 CONTINUE +* +* Step (4R): apply back the Givens rotations performed. +* + DO 100 I = GIVPTR, 1, -1 + CALL DROT( NRHS, B( GIVCOL( I, 2 ), 1 ), LDB, + $ B( GIVCOL( I, 1 ), 1 ), LDB, GIVNUM( I, 2 ), + $ -GIVNUM( I, 1 ) ) + 100 CONTINUE + END IF +* + RETURN +* +* End of DLALS0 +* + END diff --git a/lib/linalg/dlalsa.f b/lib/linalg/dlalsa.f new file mode 100644 index 0000000000000000000000000000000000000000..b643f11c0b65a4b9aacc39ed9a768be2979dc72f --- /dev/null +++ b/lib/linalg/dlalsa.f @@ -0,0 +1,493 @@ +*> \brief \b DLALSA computes the SVD of the coefficient matrix in compact form. Used by sgelsd. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLALSA + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLALSA( ICOMPQ, SMLSIZ, N, NRHS, B, LDB, BX, LDBX, U, +* LDU, VT, K, DIFL, DIFR, Z, POLES, GIVPTR, +* GIVCOL, LDGCOL, PERM, GIVNUM, C, S, WORK, +* IWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER ICOMPQ, INFO, LDB, LDBX, LDGCOL, LDU, N, NRHS, +* $ SMLSIZ +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( LDGCOL, * ), GIVPTR( * ), IWORK( * ), +* $ K( * ), PERM( LDGCOL, * ) +* DOUBLE PRECISION B( LDB, * ), BX( LDBX, * ), C( * ), +* $ DIFL( LDU, * ), DIFR( LDU, * ), +* $ GIVNUM( LDU, * ), POLES( LDU, * ), S( * ), +* $ U( LDU, * ), VT( LDU, * ), WORK( * ), +* $ Z( LDU, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLALSA is an itermediate step in solving the least squares problem +*> by computing the SVD of the coefficient matrix in compact form (The +*> singular vectors are computed as products of simple orthorgonal +*> matrices.). +*> +*> If ICOMPQ = 0, DLALSA applies the inverse of the left singular vector +*> matrix of an upper bidiagonal matrix to the right hand side; and if +*> ICOMPQ = 1, DLALSA applies the right singular vector matrix to the +*> right hand side. The singular vector matrices were generated in +*> compact form by DLALSA. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether the left or the right singular vector +*> matrix is involved. +*> = 0: Left singular vector matrix +*> = 1: Right singular vector matrix +*> \endverbatim +*> +*> \param[in] SMLSIZ +*> \verbatim +*> SMLSIZ is INTEGER +*> The maximum size of the subproblems at the bottom of the +*> computation tree. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The row and column dimensions of the upper bidiagonal matrix. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of columns of B and BX. NRHS must be at least 1. +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension ( LDB, NRHS ) +*> On input, B contains the right hand sides of the least +*> squares problem in rows 1 through M. +*> On output, B contains the solution X in rows 1 through N. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of B in the calling subprogram. +*> LDB must be at least max(1,MAX( M, N ) ). +*> \endverbatim +*> +*> \param[out] BX +*> \verbatim +*> BX is DOUBLE PRECISION array, dimension ( LDBX, NRHS ) +*> On exit, the result of applying the left or right singular +*> vector matrix to B. +*> \endverbatim +*> +*> \param[in] LDBX +*> \verbatim +*> LDBX is INTEGER +*> The leading dimension of BX. +*> \endverbatim +*> +*> \param[in] U +*> \verbatim +*> U is DOUBLE PRECISION array, dimension ( LDU, SMLSIZ ). +*> On entry, U contains the left singular vector matrices of all +*> subproblems at the bottom level. +*> \endverbatim +*> +*> \param[in] LDU +*> \verbatim +*> LDU is INTEGER, LDU = > N. +*> The leading dimension of arrays U, VT, DIFL, DIFR, +*> POLES, GIVNUM, and Z. +*> \endverbatim +*> +*> \param[in] VT +*> \verbatim +*> VT is DOUBLE PRECISION array, dimension ( LDU, SMLSIZ+1 ). +*> On entry, VT**T contains the right singular vector matrices of +*> all subproblems at the bottom level. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER array, dimension ( N ). +*> \endverbatim +*> +*> \param[in] DIFL +*> \verbatim +*> DIFL is DOUBLE PRECISION array, dimension ( LDU, NLVL ). +*> where NLVL = INT(log_2 (N/(SMLSIZ+1))) + 1. +*> \endverbatim +*> +*> \param[in] DIFR +*> \verbatim +*> DIFR is DOUBLE PRECISION array, dimension ( LDU, 2 * NLVL ). +*> On entry, DIFL(*, I) and DIFR(*, 2 * I -1) record +*> distances between singular values on the I-th level and +*> singular values on the (I -1)-th level, and DIFR(*, 2 * I) +*> record the normalizing factors of the right singular vectors +*> matrices of subproblems on I-th level. +*> \endverbatim +*> +*> \param[in] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( LDU, NLVL ). +*> On entry, Z(1, I) contains the components of the deflation- +*> adjusted updating row vector for subproblems on the I-th +*> level. +*> \endverbatim +*> +*> \param[in] POLES +*> \verbatim +*> POLES is DOUBLE PRECISION array, dimension ( LDU, 2 * NLVL ). +*> On entry, POLES(*, 2 * I -1: 2 * I) contains the new and old +*> singular values involved in the secular equations on the I-th +*> level. +*> \endverbatim +*> +*> \param[in] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER array, dimension ( N ). +*> On entry, GIVPTR( I ) records the number of Givens +*> rotations performed on the I-th problem on the computation +*> tree. +*> \endverbatim +*> +*> \param[in] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension ( LDGCOL, 2 * NLVL ). +*> On entry, for each I, GIVCOL(*, 2 * I - 1: 2 * I) records the +*> locations of Givens rotations performed on the I-th level on +*> the computation tree. +*> \endverbatim +*> +*> \param[in] LDGCOL +*> \verbatim +*> LDGCOL is INTEGER, LDGCOL = > N. +*> The leading dimension of arrays GIVCOL and PERM. +*> \endverbatim +*> +*> \param[in] PERM +*> \verbatim +*> PERM is INTEGER array, dimension ( LDGCOL, NLVL ). +*> On entry, PERM(*, I) records permutations done on the I-th +*> level of the computation tree. +*> \endverbatim +*> +*> \param[in] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension ( LDU, 2 * NLVL ). +*> On entry, GIVNUM(*, 2 *I -1 : 2 * I) records the C- and S- +*> values of Givens rotations performed on the I-th level on the +*> computation tree. +*> \endverbatim +*> +*> \param[in] C +*> \verbatim +*> C is DOUBLE PRECISION array, dimension ( N ). +*> On entry, if the I-th subproblem is not square, +*> C( I ) contains the C-value of a Givens rotation related to +*> the right null space of the I-th subproblem. +*> \endverbatim +*> +*> \param[in] S +*> \verbatim +*> S is DOUBLE PRECISION array, dimension ( N ). +*> On entry, if the I-th subproblem is not square, +*> S( I ) contains the S-value of a Givens rotation related to +*> the right null space of the I-th subproblem. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension (N) +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (3*N) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2017 +* +*> \ingroup doubleOTHERcomputational +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Ren-Cang Li, Computer Science Division, University of +*> California at Berkeley, USA \n +*> Osni Marques, LBNL/NERSC, USA \n +* +* ===================================================================== + SUBROUTINE DLALSA( ICOMPQ, SMLSIZ, N, NRHS, B, LDB, BX, LDBX, U, + $ LDU, VT, K, DIFL, DIFR, Z, POLES, GIVPTR, + $ GIVCOL, LDGCOL, PERM, GIVNUM, C, S, WORK, + $ IWORK, INFO ) +* +* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2017 +* +* .. Scalar Arguments .. + INTEGER ICOMPQ, INFO, LDB, LDBX, LDGCOL, LDU, N, NRHS, + $ SMLSIZ +* .. +* .. Array Arguments .. + INTEGER GIVCOL( LDGCOL, * ), GIVPTR( * ), IWORK( * ), + $ K( * ), PERM( LDGCOL, * ) + DOUBLE PRECISION B( LDB, * ), BX( LDBX, * ), C( * ), + $ DIFL( LDU, * ), DIFR( LDU, * ), + $ GIVNUM( LDU, * ), POLES( LDU, * ), S( * ), + $ U( LDU, * ), VT( LDU, * ), WORK( * ), + $ Z( LDU, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE + PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0 ) +* .. +* .. Local Scalars .. + INTEGER I, I1, IC, IM1, INODE, J, LF, LL, LVL, LVL2, + $ ND, NDB1, NDIML, NDIMR, NL, NLF, NLP1, NLVL, + $ NR, NRF, NRP1, SQRE +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DGEMM, DLALS0, DLASDT, XERBLA +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( SMLSIZ.LT.3 ) THEN + INFO = -2 + ELSE IF( N.LT.SMLSIZ ) THEN + INFO = -3 + ELSE IF( NRHS.LT.1 ) THEN + INFO = -4 + ELSE IF( LDB.LT.N ) THEN + INFO = -6 + ELSE IF( LDBX.LT.N ) THEN + INFO = -8 + ELSE IF( LDU.LT.N ) THEN + INFO = -10 + ELSE IF( LDGCOL.LT.N ) THEN + INFO = -19 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLALSA', -INFO ) + RETURN + END IF +* +* Book-keeping and setting up the computation tree. +* + INODE = 1 + NDIML = INODE + N + NDIMR = NDIML + N +* + CALL DLASDT( N, NLVL, ND, IWORK( INODE ), IWORK( NDIML ), + $ IWORK( NDIMR ), SMLSIZ ) +* +* The following code applies back the left singular vector factors. +* For applying back the right singular vector factors, go to 50. +* + IF( ICOMPQ.EQ.1 ) THEN + GO TO 50 + END IF +* +* The nodes on the bottom level of the tree were solved +* by DLASDQ. The corresponding left and right singular vector +* matrices are in explicit form. First apply back the left +* singular vector matrices. +* + NDB1 = ( ND+1 ) / 2 + DO 10 I = NDB1, ND +* +* IC : center row of each node +* NL : number of rows of left subproblem +* NR : number of rows of right subproblem +* NLF: starting row of the left subproblem +* NRF: starting row of the right subproblem +* + I1 = I - 1 + IC = IWORK( INODE+I1 ) + NL = IWORK( NDIML+I1 ) + NR = IWORK( NDIMR+I1 ) + NLF = IC - NL + NRF = IC + 1 + CALL DGEMM( 'T', 'N', NL, NRHS, NL, ONE, U( NLF, 1 ), LDU, + $ B( NLF, 1 ), LDB, ZERO, BX( NLF, 1 ), LDBX ) + CALL DGEMM( 'T', 'N', NR, NRHS, NR, ONE, U( NRF, 1 ), LDU, + $ B( NRF, 1 ), LDB, ZERO, BX( NRF, 1 ), LDBX ) + 10 CONTINUE +* +* Next copy the rows of B that correspond to unchanged rows +* in the bidiagonal matrix to BX. +* + DO 20 I = 1, ND + IC = IWORK( INODE+I-1 ) + CALL DCOPY( NRHS, B( IC, 1 ), LDB, BX( IC, 1 ), LDBX ) + 20 CONTINUE +* +* Finally go through the left singular vector matrices of all +* the other subproblems bottom-up on the tree. +* + J = 2**NLVL + SQRE = 0 +* + DO 40 LVL = NLVL, 1, -1 + LVL2 = 2*LVL - 1 +* +* find the first node LF and last node LL on +* the current level LVL +* + IF( LVL.EQ.1 ) THEN + LF = 1 + LL = 1 + ELSE + LF = 2**( LVL-1 ) + LL = 2*LF - 1 + END IF + DO 30 I = LF, LL + IM1 = I - 1 + IC = IWORK( INODE+IM1 ) + NL = IWORK( NDIML+IM1 ) + NR = IWORK( NDIMR+IM1 ) + NLF = IC - NL + NRF = IC + 1 + J = J - 1 + CALL DLALS0( ICOMPQ, NL, NR, SQRE, NRHS, BX( NLF, 1 ), LDBX, + $ B( NLF, 1 ), LDB, PERM( NLF, LVL ), + $ GIVPTR( J ), GIVCOL( NLF, LVL2 ), LDGCOL, + $ GIVNUM( NLF, LVL2 ), LDU, POLES( NLF, LVL2 ), + $ DIFL( NLF, LVL ), DIFR( NLF, LVL2 ), + $ Z( NLF, LVL ), K( J ), C( J ), S( J ), WORK, + $ INFO ) + 30 CONTINUE + 40 CONTINUE + GO TO 90 +* +* ICOMPQ = 1: applying back the right singular vector factors. +* + 50 CONTINUE +* +* First now go through the right singular vector matrices of all +* the tree nodes top-down. +* + J = 0 + DO 70 LVL = 1, NLVL + LVL2 = 2*LVL - 1 +* +* Find the first node LF and last node LL on +* the current level LVL. +* + IF( LVL.EQ.1 ) THEN + LF = 1 + LL = 1 + ELSE + LF = 2**( LVL-1 ) + LL = 2*LF - 1 + END IF + DO 60 I = LL, LF, -1 + IM1 = I - 1 + IC = IWORK( INODE+IM1 ) + NL = IWORK( NDIML+IM1 ) + NR = IWORK( NDIMR+IM1 ) + NLF = IC - NL + NRF = IC + 1 + IF( I.EQ.LL ) THEN + SQRE = 0 + ELSE + SQRE = 1 + END IF + J = J + 1 + CALL DLALS0( ICOMPQ, NL, NR, SQRE, NRHS, B( NLF, 1 ), LDB, + $ BX( NLF, 1 ), LDBX, PERM( NLF, LVL ), + $ GIVPTR( J ), GIVCOL( NLF, LVL2 ), LDGCOL, + $ GIVNUM( NLF, LVL2 ), LDU, POLES( NLF, LVL2 ), + $ DIFL( NLF, LVL ), DIFR( NLF, LVL2 ), + $ Z( NLF, LVL ), K( J ), C( J ), S( J ), WORK, + $ INFO ) + 60 CONTINUE + 70 CONTINUE +* +* The nodes on the bottom level of the tree were solved +* by DLASDQ. The corresponding right singular vector +* matrices are in explicit form. Apply them back. +* + NDB1 = ( ND+1 ) / 2 + DO 80 I = NDB1, ND + I1 = I - 1 + IC = IWORK( INODE+I1 ) + NL = IWORK( NDIML+I1 ) + NR = IWORK( NDIMR+I1 ) + NLP1 = NL + 1 + IF( I.EQ.ND ) THEN + NRP1 = NR + ELSE + NRP1 = NR + 1 + END IF + NLF = IC - NL + NRF = IC + 1 + CALL DGEMM( 'T', 'N', NLP1, NRHS, NLP1, ONE, VT( NLF, 1 ), LDU, + $ B( NLF, 1 ), LDB, ZERO, BX( NLF, 1 ), LDBX ) + CALL DGEMM( 'T', 'N', NRP1, NRHS, NRP1, ONE, VT( NRF, 1 ), LDU, + $ B( NRF, 1 ), LDB, ZERO, BX( NRF, 1 ), LDBX ) + 80 CONTINUE +* + 90 CONTINUE +* + RETURN +* +* End of DLALSA +* + END diff --git a/lib/linalg/dlalsd.f b/lib/linalg/dlalsd.f new file mode 100644 index 0000000000000000000000000000000000000000..510e0455a6a922ab462d57bd12024aa9bb4a9188 --- /dev/null +++ b/lib/linalg/dlalsd.f @@ -0,0 +1,523 @@ +*> \brief \b DLALSD uses the singular value decomposition of A to solve the least squares problem. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLALSD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLALSD( UPLO, SMLSIZ, N, NRHS, D, E, B, LDB, RCOND, +* RANK, WORK, IWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER INFO, LDB, N, NRHS, RANK, SMLSIZ +* DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. +* INTEGER IWORK( * ) +* DOUBLE PRECISION B( LDB, * ), D( * ), E( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLALSD uses the singular value decomposition of A to solve the least +*> squares problem of finding X to minimize the Euclidean norm of each +*> column of A*X-B, where A is N-by-N upper bidiagonal, and X and B +*> are N-by-NRHS. The solution X overwrites B. +*> +*> The singular values of A smaller than RCOND times the largest +*> singular value are treated as zero in solving the least squares +*> problem; in this case a minimum norm solution is returned. +*> The actual singular values are returned in D in ascending order. +*> +*> This code makes very mild assumptions about floating point +*> arithmetic. It will work on machines with a guard digit in +*> add/subtract, or on those binary machines without guard digits +*> which subtract like the Cray XMP, Cray YMP, Cray C 90, or Cray 2. +*> It could conceivably fail on hexadecimal or decimal machines +*> without guard digits, but we know of none. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': D and E define an upper bidiagonal matrix. +*> = 'L': D and E define a lower bidiagonal matrix. +*> \endverbatim +*> +*> \param[in] SMLSIZ +*> \verbatim +*> SMLSIZ is INTEGER +*> The maximum size of the subproblems at the bottom of the +*> computation tree. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The dimension of the bidiagonal matrix. N >= 0. +*> \endverbatim +*> +*> \param[in] NRHS +*> \verbatim +*> NRHS is INTEGER +*> The number of columns of B. NRHS must be at least 1. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry D contains the main diagonal of the bidiagonal +*> matrix. On exit, if INFO = 0, D contains its singular values. +*> \endverbatim +*> +*> \param[in,out] E +*> \verbatim +*> E is DOUBLE PRECISION array, dimension (N-1) +*> Contains the super-diagonal entries of the bidiagonal matrix. +*> On exit, E has been destroyed. +*> \endverbatim +*> +*> \param[in,out] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB,NRHS) +*> On input, B contains the right hand sides of the least +*> squares problem. On output, B contains the solution X. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of B in the calling subprogram. +*> LDB must be at least max(1,N). +*> \endverbatim +*> +*> \param[in] RCOND +*> \verbatim +*> RCOND is DOUBLE PRECISION +*> The singular values of A less than or equal to RCOND times +*> the largest singular value are treated as zero in solving +*> the least squares problem. If RCOND is negative, +*> machine precision is used instead. +*> For example, if diag(S)*X=B were the least squares problem, +*> where diag(S) is a diagonal matrix of singular values, the +*> solution would be X(i) = B(i) / S(i) if S(i) is greater than +*> RCOND*max(S), and X(i) = 0 if S(i) is less than or equal to +*> RCOND*max(S). +*> \endverbatim +*> +*> \param[out] RANK +*> \verbatim +*> RANK is INTEGER +*> The number of singular values of A greater than RCOND times +*> the largest singular value. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension at least +*> (9*N + 2*N*SMLSIZ + 8*N*NLVL + N*NRHS + (SMLSIZ+1)**2), +*> where NLVL = max(0, INT(log_2 (N/(SMLSIZ+1))) + 1). +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension at least +*> (3*N*NLVL + 11*N) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: The algorithm failed to compute a singular value while +*> working on the submatrix lying in rows and columns +*> INFO/(N+1) through MOD(INFO,N+1). +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup doubleOTHERcomputational +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Ren-Cang Li, Computer Science Division, University of +*> California at Berkeley, USA \n +*> Osni Marques, LBNL/NERSC, USA \n +* +* ===================================================================== + SUBROUTINE DLALSD( UPLO, SMLSIZ, N, NRHS, D, E, B, LDB, RCOND, + $ RANK, WORK, IWORK, INFO ) +* +* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDB, N, NRHS, RANK, SMLSIZ + DOUBLE PRECISION RCOND +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION B( LDB, * ), D( * ), E( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE, TWO + PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0, TWO = 2.0D0 ) +* .. +* .. Local Scalars .. + INTEGER BX, BXST, C, DIFL, DIFR, GIVCOL, GIVNUM, + $ GIVPTR, I, ICMPQ1, ICMPQ2, IWK, J, K, NLVL, + $ NM1, NSIZE, NSUB, NWORK, PERM, POLES, S, SIZEI, + $ SMLSZP, SQRE, ST, ST1, U, VT, Z + DOUBLE PRECISION CS, EPS, ORGNRM, R, RCND, SN, TOL +* .. +* .. External Functions .. + INTEGER IDAMAX + DOUBLE PRECISION DLAMCH, DLANST + EXTERNAL IDAMAX, DLAMCH, DLANST +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DGEMM, DLACPY, DLALSA, DLARTG, DLASCL, + $ DLASDA, DLASDQ, DLASET, DLASRT, DROT, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, DBLE, INT, LOG, SIGN +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* + IF( N.LT.0 ) THEN + INFO = -3 + ELSE IF( NRHS.LT.1 ) THEN + INFO = -4 + ELSE IF( ( LDB.LT.1 ) .OR. ( LDB.LT.N ) ) THEN + INFO = -8 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLALSD', -INFO ) + RETURN + END IF +* + EPS = DLAMCH( 'Epsilon' ) +* +* Set up the tolerance. +* + IF( ( RCOND.LE.ZERO ) .OR. ( RCOND.GE.ONE ) ) THEN + RCND = EPS + ELSE + RCND = RCOND + END IF +* + RANK = 0 +* +* Quick return if possible. +* + IF( N.EQ.0 ) THEN + RETURN + ELSE IF( N.EQ.1 ) THEN + IF( D( 1 ).EQ.ZERO ) THEN + CALL DLASET( 'A', 1, NRHS, ZERO, ZERO, B, LDB ) + ELSE + RANK = 1 + CALL DLASCL( 'G', 0, 0, D( 1 ), ONE, 1, NRHS, B, LDB, INFO ) + D( 1 ) = ABS( D( 1 ) ) + END IF + RETURN + END IF +* +* Rotate the matrix if it is lower bidiagonal. +* + IF( UPLO.EQ.'L' ) THEN + DO 10 I = 1, N - 1 + CALL DLARTG( D( I ), E( I ), CS, SN, R ) + D( I ) = R + E( I ) = SN*D( I+1 ) + D( I+1 ) = CS*D( I+1 ) + IF( NRHS.EQ.1 ) THEN + CALL DROT( 1, B( I, 1 ), 1, B( I+1, 1 ), 1, CS, SN ) + ELSE + WORK( I*2-1 ) = CS + WORK( I*2 ) = SN + END IF + 10 CONTINUE + IF( NRHS.GT.1 ) THEN + DO 30 I = 1, NRHS + DO 20 J = 1, N - 1 + CS = WORK( J*2-1 ) + SN = WORK( J*2 ) + CALL DROT( 1, B( J, I ), 1, B( J+1, I ), 1, CS, SN ) + 20 CONTINUE + 30 CONTINUE + END IF + END IF +* +* Scale. +* + NM1 = N - 1 + ORGNRM = DLANST( 'M', N, D, E ) + IF( ORGNRM.EQ.ZERO ) THEN + CALL DLASET( 'A', N, NRHS, ZERO, ZERO, B, LDB ) + RETURN + END IF +* + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, N, 1, D, N, INFO ) + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, NM1, 1, E, NM1, INFO ) +* +* If N is smaller than the minimum divide size SMLSIZ, then solve +* the problem with another solver. +* + IF( N.LE.SMLSIZ ) THEN + NWORK = 1 + N*N + CALL DLASET( 'A', N, N, ZERO, ONE, WORK, N ) + CALL DLASDQ( 'U', 0, N, N, 0, NRHS, D, E, WORK, N, WORK, N, B, + $ LDB, WORK( NWORK ), INFO ) + IF( INFO.NE.0 ) THEN + RETURN + END IF + TOL = RCND*ABS( D( IDAMAX( N, D, 1 ) ) ) + DO 40 I = 1, N + IF( D( I ).LE.TOL ) THEN + CALL DLASET( 'A', 1, NRHS, ZERO, ZERO, B( I, 1 ), LDB ) + ELSE + CALL DLASCL( 'G', 0, 0, D( I ), ONE, 1, NRHS, B( I, 1 ), + $ LDB, INFO ) + RANK = RANK + 1 + END IF + 40 CONTINUE + CALL DGEMM( 'T', 'N', N, NRHS, N, ONE, WORK, N, B, LDB, ZERO, + $ WORK( NWORK ), N ) + CALL DLACPY( 'A', N, NRHS, WORK( NWORK ), N, B, LDB ) +* +* Unscale. +* + CALL DLASCL( 'G', 0, 0, ONE, ORGNRM, N, 1, D, N, INFO ) + CALL DLASRT( 'D', N, D, INFO ) + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, N, NRHS, B, LDB, INFO ) +* + RETURN + END IF +* +* Book-keeping and setting up some constants. +* + NLVL = INT( LOG( DBLE( N ) / DBLE( SMLSIZ+1 ) ) / LOG( TWO ) ) + 1 +* + SMLSZP = SMLSIZ + 1 +* + U = 1 + VT = 1 + SMLSIZ*N + DIFL = VT + SMLSZP*N + DIFR = DIFL + NLVL*N + Z = DIFR + NLVL*N*2 + C = Z + NLVL*N + S = C + N + POLES = S + N + GIVNUM = POLES + 2*NLVL*N + BX = GIVNUM + 2*NLVL*N + NWORK = BX + N*NRHS +* + SIZEI = 1 + N + K = SIZEI + N + GIVPTR = K + N + PERM = GIVPTR + N + GIVCOL = PERM + NLVL*N + IWK = GIVCOL + NLVL*N*2 +* + ST = 1 + SQRE = 0 + ICMPQ1 = 1 + ICMPQ2 = 0 + NSUB = 0 +* + DO 50 I = 1, N + IF( ABS( D( I ) ).LT.EPS ) THEN + D( I ) = SIGN( EPS, D( I ) ) + END IF + 50 CONTINUE +* + DO 60 I = 1, NM1 + IF( ( ABS( E( I ) ).LT.EPS ) .OR. ( I.EQ.NM1 ) ) THEN + NSUB = NSUB + 1 + IWORK( NSUB ) = ST +* +* Subproblem found. First determine its size and then +* apply divide and conquer on it. +* + IF( I.LT.NM1 ) THEN +* +* A subproblem with E(I) small for I < NM1. +* + NSIZE = I - ST + 1 + IWORK( SIZEI+NSUB-1 ) = NSIZE + ELSE IF( ABS( E( I ) ).GE.EPS ) THEN +* +* A subproblem with E(NM1) not too small but I = NM1. +* + NSIZE = N - ST + 1 + IWORK( SIZEI+NSUB-1 ) = NSIZE + ELSE +* +* A subproblem with E(NM1) small. This implies an +* 1-by-1 subproblem at D(N), which is not solved +* explicitly. +* + NSIZE = I - ST + 1 + IWORK( SIZEI+NSUB-1 ) = NSIZE + NSUB = NSUB + 1 + IWORK( NSUB ) = N + IWORK( SIZEI+NSUB-1 ) = 1 + CALL DCOPY( NRHS, B( N, 1 ), LDB, WORK( BX+NM1 ), N ) + END IF + ST1 = ST - 1 + IF( NSIZE.EQ.1 ) THEN +* +* This is a 1-by-1 subproblem and is not solved +* explicitly. +* + CALL DCOPY( NRHS, B( ST, 1 ), LDB, WORK( BX+ST1 ), N ) + ELSE IF( NSIZE.LE.SMLSIZ ) THEN +* +* This is a small subproblem and is solved by DLASDQ. +* + CALL DLASET( 'A', NSIZE, NSIZE, ZERO, ONE, + $ WORK( VT+ST1 ), N ) + CALL DLASDQ( 'U', 0, NSIZE, NSIZE, 0, NRHS, D( ST ), + $ E( ST ), WORK( VT+ST1 ), N, WORK( NWORK ), + $ N, B( ST, 1 ), LDB, WORK( NWORK ), INFO ) + IF( INFO.NE.0 ) THEN + RETURN + END IF + CALL DLACPY( 'A', NSIZE, NRHS, B( ST, 1 ), LDB, + $ WORK( BX+ST1 ), N ) + ELSE +* +* A large problem. Solve it using divide and conquer. +* + CALL DLASDA( ICMPQ1, SMLSIZ, NSIZE, SQRE, D( ST ), + $ E( ST ), WORK( U+ST1 ), N, WORK( VT+ST1 ), + $ IWORK( K+ST1 ), WORK( DIFL+ST1 ), + $ WORK( DIFR+ST1 ), WORK( Z+ST1 ), + $ WORK( POLES+ST1 ), IWORK( GIVPTR+ST1 ), + $ IWORK( GIVCOL+ST1 ), N, IWORK( PERM+ST1 ), + $ WORK( GIVNUM+ST1 ), WORK( C+ST1 ), + $ WORK( S+ST1 ), WORK( NWORK ), IWORK( IWK ), + $ INFO ) + IF( INFO.NE.0 ) THEN + RETURN + END IF + BXST = BX + ST1 + CALL DLALSA( ICMPQ2, SMLSIZ, NSIZE, NRHS, B( ST, 1 ), + $ LDB, WORK( BXST ), N, WORK( U+ST1 ), N, + $ WORK( VT+ST1 ), IWORK( K+ST1 ), + $ WORK( DIFL+ST1 ), WORK( DIFR+ST1 ), + $ WORK( Z+ST1 ), WORK( POLES+ST1 ), + $ IWORK( GIVPTR+ST1 ), IWORK( GIVCOL+ST1 ), N, + $ IWORK( PERM+ST1 ), WORK( GIVNUM+ST1 ), + $ WORK( C+ST1 ), WORK( S+ST1 ), WORK( NWORK ), + $ IWORK( IWK ), INFO ) + IF( INFO.NE.0 ) THEN + RETURN + END IF + END IF + ST = I + 1 + END IF + 60 CONTINUE +* +* Apply the singular values and treat the tiny ones as zero. +* + TOL = RCND*ABS( D( IDAMAX( N, D, 1 ) ) ) +* + DO 70 I = 1, N +* +* Some of the elements in D can be negative because 1-by-1 +* subproblems were not solved explicitly. +* + IF( ABS( D( I ) ).LE.TOL ) THEN + CALL DLASET( 'A', 1, NRHS, ZERO, ZERO, WORK( BX+I-1 ), N ) + ELSE + RANK = RANK + 1 + CALL DLASCL( 'G', 0, 0, D( I ), ONE, 1, NRHS, + $ WORK( BX+I-1 ), N, INFO ) + END IF + D( I ) = ABS( D( I ) ) + 70 CONTINUE +* +* Now apply back the right singular vectors. +* + ICMPQ2 = 1 + DO 80 I = 1, NSUB + ST = IWORK( I ) + ST1 = ST - 1 + NSIZE = IWORK( SIZEI+I-1 ) + BXST = BX + ST1 + IF( NSIZE.EQ.1 ) THEN + CALL DCOPY( NRHS, WORK( BXST ), N, B( ST, 1 ), LDB ) + ELSE IF( NSIZE.LE.SMLSIZ ) THEN + CALL DGEMM( 'T', 'N', NSIZE, NRHS, NSIZE, ONE, + $ WORK( VT+ST1 ), N, WORK( BXST ), N, ZERO, + $ B( ST, 1 ), LDB ) + ELSE + CALL DLALSA( ICMPQ2, SMLSIZ, NSIZE, NRHS, WORK( BXST ), N, + $ B( ST, 1 ), LDB, WORK( U+ST1 ), N, + $ WORK( VT+ST1 ), IWORK( K+ST1 ), + $ WORK( DIFL+ST1 ), WORK( DIFR+ST1 ), + $ WORK( Z+ST1 ), WORK( POLES+ST1 ), + $ IWORK( GIVPTR+ST1 ), IWORK( GIVCOL+ST1 ), N, + $ IWORK( PERM+ST1 ), WORK( GIVNUM+ST1 ), + $ WORK( C+ST1 ), WORK( S+ST1 ), WORK( NWORK ), + $ IWORK( IWK ), INFO ) + IF( INFO.NE.0 ) THEN + RETURN + END IF + END IF + 80 CONTINUE +* +* Unscale and sort the singular values. +* + CALL DLASCL( 'G', 0, 0, ONE, ORGNRM, N, 1, D, N, INFO ) + CALL DLASRT( 'D', N, D, INFO ) + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, N, NRHS, B, LDB, INFO ) +* + RETURN +* +* End of DLALSD +* + END diff --git a/lib/linalg/dlamch.f b/lib/linalg/dlamch.f index 8f830e87cd94024cc83feb2eecd26e137f25f24c..76f875cef65d732143f6a48d9dbda2bc652c445e 100644 --- a/lib/linalg/dlamch.f +++ b/lib/linalg/dlamch.f @@ -1,47 +1,77 @@ +*> \brief \b DLAMCH +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +* Definition: +* =========== +* +* DOUBLE PRECISION FUNCTION DLAMCH( CMACH ) +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLAMCH determines double precision machine parameters. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] CMACH +*> \verbatim +*> Specifies the value to be returned by DLAMCH: +*> = 'E' or 'e', DLAMCH := eps +*> = 'S' or 's , DLAMCH := sfmin +*> = 'B' or 'b', DLAMCH := base +*> = 'P' or 'p', DLAMCH := eps*base +*> = 'N' or 'n', DLAMCH := t +*> = 'R' or 'r', DLAMCH := rnd +*> = 'M' or 'm', DLAMCH := emin +*> = 'U' or 'u', DLAMCH := rmin +*> = 'L' or 'l', DLAMCH := emax +*> = 'O' or 'o', DLAMCH := rmax +*> where +*> eps = relative machine precision +*> sfmin = safe minimum, such that 1/sfmin does not overflow +*> base = base of the machine +*> prec = eps*base +*> t = number of (base) digits in the mantissa +*> rnd = 1.0 when rounding occurs in addition, 0.0 otherwise +*> emin = minimum exponent before (gradual) underflow +*> rmin = underflow threshold - base**(emin-1) +*> emax = largest exponent before overflow +*> rmax = overflow threshold - (base**emax)*(1-eps) +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup auxOTHERauxiliary +* +* ===================================================================== DOUBLE PRECISION FUNCTION DLAMCH( CMACH ) * -* -- LAPACK auxiliary routine (version 3.2) -- -* Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 * * .. Scalar Arguments .. CHARACTER CMACH * .. * -* Purpose -* ======= -* -* DLAMCH determines double precision machine parameters. -* -* Arguments -* ========= -* -* CMACH (input) CHARACTER*1 -* Specifies the value to be returned by DLAMCH: -* = 'E' or 'e', DLAMCH := eps -* = 'S' or 's , DLAMCH := sfmin -* = 'B' or 'b', DLAMCH := base -* = 'P' or 'p', DLAMCH := eps*base -* = 'N' or 'n', DLAMCH := t -* = 'R' or 'r', DLAMCH := rnd -* = 'M' or 'm', DLAMCH := emin -* = 'U' or 'u', DLAMCH := rmin -* = 'L' or 'l', DLAMCH := emax -* = 'O' or 'o', DLAMCH := rmax -* -* where -* -* eps = relative machine precision -* sfmin = safe minimum, such that 1/sfmin does not overflow -* base = base of the machine -* prec = eps*base -* t = number of (base) digits in the mantissa -* rnd = 1.0 when rounding occurs in addition, 0.0 otherwise -* emin = minimum exponent before (gradual) underflow -* rmin = underflow threshold - base**(emin-1) -* emax = largest exponent before overflow -* rmax = overflow threshold - (base**emax)*(1-eps) -* * ===================================================================== * * .. Parameters .. @@ -49,552 +79,101 @@ PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) * .. * .. Local Scalars .. - LOGICAL FIRST, LRND - INTEGER BETA, IMAX, IMIN, IT - DOUBLE PRECISION BASE, EMAX, EMIN, EPS, PREC, RMACH, RMAX, RMIN, - $ RND, SFMIN, SMALL, T + DOUBLE PRECISION RND, EPS, SFMIN, SMALL, RMACH * .. * .. External Functions .. LOGICAL LSAME EXTERNAL LSAME * .. -* .. External Subroutines .. - EXTERNAL DLAMC2 -* .. -* .. Save statement .. - SAVE FIRST, EPS, SFMIN, BASE, T, RND, EMIN, RMIN, - $ EMAX, RMAX, PREC -* .. -* .. Data statements .. - DATA FIRST / .TRUE. / +* .. Intrinsic Functions .. + INTRINSIC DIGITS, EPSILON, HUGE, MAXEXPONENT, + $ MINEXPONENT, RADIX, TINY * .. * .. Executable Statements .. * - IF( FIRST ) THEN - CALL DLAMC2( BETA, IT, LRND, EPS, IMIN, RMIN, IMAX, RMAX ) - BASE = BETA - T = IT - IF( LRND ) THEN - RND = ONE - EPS = ( BASE**( 1-IT ) ) / 2 - ELSE - RND = ZERO - EPS = BASE**( 1-IT ) - END IF - PREC = EPS*BASE - EMIN = IMIN - EMAX = IMAX - SFMIN = RMIN - SMALL = ONE / RMAX - IF( SMALL.GE.SFMIN ) THEN * -* Use SMALL plus a bit, to avoid the possibility of rounding -* causing overflow when computing 1/sfmin. +* Assume rounding, not chopping. Always. * - SFMIN = SMALL*( ONE+EPS ) - END IF + RND = ONE +* + IF( ONE.EQ.RND ) THEN + EPS = EPSILON(ZERO) * 0.5 + ELSE + EPS = EPSILON(ZERO) END IF * IF( LSAME( CMACH, 'E' ) ) THEN RMACH = EPS ELSE IF( LSAME( CMACH, 'S' ) ) THEN + SFMIN = TINY(ZERO) + SMALL = ONE / HUGE(ZERO) + IF( SMALL.GE.SFMIN ) THEN +* +* Use SMALL plus a bit, to avoid the possibility of rounding +* causing overflow when computing 1/sfmin. +* + SFMIN = SMALL*( ONE+EPS ) + END IF RMACH = SFMIN ELSE IF( LSAME( CMACH, 'B' ) ) THEN - RMACH = BASE + RMACH = RADIX(ZERO) ELSE IF( LSAME( CMACH, 'P' ) ) THEN - RMACH = PREC + RMACH = EPS * RADIX(ZERO) ELSE IF( LSAME( CMACH, 'N' ) ) THEN - RMACH = T + RMACH = DIGITS(ZERO) ELSE IF( LSAME( CMACH, 'R' ) ) THEN RMACH = RND ELSE IF( LSAME( CMACH, 'M' ) ) THEN - RMACH = EMIN + RMACH = MINEXPONENT(ZERO) ELSE IF( LSAME( CMACH, 'U' ) ) THEN - RMACH = RMIN + RMACH = tiny(zero) ELSE IF( LSAME( CMACH, 'L' ) ) THEN - RMACH = EMAX + RMACH = MAXEXPONENT(ZERO) ELSE IF( LSAME( CMACH, 'O' ) ) THEN - RMACH = RMAX + RMACH = HUGE(ZERO) + ELSE + RMACH = ZERO END IF * DLAMCH = RMACH - FIRST = .FALSE. RETURN * * End of DLAMCH * END -* -************************************************************************ -* - SUBROUTINE DLAMC1( BETA, T, RND, IEEE1 ) -* -* -- LAPACK auxiliary routine (version 3.2) -- -* Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 -* -* .. Scalar Arguments .. - LOGICAL IEEE1, RND - INTEGER BETA, T -* .. -* -* Purpose -* ======= -* -* DLAMC1 determines the machine parameters given by BETA, T, RND, and -* IEEE1. -* -* Arguments -* ========= -* -* BETA (output) INTEGER -* The base of the machine. -* -* T (output) INTEGER -* The number of ( BETA ) digits in the mantissa. -* -* RND (output) LOGICAL -* Specifies whether proper rounding ( RND = .TRUE. ) or -* chopping ( RND = .FALSE. ) occurs in addition. This may not -* be a reliable guide to the way in which the machine performs -* its arithmetic. -* -* IEEE1 (output) LOGICAL -* Specifies whether rounding appears to be done in the IEEE -* 'round to nearest' style. -* -* Further Details -* =============== -* -* The routine is based on the routine ENVRON by Malcolm and -* incorporates suggestions by Gentleman and Marovich. See -* -* Malcolm M. A. (1972) Algorithms to reveal properties of -* floating-point arithmetic. Comms. of the ACM, 15, 949-951. -* -* Gentleman W. M. and Marovich S. B. (1974) More on algorithms -* that reveal properties of floating point arithmetic units. -* Comms. of the ACM, 17, 276-277. -* -* ===================================================================== -* -* .. Local Scalars .. - LOGICAL FIRST, LIEEE1, LRND - INTEGER LBETA, LT - DOUBLE PRECISION A, B, C, F, ONE, QTR, SAVEC, T1, T2 -* .. -* .. External Functions .. - DOUBLE PRECISION DLAMC3 - EXTERNAL DLAMC3 -* .. -* .. Save statement .. - SAVE FIRST, LIEEE1, LBETA, LRND, LT -* .. -* .. Data statements .. - DATA FIRST / .TRUE. / -* .. -* .. Executable Statements .. -* - IF( FIRST ) THEN - ONE = 1 -* -* LBETA, LIEEE1, LT and LRND are the local values of BETA, -* IEEE1, T and RND. -* -* Throughout this routine we use the function DLAMC3 to ensure -* that relevant values are stored and not held in registers, or -* are not affected by optimizers. -* -* Compute a = 2.0**m with the smallest positive integer m such -* that -* -* fl( a + 1.0 ) = a. -* - A = 1 - C = 1 -* -*+ WHILE( C.EQ.ONE )LOOP - 10 CONTINUE - IF( C.EQ.ONE ) THEN - A = 2*A - C = DLAMC3( A, ONE ) - C = DLAMC3( C, -A ) - GO TO 10 - END IF -*+ END WHILE -* -* Now compute b = 2.0**m with the smallest positive integer m -* such that -* -* fl( a + b ) .gt. a. -* - B = 1 - C = DLAMC3( A, B ) -* -*+ WHILE( C.EQ.A )LOOP - 20 CONTINUE - IF( C.EQ.A ) THEN - B = 2*B - C = DLAMC3( A, B ) - GO TO 20 - END IF -*+ END WHILE -* -* Now compute the base. a and c are neighbouring floating point -* numbers in the interval ( beta**t, beta**( t + 1 ) ) and so -* their difference is beta. Adding 0.25 to c is to ensure that it -* is truncated to beta and not ( beta - 1 ). -* - QTR = ONE / 4 - SAVEC = C - C = DLAMC3( C, -A ) - LBETA = C + QTR -* -* Now determine whether rounding or chopping occurs, by adding a -* bit less than beta/2 and a bit more than beta/2 to a. -* - B = LBETA - F = DLAMC3( B / 2, -B / 100 ) - C = DLAMC3( F, A ) - IF( C.EQ.A ) THEN - LRND = .TRUE. - ELSE - LRND = .FALSE. - END IF - F = DLAMC3( B / 2, B / 100 ) - C = DLAMC3( F, A ) - IF( ( LRND ) .AND. ( C.EQ.A ) ) - $ LRND = .FALSE. -* -* Try and decide whether rounding is done in the IEEE 'round to -* nearest' style. B/2 is half a unit in the last place of the two -* numbers A and SAVEC. Furthermore, A is even, i.e. has last bit -* zero, and SAVEC is odd. Thus adding B/2 to A should not change -* A, but adding B/2 to SAVEC should change SAVEC. -* - T1 = DLAMC3( B / 2, A ) - T2 = DLAMC3( B / 2, SAVEC ) - LIEEE1 = ( T1.EQ.A ) .AND. ( T2.GT.SAVEC ) .AND. LRND -* -* Now find the mantissa, t. It should be the integer part of -* log to the base beta of a, however it is safer to determine t -* by powering. So we find t as the smallest positive integer for -* which -* -* fl( beta**t + 1.0 ) = 1.0. -* - LT = 0 - A = 1 - C = 1 -* -*+ WHILE( C.EQ.ONE )LOOP - 30 CONTINUE - IF( C.EQ.ONE ) THEN - LT = LT + 1 - A = A*LBETA - C = DLAMC3( A, ONE ) - C = DLAMC3( C, -A ) - GO TO 30 - END IF -*+ END WHILE -* - END IF -* - BETA = LBETA - T = LT - RND = LRND - IEEE1 = LIEEE1 - FIRST = .FALSE. - RETURN -* -* End of DLAMC1 -* - END -* -************************************************************************ -* - SUBROUTINE DLAMC2( BETA, T, RND, EPS, EMIN, RMIN, EMAX, RMAX ) -* -* -- LAPACK auxiliary routine (version 3.2) -- -* Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 -* -* .. Scalar Arguments .. - LOGICAL RND - INTEGER BETA, EMAX, EMIN, T - DOUBLE PRECISION EPS, RMAX, RMIN -* .. -* -* Purpose -* ======= -* -* DLAMC2 determines the machine parameters specified in its argument -* list. -* -* Arguments -* ========= -* -* BETA (output) INTEGER -* The base of the machine. -* -* T (output) INTEGER -* The number of ( BETA ) digits in the mantissa. -* -* RND (output) LOGICAL -* Specifies whether proper rounding ( RND = .TRUE. ) or -* chopping ( RND = .FALSE. ) occurs in addition. This may not -* be a reliable guide to the way in which the machine performs -* its arithmetic. -* -* EPS (output) DOUBLE PRECISION -* The smallest positive number such that -* -* fl( 1.0 - EPS ) .LT. 1.0, -* -* where fl denotes the computed value. -* -* EMIN (output) INTEGER -* The minimum exponent before (gradual) underflow occurs. -* -* RMIN (output) DOUBLE PRECISION -* The smallest normalized number for the machine, given by -* BASE**( EMIN - 1 ), where BASE is the floating point value -* of BETA. -* -* EMAX (output) INTEGER -* The maximum exponent before overflow occurs. -* -* RMAX (output) DOUBLE PRECISION -* The largest positive number for the machine, given by -* BASE**EMAX * ( 1 - EPS ), where BASE is the floating point -* value of BETA. -* -* Further Details -* =============== -* -* The computation of EPS is based on a routine PARANOIA by -* W. Kahan of the University of California at Berkeley. -* -* ===================================================================== -* -* .. Local Scalars .. - LOGICAL FIRST, IEEE, IWARN, LIEEE1, LRND - INTEGER GNMIN, GPMIN, I, LBETA, LEMAX, LEMIN, LT, - $ NGNMIN, NGPMIN - DOUBLE PRECISION A, B, C, HALF, LEPS, LRMAX, LRMIN, ONE, RBASE, - $ SIXTH, SMALL, THIRD, TWO, ZERO -* .. -* .. External Functions .. - DOUBLE PRECISION DLAMC3 - EXTERNAL DLAMC3 -* .. -* .. External Subroutines .. - EXTERNAL DLAMC1, DLAMC4, DLAMC5 -* .. -* .. Intrinsic Functions .. - INTRINSIC ABS, MAX, MIN -* .. -* .. Save statement .. - SAVE FIRST, IWARN, LBETA, LEMAX, LEMIN, LEPS, LRMAX, - $ LRMIN, LT -* .. -* .. Data statements .. - DATA FIRST / .TRUE. / , IWARN / .FALSE. / -* .. -* .. Executable Statements .. -* - IF( FIRST ) THEN - ZERO = 0 - ONE = 1 - TWO = 2 -* -* LBETA, LT, LRND, LEPS, LEMIN and LRMIN are the local values of -* BETA, T, RND, EPS, EMIN and RMIN. -* -* Throughout this routine we use the function DLAMC3 to ensure -* that relevant values are stored and not held in registers, or -* are not affected by optimizers. -* -* DLAMC1 returns the parameters LBETA, LT, LRND and LIEEE1. -* - CALL DLAMC1( LBETA, LT, LRND, LIEEE1 ) -* -* Start to find EPS. -* - B = LBETA - A = B**( -LT ) - LEPS = A -* -* Try some tricks to see whether or not this is the correct EPS. -* - B = TWO / 3 - HALF = ONE / 2 - SIXTH = DLAMC3( B, -HALF ) - THIRD = DLAMC3( SIXTH, SIXTH ) - B = DLAMC3( THIRD, -HALF ) - B = DLAMC3( B, SIXTH ) - B = ABS( B ) - IF( B.LT.LEPS ) - $ B = LEPS -* - LEPS = 1 -* -*+ WHILE( ( LEPS.GT.B ).AND.( B.GT.ZERO ) )LOOP - 10 CONTINUE - IF( ( LEPS.GT.B ) .AND. ( B.GT.ZERO ) ) THEN - LEPS = B - C = DLAMC3( HALF*LEPS, ( TWO**5 )*( LEPS**2 ) ) - C = DLAMC3( HALF, -C ) - B = DLAMC3( HALF, C ) - C = DLAMC3( HALF, -B ) - B = DLAMC3( HALF, C ) - GO TO 10 - END IF -*+ END WHILE -* - IF( A.LT.LEPS ) - $ LEPS = A -* -* Computation of EPS complete. -* -* Now find EMIN. Let A = + or - 1, and + or - (1 + BASE**(-3)). -* Keep dividing A by BETA until (gradual) underflow occurs. This -* is detected when we cannot recover the previous A. -* - RBASE = ONE / LBETA - SMALL = ONE - DO 20 I = 1, 3 - SMALL = DLAMC3( SMALL*RBASE, ZERO ) - 20 CONTINUE - A = DLAMC3( ONE, SMALL ) - CALL DLAMC4( NGPMIN, ONE, LBETA ) - CALL DLAMC4( NGNMIN, -ONE, LBETA ) - CALL DLAMC4( GPMIN, A, LBETA ) - CALL DLAMC4( GNMIN, -A, LBETA ) - IEEE = .FALSE. -* - IF( ( NGPMIN.EQ.NGNMIN ) .AND. ( GPMIN.EQ.GNMIN ) ) THEN - IF( NGPMIN.EQ.GPMIN ) THEN - LEMIN = NGPMIN -* ( Non twos-complement machines, no gradual underflow; -* e.g., VAX ) - ELSE IF( ( GPMIN-NGPMIN ).EQ.3 ) THEN - LEMIN = NGPMIN - 1 + LT - IEEE = .TRUE. -* ( Non twos-complement machines, with gradual underflow; -* e.g., IEEE standard followers ) - ELSE - LEMIN = MIN( NGPMIN, GPMIN ) -* ( A guess; no known machine ) - IWARN = .TRUE. - END IF -* - ELSE IF( ( NGPMIN.EQ.GPMIN ) .AND. ( NGNMIN.EQ.GNMIN ) ) THEN - IF( ABS( NGPMIN-NGNMIN ).EQ.1 ) THEN - LEMIN = MAX( NGPMIN, NGNMIN ) -* ( Twos-complement machines, no gradual underflow; -* e.g., CYBER 205 ) - ELSE - LEMIN = MIN( NGPMIN, NGNMIN ) -* ( A guess; no known machine ) - IWARN = .TRUE. - END IF -* - ELSE IF( ( ABS( NGPMIN-NGNMIN ).EQ.1 ) .AND. - $ ( GPMIN.EQ.GNMIN ) ) THEN - IF( ( GPMIN-MIN( NGPMIN, NGNMIN ) ).EQ.3 ) THEN - LEMIN = MAX( NGPMIN, NGNMIN ) - 1 + LT -* ( Twos-complement machines with gradual underflow; -* no known machine ) - ELSE - LEMIN = MIN( NGPMIN, NGNMIN ) -* ( A guess; no known machine ) - IWARN = .TRUE. - END IF -* - ELSE - LEMIN = MIN( NGPMIN, NGNMIN, GPMIN, GNMIN ) -* ( A guess; no known machine ) - IWARN = .TRUE. - END IF - FIRST = .FALSE. -*** -* Comment out this if block if EMIN is ok - IF( IWARN ) THEN - FIRST = .TRUE. - WRITE( 6, FMT = 9999 )LEMIN - END IF -*** -* -* Assume IEEE arithmetic if we found denormalised numbers above, -* or if arithmetic seems to round in the IEEE style, determined -* in routine DLAMC1. A true IEEE machine should have both things -* true; however, faulty machines may have one or the other. -* - IEEE = IEEE .OR. LIEEE1 -* -* Compute RMIN by successive division by BETA. We could compute -* RMIN as BASE**( EMIN - 1 ), but some machines underflow during -* this computation. -* - LRMIN = 1 - DO 30 I = 1, 1 - LEMIN - LRMIN = DLAMC3( LRMIN*RBASE, ZERO ) - 30 CONTINUE -* -* Finally, call DLAMC5 to compute EMAX and RMAX. -* - CALL DLAMC5( LBETA, LT, LEMIN, IEEE, LEMAX, LRMAX ) - END IF -* - BETA = LBETA - T = LT - RND = LRND - EPS = LEPS - EMIN = LEMIN - RMIN = LRMIN - EMAX = LEMAX - RMAX = LRMAX -* - RETURN -* - 9999 FORMAT( / / ' WARNING. The value EMIN may be incorrect:-', - $ ' EMIN = ', I8, / - $ ' If, after inspection, the value EMIN looks', - $ ' acceptable please comment out ', - $ / ' the IF block as marked within the code of routine', - $ ' DLAMC2,', / ' otherwise supply EMIN explicitly.', / ) -* -* End of DLAMC2 -* - END -* ************************************************************************ -* +*> \brief \b DLAMC3 +*> \details +*> \b Purpose: +*> \verbatim +*> DLAMC3 is intended to force A and B to be stored prior to doing +*> the addition of A and B , for use in situations where optimizers +*> might hold one of these in a register. +*> \endverbatim +*> \author LAPACK is a software package provided by Univ. of Tennessee, Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd.. +*> \date December 2016 +*> \ingroup auxOTHERauxiliary +*> +*> \param[in] A +*> \verbatim +*> A is a DOUBLE PRECISION +*> \endverbatim +*> +*> \param[in] B +*> \verbatim +*> B is a DOUBLE PRECISION +*> The values A and B. +*> \endverbatim +*> DOUBLE PRECISION FUNCTION DLAMC3( A, B ) * -* -- LAPACK auxiliary routine (version 3.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 +* November 2010 * * .. Scalar Arguments .. DOUBLE PRECISION A, B * .. -* -* Purpose -* ======= -* -* DLAMC3 is intended to force A and B to be stored prior to doing -* the addition of A and B , for use in situations where optimizers -* might hold one of these in a register. -* -* Arguments -* ========= -* -* A (input) DOUBLE PRECISION -* B (input) DOUBLE PRECISION -* The values A and B. -* * ===================================================================== * * .. Executable Statements .. @@ -608,245 +187,3 @@ END * ************************************************************************ -* - SUBROUTINE DLAMC4( EMIN, START, BASE ) -* -* -- LAPACK auxiliary routine (version 3.2) -- -* Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 -* -* .. Scalar Arguments .. - INTEGER BASE, EMIN - DOUBLE PRECISION START -* .. -* -* Purpose -* ======= -* -* DLAMC4 is a service routine for DLAMC2. -* -* Arguments -* ========= -* -* EMIN (output) INTEGER -* The minimum exponent before (gradual) underflow, computed by -* setting A = START and dividing by BASE until the previous A -* can not be recovered. -* -* START (input) DOUBLE PRECISION -* The starting point for determining EMIN. -* -* BASE (input) INTEGER -* The base of the machine. -* -* ===================================================================== -* -* .. Local Scalars .. - INTEGER I - DOUBLE PRECISION A, B1, B2, C1, C2, D1, D2, ONE, RBASE, ZERO -* .. -* .. External Functions .. - DOUBLE PRECISION DLAMC3 - EXTERNAL DLAMC3 -* .. -* .. Executable Statements .. -* - A = START - ONE = 1 - RBASE = ONE / BASE - ZERO = 0 - EMIN = 1 - B1 = DLAMC3( A*RBASE, ZERO ) - C1 = A - C2 = A - D1 = A - D2 = A -*+ WHILE( ( C1.EQ.A ).AND.( C2.EQ.A ).AND. -* $ ( D1.EQ.A ).AND.( D2.EQ.A ) )LOOP - 10 CONTINUE - IF( ( C1.EQ.A ) .AND. ( C2.EQ.A ) .AND. ( D1.EQ.A ) .AND. - $ ( D2.EQ.A ) ) THEN - EMIN = EMIN - 1 - A = B1 - B1 = DLAMC3( A / BASE, ZERO ) - C1 = DLAMC3( B1*BASE, ZERO ) - D1 = ZERO - DO 20 I = 1, BASE - D1 = D1 + B1 - 20 CONTINUE - B2 = DLAMC3( A*RBASE, ZERO ) - C2 = DLAMC3( B2 / RBASE, ZERO ) - D2 = ZERO - DO 30 I = 1, BASE - D2 = D2 + B2 - 30 CONTINUE - GO TO 10 - END IF -*+ END WHILE -* - RETURN -* -* End of DLAMC4 -* - END -* -************************************************************************ -* - SUBROUTINE DLAMC5( BETA, P, EMIN, IEEE, EMAX, RMAX ) -* -* -- LAPACK auxiliary routine (version 3.2) -- -* Univ. of Tennessee, Univ. of California Berkeley and NAG Ltd.. -* November 2006 -* -* .. Scalar Arguments .. - LOGICAL IEEE - INTEGER BETA, EMAX, EMIN, P - DOUBLE PRECISION RMAX -* .. -* -* Purpose -* ======= -* -* DLAMC5 attempts to compute RMAX, the largest machine floating-point -* number, without overflow. It assumes that EMAX + abs(EMIN) sum -* approximately to a power of 2. It will fail on machines where this -* assumption does not hold, for example, the Cyber 205 (EMIN = -28625, -* EMAX = 28718). It will also fail if the value supplied for EMIN is -* too large (i.e. too close to zero), probably with overflow. -* -* Arguments -* ========= -* -* BETA (input) INTEGER -* The base of floating-point arithmetic. -* -* P (input) INTEGER -* The number of base BETA digits in the mantissa of a -* floating-point value. -* -* EMIN (input) INTEGER -* The minimum exponent before (gradual) underflow. -* -* IEEE (input) LOGICAL -* A logical flag specifying whether or not the arithmetic -* system is thought to comply with the IEEE standard. -* -* EMAX (output) INTEGER -* The largest exponent before overflow -* -* RMAX (output) DOUBLE PRECISION -* The largest machine floating-point number. -* -* ===================================================================== -* -* .. Parameters .. - DOUBLE PRECISION ZERO, ONE - PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0 ) -* .. -* .. Local Scalars .. - INTEGER EXBITS, EXPSUM, I, LEXP, NBITS, TRY, UEXP - DOUBLE PRECISION OLDY, RECBAS, Y, Z -* .. -* .. External Functions .. - DOUBLE PRECISION DLAMC3 - EXTERNAL DLAMC3 -* .. -* .. Intrinsic Functions .. - INTRINSIC MOD -* .. -* .. Executable Statements .. -* -* First compute LEXP and UEXP, two powers of 2 that bound -* abs(EMIN). We then assume that EMAX + abs(EMIN) will sum -* approximately to the bound that is closest to abs(EMIN). -* (EMAX is the exponent of the required number RMAX). -* - LEXP = 1 - EXBITS = 1 - 10 CONTINUE - TRY = LEXP*2 - IF( TRY.LE.( -EMIN ) ) THEN - LEXP = TRY - EXBITS = EXBITS + 1 - GO TO 10 - END IF - IF( LEXP.EQ.-EMIN ) THEN - UEXP = LEXP - ELSE - UEXP = TRY - EXBITS = EXBITS + 1 - END IF -* -* Now -LEXP is less than or equal to EMIN, and -UEXP is greater -* than or equal to EMIN. EXBITS is the number of bits needed to -* store the exponent. -* - IF( ( UEXP+EMIN ).GT.( -LEXP-EMIN ) ) THEN - EXPSUM = 2*LEXP - ELSE - EXPSUM = 2*UEXP - END IF -* -* EXPSUM is the exponent range, approximately equal to -* EMAX - EMIN + 1 . -* - EMAX = EXPSUM + EMIN - 1 - NBITS = 1 + EXBITS + P -* -* NBITS is the total number of bits needed to store a -* floating-point number. -* - IF( ( MOD( NBITS, 2 ).EQ.1 ) .AND. ( BETA.EQ.2 ) ) THEN -* -* Either there are an odd number of bits used to store a -* floating-point number, which is unlikely, or some bits are -* not used in the representation of numbers, which is possible, -* (e.g. Cray machines) or the mantissa has an implicit bit, -* (e.g. IEEE machines, Dec Vax machines), which is perhaps the -* most likely. We have to assume the last alternative. -* If this is true, then we need to reduce EMAX by one because -* there must be some way of representing zero in an implicit-bit -* system. On machines like Cray, we are reducing EMAX by one -* unnecessarily. -* - EMAX = EMAX - 1 - END IF -* - IF( IEEE ) THEN -* -* Assume we are on an IEEE machine which reserves one exponent -* for infinity and NaN. -* - EMAX = EMAX - 1 - END IF -* -* Now create RMAX, the largest machine number, which should -* be equal to (1.0 - BETA**(-P)) * BETA**EMAX . -* -* First compute 1.0 - BETA**(-P), being careful that the -* result is less than 1.0 . -* - RECBAS = ONE / BETA - Z = BETA - ONE - Y = ZERO - DO 20 I = 1, P - Z = Z*RECBAS - IF( Y.LT.ONE ) - $ OLDY = Y - Y = DLAMC3( Y, Z ) - 20 CONTINUE - IF( Y.GE.ONE ) - $ Y = OLDY -* -* Now multiply by BETA**EMAX to get RMAX. -* - DO 30 I = 1, EMAX - Y = DLAMC3( Y*BETA, ZERO ) - 30 CONTINUE -* - RMAX = Y - RETURN -* -* End of DLAMC5 -* - END diff --git a/lib/linalg/dlamrg.f b/lib/linalg/dlamrg.f index 7126053e8a43ebeb48290cbda628d4d82810681f..de19508e459695e7132a8fb7806b7310003d3333 100644 --- a/lib/linalg/dlamrg.f +++ b/lib/linalg/dlamrg.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAMRG + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAMRG + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAMRG( N1, N2, A, DTRD1, DTRD2, INDEX ) -* +* * .. Scalar Arguments .. * INTEGER DTRD1, DTRD2, N1, N2 * .. @@ -27,7 +27,7 @@ * INTEGER INDEX( * ) * DOUBLE PRECISION A( * ) * .. -* +* * *> \par Purpose: * ============= @@ -50,7 +50,7 @@ *> \param[in] N2 *> \verbatim *> N2 is INTEGER -*> These arguements contain the respective lengths of the two +*> These arguments contain the respective lengths of the two *> sorted lists to be merged. *> \endverbatim *> @@ -87,22 +87,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLAMRG( N1, N2, A, DTRD1, DTRD2, INDEX ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. INTEGER DTRD1, DTRD2, N1, N2 diff --git a/lib/linalg/dlange.f b/lib/linalg/dlange.f index bec815d1efc1a98ec3caa34e982d0f9624c5b13c..9dbf45e81827f751a7842d8011c48f8cdd507483 100644 --- a/lib/linalg/dlange.f +++ b/lib/linalg/dlange.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLANGE + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLANGE + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DLANGE( NORM, M, N, A, LDA, WORK ) -* +* * .. Scalar Arguments .. * CHARACTER NORM * INTEGER LDA, M, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleGEauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANGE( NORM, M, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dlanst.f b/lib/linalg/dlanst.f index 213b06ada0f8b083198f2e6e2f285d7488559ae4..e952e2dd212d40cfe38af43a6c0043aa9aa114a7 100644 --- a/lib/linalg/dlanst.f +++ b/lib/linalg/dlanst.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLANST + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLANST + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DLANST( NORM, N, D, E ) -* +* * .. Scalar Arguments .. * CHARACTER NORM * INTEGER N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( * ), E( * ) * .. -* +* * *> \par Purpose: * ============= @@ -88,22 +88,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANST( NORM, N, D, E ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dlansy.f b/lib/linalg/dlansy.f index bc70ab8edacd3e015294c6faeb001ff7cfb70b12..2372fce0a8f4868a5f123ec9815c0cc1f6d6ce4c 100644 --- a/lib/linalg/dlansy.f +++ b/lib/linalg/dlansy.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLANSY + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLANSY + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DLANSY( NORM, UPLO, N, A, LDA, WORK ) -* +* * .. Scalar Arguments .. * CHARACTER NORM, UPLO * INTEGER LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -110,22 +110,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleSYauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANSY( NORM, UPLO, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER NORM, UPLO diff --git a/lib/linalg/dlapy2.f b/lib/linalg/dlapy2.f index d43b0d5d14ce0d6ec97a9eab066b0316ac2a8bf5..bc01829a24ed7ab572f8f5f11cadd53dc6b1589c 100644 --- a/lib/linalg/dlapy2.f +++ b/lib/linalg/dlapy2.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAPY2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAPY2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DLAPY2( X, Y ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION X, Y * .. -* +* * *> \par Purpose: * ============= @@ -51,22 +51,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLAPY2( X, Y ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. DOUBLE PRECISION X, Y @@ -82,20 +82,32 @@ * .. * .. Local Scalars .. DOUBLE PRECISION W, XABS, YABS, Z + LOGICAL X_IS_NAN, Y_IS_NAN +* .. +* .. External Functions .. + LOGICAL DISNAN + EXTERNAL DISNAN * .. * .. Intrinsic Functions .. INTRINSIC ABS, MAX, MIN, SQRT * .. * .. Executable Statements .. * - XABS = ABS( X ) - YABS = ABS( Y ) - W = MAX( XABS, YABS ) - Z = MIN( XABS, YABS ) - IF( Z.EQ.ZERO ) THEN - DLAPY2 = W - ELSE - DLAPY2 = W*SQRT( ONE+( Z / W )**2 ) + X_IS_NAN = DISNAN( X ) + Y_IS_NAN = DISNAN( Y ) + IF ( X_IS_NAN ) DLAPY2 = X + IF ( Y_IS_NAN ) DLAPY2 = Y +* + IF ( .NOT.( X_IS_NAN.OR.Y_IS_NAN ) ) THEN + XABS = ABS( X ) + YABS = ABS( Y ) + W = MAX( XABS, YABS ) + Z = MIN( XABS, YABS ) + IF( Z.EQ.ZERO ) THEN + DLAPY2 = W + ELSE + DLAPY2 = W*SQRT( ONE+( Z / W )**2 ) + END IF END IF RETURN * diff --git a/lib/linalg/dlapy3.f b/lib/linalg/dlapy3.f index 23feecc4478a3ed002b7bdd5ec5c4c00c98603f6..3bbba88875c8e0572b920b1bb7f009006e747806 100644 --- a/lib/linalg/dlapy3.f +++ b/lib/linalg/dlapy3.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAPY3 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAPY3 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DLAPY3( X, Y, Z ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION X, Y, Z * .. -* +* * *> \par Purpose: * ============= @@ -56,22 +56,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLAPY3( X, Y, Z ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION X, Y, Z diff --git a/lib/linalg/dlarf.f b/lib/linalg/dlarf.f index 80dca69af7f6e36073fc5cbf1f6eef0ca7fb4a45..e99d0bb2a914323352b61232d134999c36f6d0df 100644 --- a/lib/linalg/dlarf.f +++ b/lib/linalg/dlarf.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLARF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLARF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE * INTEGER INCV, LDC, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION C( LDC, * ), V( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -112,22 +112,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE diff --git a/lib/linalg/dlarfb.f b/lib/linalg/dlarfb.f index 17218478af31abe795d5972fec7d5c99937048f1..5b2cc2ba800f3d53bb1d990ad69ceebc6e4c105e 100644 --- a/lib/linalg/dlarfb.f +++ b/lib/linalg/dlarfb.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLARFB + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLARFB + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, * T, LDT, C, LDC, WORK, LDWORK ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, SIDE, STOREV, TRANS * INTEGER K, LDC, LDT, LDV, LDWORK, M, N @@ -29,7 +29,7 @@ * DOUBLE PRECISION C( LDC, * ), T( LDT, * ), V( LDV, * ), * $ WORK( LDWORK, * ) * .. -* +* * *> \par Purpose: * ============= @@ -154,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2013 * *> \ingroup doubleOTHERauxiliary * @@ -195,10 +195,10 @@ SUBROUTINE DLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, $ T, LDT, C, LDC, WORK, LDWORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2013 * * .. Scalar Arguments .. CHARACTER DIRECT, SIDE, STOREV, TRANS @@ -217,12 +217,11 @@ * .. * .. Local Scalars .. CHARACTER TRANST - INTEGER I, J, LASTV, LASTC, lastv2 + INTEGER I, J * .. * .. External Functions .. LOGICAL LSAME - INTEGER ILADLR, ILADLC - EXTERNAL LSAME, ILADLR, ILADLC + EXTERNAL LSAME * .. * .. External Subroutines .. EXTERNAL DCOPY, DGEMM, DTRMM @@ -252,58 +251,53 @@ * * Form H * C or H**T * C where C = ( C1 ) * ( C2 ) -* - LASTV = MAX( K, ILADLR( M, K, V, LDV ) ) - LASTC = ILADLC( LASTV, N, C, LDC ) * * W := C**T * V = (C1**T * V1 + C2**T * V2) (stored in WORK) * * W := C1**T * DO 10 J = 1, K - CALL DCOPY( LASTC, C( J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL DCOPY( N, C( J, 1 ), LDC, WORK( 1, J ), 1 ) 10 CONTINUE * * W := W * V1 * - CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', N, + $ K, ONE, V, LDV, WORK, LDWORK ) + IF( M.GT.K ) THEN * -* W := W + C2**T *V2 +* W := W + C2**T * V2 * - CALL DGEMM( 'Transpose', 'No transpose', - $ LASTC, K, LASTV-K, - $ ONE, C( K+1, 1 ), LDC, V( K+1, 1 ), LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'Transpose', 'No transpose', N, K, M-K, + $ ONE, C( K+1, 1 ), LDC, V( K+1, 1 ), LDV, + $ ONE, WORK, LDWORK ) END IF * * W := W * T**T or W * T * - CALL DTRMM( 'Right', 'Upper', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V * W**T * - IF( LASTV.GT.K ) THEN + IF( M.GT.K ) THEN * * C2 := C2 - V2 * W**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ LASTV-K, LASTC, K, - $ -ONE, V( K+1, 1 ), LDV, WORK, LDWORK, ONE, - $ C( K+1, 1 ), LDC ) + CALL DGEMM( 'No transpose', 'Transpose', M-K, N, K, + $ -ONE, V( K+1, 1 ), LDV, WORK, LDWORK, ONE, + $ C( K+1, 1 ), LDC ) END IF * * W := W * V1**T * - CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', N, K, + $ ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W**T * DO 30 J = 1, K - DO 20 I = 1, LASTC + DO 20 I = 1, N C( J, I ) = C( J, I ) - WORK( I, J ) 20 CONTINUE 30 CONTINUE @@ -311,58 +305,53 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**T where C = ( C1 C2 ) -* - LASTV = MAX( K, ILADLR( N, K, V, LDV ) ) - LASTC = ILADLR( M, LASTV, C, LDC ) * * W := C * V = (C1*V1 + C2*V2) (stored in WORK) * * W := C1 * DO 40 J = 1, K - CALL DCOPY( LASTC, C( 1, J ), 1, WORK( 1, J ), 1 ) + CALL DCOPY( M, C( 1, J ), 1, WORK( 1, J ), 1 ) 40 CONTINUE * * W := W * V1 * - CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', M, + $ K, ONE, V, LDV, WORK, LDWORK ) + IF( N.GT.K ) THEN * * W := W + C2 * V2 * - CALL DGEMM( 'No transpose', 'No transpose', - $ LASTC, K, LASTV-K, - $ ONE, C( 1, K+1 ), LDC, V( K+1, 1 ), LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'No transpose', 'No transpose', M, K, N-K, + $ ONE, C( 1, K+1 ), LDC, V( K+1, 1 ), LDV, + $ ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**T * - CALL DTRMM( 'Right', 'Upper', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V**T * - IF( LASTV.GT.K ) THEN + IF( N.GT.K ) THEN * * C2 := C2 - W * V2**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ LASTC, LASTV-K, K, - $ -ONE, WORK, LDWORK, V( K+1, 1 ), LDV, ONE, - $ C( 1, K+1 ), LDC ) + CALL DGEMM( 'No transpose', 'Transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V( K+1, 1 ), LDV, ONE, + $ C( 1, K+1 ), LDC ) END IF * * W := W * V1**T * - CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', M, K, + $ ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 60 J = 1, K - DO 50 I = 1, LASTC + DO 50 I = 1, M C( I, J ) = C( I, J ) - WORK( I, J ) 50 CONTINUE 60 CONTINUE @@ -378,36 +367,31 @@ * * Form H * C or H**T * C where C = ( C1 ) * ( C2 ) -* - LASTC = ILADLC( M, N, C, LDC ) * * W := C**T * V = (C1**T * V1 + C2**T * V2) (stored in WORK) * * W := C2**T * DO 70 J = 1, K - CALL DCOPY( LASTC, C( M-K+J, 1 ), LDC, - $ WORK( 1, J ), 1 ) + CALL DCOPY( N, C( M-K+J, 1 ), LDC, WORK( 1, J ), 1 ) 70 CONTINUE * * W := W * V2 * - CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( M-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', N, + $ K, ONE, V( M-K+1, 1 ), LDV, WORK, LDWORK ) IF( M.GT.K ) THEN * -* W := W + C1**T*V1 +* W := W + C1**T * V1 * - CALL DGEMM( 'Transpose', 'No transpose', - $ LASTC, K, M-K, ONE, C, LDC, V, LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'Transpose', 'No transpose', N, K, M-K, + $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T**T or W * T * - CALL DTRMM( 'Right', 'Lower', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V * W**T * @@ -415,57 +399,51 @@ * * C1 := C1 - V1 * W**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ M-K, LASTC, K, -ONE, V, LDV, WORK, LDWORK, - $ ONE, C, LDC ) + CALL DGEMM( 'No transpose', 'Transpose', M-K, N, K, + $ -ONE, V, LDV, WORK, LDWORK, ONE, C, LDC ) END IF * * W := W * V2**T * - CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', - $ LASTC, K, ONE, V( M-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', N, K, + $ ONE, V( M-K+1, 1 ), LDV, WORK, LDWORK ) * * C2 := C2 - W**T * DO 90 J = 1, K - DO 80 I = 1, LASTC - C( M-K+J, I ) = C( M-K+J, I ) - WORK(I, J) + DO 80 I = 1, N + C( M-K+J, I ) = C( M-K+J, I ) - WORK( I, J ) 80 CONTINUE 90 CONTINUE * ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**T where C = ( C1 C2 ) -* - LASTC = ILADLR( M, N, C, LDC ) * * W := C * V = (C1*V1 + C2*V2) (stored in WORK) * * W := C2 * DO 100 J = 1, K - CALL DCOPY( LASTC, C( 1, N-K+J ), 1, WORK( 1, J ), 1 ) + CALL DCOPY( M, C( 1, N-K+J ), 1, WORK( 1, J ), 1 ) 100 CONTINUE * * W := W * V2 * - CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( N-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', M, + $ K, ONE, V( N-K+1, 1 ), LDV, WORK, LDWORK ) IF( N.GT.K ) THEN * * W := W + C1 * V1 * - CALL DGEMM( 'No transpose', 'No transpose', - $ LASTC, K, N-K, ONE, C, LDC, V, LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'No transpose', 'No transpose', M, K, N-K, + $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**T * - CALL DTRMM( 'Right', 'Lower', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V**T * @@ -473,22 +451,20 @@ * * C1 := C1 - W * V1**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ LASTC, N-K, K, -ONE, WORK, LDWORK, V, LDV, - $ ONE, C, LDC ) + CALL DGEMM( 'No transpose', 'Transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V, LDV, ONE, C, LDC ) END IF * * W := W * V2**T * - CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', - $ LASTC, K, ONE, V( N-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', M, K, + $ ONE, V( N-K+1, 1 ), LDV, WORK, LDWORK ) * * C2 := C2 - W * DO 120 J = 1, K - DO 110 I = 1, LASTC - C( I, N-K+J ) = C( I, N-K+J ) - WORK(I, J) + DO 110 I = 1, M + C( I, N-K+J ) = C( I, N-K+J ) - WORK( I, J ) 110 CONTINUE 120 CONTINUE END IF @@ -505,58 +481,53 @@ * * Form H * C or H**T * C where C = ( C1 ) * ( C2 ) -* - LASTV = MAX( K, ILADLC( K, M, V, LDV ) ) - LASTC = ILADLC( LASTV, N, C, LDC ) * * W := C**T * V**T = (C1**T * V1**T + C2**T * V2**T) (stored in WORK) * * W := C1**T * DO 130 J = 1, K - CALL DCOPY( LASTC, C( J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL DCOPY( N, C( J, 1 ), LDC, WORK( 1, J ), 1 ) 130 CONTINUE * * W := W * V1**T * - CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', N, K, + $ ONE, V, LDV, WORK, LDWORK ) + IF( M.GT.K ) THEN * -* W := W + C2**T*V2**T +* W := W + C2**T * V2**T * - CALL DGEMM( 'Transpose', 'Transpose', - $ LASTC, K, LASTV-K, - $ ONE, C( K+1, 1 ), LDC, V( 1, K+1 ), LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'Transpose', 'Transpose', N, K, M-K, ONE, + $ C( K+1, 1 ), LDC, V( 1, K+1 ), LDV, ONE, + $ WORK, LDWORK ) END IF * * W := W * T**T or W * T * - CALL DTRMM( 'Right', 'Upper', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V**T * W**T * - IF( LASTV.GT.K ) THEN + IF( M.GT.K ) THEN * * C2 := C2 - V2**T * W**T * - CALL DGEMM( 'Transpose', 'Transpose', - $ LASTV-K, LASTC, K, - $ -ONE, V( 1, K+1 ), LDV, WORK, LDWORK, - $ ONE, C( K+1, 1 ), LDC ) + CALL DGEMM( 'Transpose', 'Transpose', M-K, N, K, -ONE, + $ V( 1, K+1 ), LDV, WORK, LDWORK, ONE, + $ C( K+1, 1 ), LDC ) END IF * * W := W * V1 * - CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', N, + $ K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W**T * DO 150 J = 1, K - DO 140 I = 1, LASTC + DO 140 I = 1, N C( J, I ) = C( J, I ) - WORK( I, J ) 140 CONTINUE 150 CONTINUE @@ -564,58 +535,53 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**T where C = ( C1 C2 ) -* - LASTV = MAX( K, ILADLC( K, N, V, LDV ) ) - LASTC = ILADLR( M, LASTV, C, LDC ) * * W := C * V**T = (C1*V1**T + C2*V2**T) (stored in WORK) * * W := C1 * DO 160 J = 1, K - CALL DCOPY( LASTC, C( 1, J ), 1, WORK( 1, J ), 1 ) + CALL DCOPY( M, C( 1, J ), 1, WORK( 1, J ), 1 ) 160 CONTINUE * * W := W * V1**T * - CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL DTRMM( 'Right', 'Upper', 'Transpose', 'Unit', M, K, + $ ONE, V, LDV, WORK, LDWORK ) + IF( N.GT.K ) THEN * * W := W + C2 * V2**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ LASTC, K, LASTV-K, - $ ONE, C( 1, K+1 ), LDC, V( 1, K+1 ), LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'No transpose', 'Transpose', M, K, N-K, + $ ONE, C( 1, K+1 ), LDC, V( 1, K+1 ), LDV, + $ ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**T * - CALL DTRMM( 'Right', 'Upper', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V * - IF( LASTV.GT.K ) THEN + IF( N.GT.K ) THEN * * C2 := C2 - W * V2 * - CALL DGEMM( 'No transpose', 'No transpose', - $ LASTC, LASTV-K, K, - $ -ONE, WORK, LDWORK, V( 1, K+1 ), LDV, - $ ONE, C( 1, K+1 ), LDC ) + CALL DGEMM( 'No transpose', 'No transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V( 1, K+1 ), LDV, ONE, + $ C( 1, K+1 ), LDC ) END IF * * W := W * V1 * - CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Upper', 'No transpose', 'Unit', M, + $ K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 180 J = 1, K - DO 170 I = 1, LASTC + DO 170 I = 1, M C( I, J ) = C( I, J ) - WORK( I, J ) 170 CONTINUE 180 CONTINUE @@ -631,36 +597,31 @@ * * Form H * C or H**T * C where C = ( C1 ) * ( C2 ) -* - LASTC = ILADLC( M, N, C, LDC ) * * W := C**T * V**T = (C1**T * V1**T + C2**T * V2**T) (stored in WORK) * * W := C2**T * DO 190 J = 1, K - CALL DCOPY( LASTC, C( M-K+J, 1 ), LDC, - $ WORK( 1, J ), 1 ) + CALL DCOPY( N, C( M-K+J, 1 ), LDC, WORK( 1, J ), 1 ) 190 CONTINUE * * W := W * V2**T * - CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', - $ LASTC, K, ONE, V( 1, M-K+1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', N, K, + $ ONE, V( 1, M-K+1 ), LDV, WORK, LDWORK ) IF( M.GT.K ) THEN * * W := W + C1**T * V1**T * - CALL DGEMM( 'Transpose', 'Transpose', - $ LASTC, K, M-K, ONE, C, LDC, V, LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'Transpose', 'Transpose', N, K, M-K, ONE, + $ C, LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T**T or W * T * - CALL DTRMM( 'Right', 'Lower', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V**T * W**T * @@ -668,58 +629,51 @@ * * C1 := C1 - V1**T * W**T * - CALL DGEMM( 'Transpose', 'Transpose', - $ M-K, LASTC, K, -ONE, V, LDV, WORK, LDWORK, - $ ONE, C, LDC ) + CALL DGEMM( 'Transpose', 'Transpose', M-K, N, K, -ONE, + $ V, LDV, WORK, LDWORK, ONE, C, LDC ) END IF * * W := W * V2 * - CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( 1, M-K+1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', N, + $ K, ONE, V( 1, M-K+1 ), LDV, WORK, LDWORK ) * * C2 := C2 - W**T * DO 210 J = 1, K - DO 200 I = 1, LASTC - C( M-K+J, I ) = C( M-K+J, I ) - WORK(I, J) + DO 200 I = 1, N + C( M-K+J, I ) = C( M-K+J, I ) - WORK( I, J ) 200 CONTINUE 210 CONTINUE * ELSE IF( LSAME( SIDE, 'R' ) ) THEN * -* Form C * H or C * H**T where C = ( C1 C2 ) -* - LASTC = ILADLR( M, N, C, LDC ) +* Form C * H or C * H' where C = ( C1 C2 ) * * W := C * V**T = (C1*V1**T + C2*V2**T) (stored in WORK) * * W := C2 * DO 220 J = 1, K - CALL DCOPY( LASTC, C( 1, N-K+J ), 1, - $ WORK( 1, J ), 1 ) + CALL DCOPY( M, C( 1, N-K+J ), 1, WORK( 1, J ), 1 ) 220 CONTINUE * * W := W * V2**T * - CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', - $ LASTC, K, ONE, V( 1, N-K+1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'Transpose', 'Unit', M, K, + $ ONE, V( 1, N-K+1 ), LDV, WORK, LDWORK ) IF( N.GT.K ) THEN * * W := W + C1 * V1**T * - CALL DGEMM( 'No transpose', 'Transpose', - $ LASTC, K, N-K, ONE, C, LDC, V, LDV, - $ ONE, WORK, LDWORK ) + CALL DGEMM( 'No transpose', 'Transpose', M, K, N-K, + $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**T * - CALL DTRMM( 'Right', 'Lower', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V * @@ -727,22 +681,20 @@ * * C1 := C1 - W * V1 * - CALL DGEMM( 'No transpose', 'No transpose', - $ LASTC, N-K, K, -ONE, WORK, LDWORK, V, LDV, - $ ONE, C, LDC ) + CALL DGEMM( 'No transpose', 'No transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V, LDV, ONE, C, LDC ) END IF * * W := W * V2 * - CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( 1, N-K+1 ), LDV, - $ WORK, LDWORK ) + CALL DTRMM( 'Right', 'Lower', 'No transpose', 'Unit', M, + $ K, ONE, V( 1, N-K+1 ), LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 240 J = 1, K - DO 230 I = 1, LASTC - C( I, N-K+J ) = C( I, N-K+J ) - WORK(I, J) + DO 230 I = 1, M + C( I, N-K+J ) = C( I, N-K+J ) - WORK( I, J ) 230 CONTINUE 240 CONTINUE * diff --git a/lib/linalg/dlarfg.f b/lib/linalg/dlarfg.f index ce91d33c1af5474e49f6ffb90303f8028218813c..cb177a57035aa4995a2d56cc4a70b765a9fdbf7a 100644 --- a/lib/linalg/dlarfg.f +++ b/lib/linalg/dlarfg.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLARFG + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLARFG + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLARFG( N, ALPHA, X, INCX, TAU ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * DOUBLE PRECISION ALPHA, TAU @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -94,22 +94,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLARFG( N, ALPHA, X, INCX, TAU ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/dlarft.f b/lib/linalg/dlarft.f index bc1b53b2ce746387ae1476e64369a723c67d8712..e69a6b792ee3005a544f26fdbbde8014b96d2620 100644 --- a/lib/linalg/dlarft.f +++ b/lib/linalg/dlarft.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLARFT + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLARFT + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, STOREV * INTEGER K, LDT, LDV, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION T( LDT, * ), TAU( * ), V( LDV, * ) * .. -* +* * *> \par Purpose: * ============= @@ -125,12 +125,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * @@ -163,10 +163,10 @@ * ===================================================================== SUBROUTINE DLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, STOREV @@ -221,13 +221,13 @@ END DO DO J = 1, I-1 T( J, I ) = -TAU( I ) * V( I , J ) - END DO + END DO J = MIN( LASTV, PREVLASTV ) * * T(1:i-1,i) := - tau(i) * V(i:j,1:i-1)**T * V(i:j,i) * - CALL DGEMV( 'Transpose', J-I, I-1, -TAU( I ), - $ V( I+1, 1 ), LDV, V( I+1, I ), 1, ONE, + CALL DGEMV( 'Transpose', J-I, I-1, -TAU( I ), + $ V( I+1, 1 ), LDV, V( I+1, I ), 1, ONE, $ T( 1, I ), 1 ) ELSE * Skip any trailing zeros. @@ -236,7 +236,7 @@ END DO DO J = 1, I-1 T( J, I ) = -TAU( I ) * V( J , I ) - END DO + END DO J = MIN( LASTV, PREVLASTV ) * * T(1:i-1,i) := - tau(i) * V(1:i-1,i:j) * V(i,i:j)**T @@ -280,7 +280,7 @@ END DO DO J = I+1, K T( J, I ) = -TAU( I ) * V( N-K+I , J ) - END DO + END DO J = MAX( LASTV, PREVLASTV ) * * T(i+1:k,i) = -tau(i) * V(j:n-k+i,i+1:k)**T * V(j:n-k+i,i) @@ -295,7 +295,7 @@ END DO DO J = I+1, K T( J, I ) = -TAU( I ) * V( J, N-K+I ) - END DO + END DO J = MAX( LASTV, PREVLASTV ) * * T(i+1:k,i) = -tau(i) * V(i+1:k,j:n-k+i) * V(i,j:n-k+i)**T diff --git a/lib/linalg/dlartg.f b/lib/linalg/dlartg.f index bf74c4365c3f0c3f86e9ca45d34f1d6bb7862f31..1c7c46f638b731c40f7ddab9a15e5321da46448d 100644 --- a/lib/linalg/dlartg.f +++ b/lib/linalg/dlartg.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLARTG + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLARTG + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLARTG( F, G, CS, SN, R ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION CS, F, G, R, SN * .. -* +* * *> \par Purpose: * ============= @@ -85,22 +85,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLARTG( F, G, CS, SN, R ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION CS, F, G, R, SN diff --git a/lib/linalg/dlas2.f b/lib/linalg/dlas2.f index 81077f940d3dbe6f589e2ebf2d3e79dc0dd96dbf..83873bc612822f7448d7d3698024c56c2d6c655f 100644 --- a/lib/linalg/dlas2.f +++ b/lib/linalg/dlas2.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLAS2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLAS2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLAS2( F, G, H, SSMIN, SSMAX ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION F, G, H, SSMAX, SSMIN * .. -* +* * *> \par Purpose: * ============= @@ -73,14 +73,14 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -107,10 +107,10 @@ * ===================================================================== SUBROUTINE DLAS2( F, G, H, SSMIN, SSMAX ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION F, G, H, SSMAX, SSMIN diff --git a/lib/linalg/dlascl.f b/lib/linalg/dlascl.f index 9b9b33c0c1482888394180502b453a93f62e8c26..03e1000a8784ae181cd73a76aee8acbb96448db4 100644 --- a/lib/linalg/dlascl.f +++ b/lib/linalg/dlascl.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASCL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASCL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER TYPE * INTEGER INFO, KL, KU, LDA, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -114,7 +114,11 @@ *> \param[in] LDA *> \verbatim *> LDA is INTEGER -*> The leading dimension of the array A. LDA >= max(1,M). +*> The leading dimension of the array A. +*> If TYPE = 'G', 'L', 'U', 'H', LDA >= max(1,M); +*> TYPE = 'B', LDA >= KL+1; +*> TYPE = 'Q', LDA >= KU+1; +*> TYPE = 'Z', LDA >= 2*KL+KU+1. *> \endverbatim *> *> \param[out] INFO @@ -127,22 +131,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. CHARACTER TYPE diff --git a/lib/linalg/dlasd4.f b/lib/linalg/dlasd4.f new file mode 100644 index 0000000000000000000000000000000000000000..8b4a8762c877ef4093462a88269209bb7e228c65 --- /dev/null +++ b/lib/linalg/dlasd4.f @@ -0,0 +1,1061 @@ +*> \brief \b DLASD4 computes the square root of the i-th updated eigenvalue of a positive symmetric rank-one modification to a positive diagonal matrix. Used by dbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASD4 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASD4( N, I, D, Z, DELTA, RHO, SIGMA, WORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER I, INFO, N +* DOUBLE PRECISION RHO, SIGMA +* .. +* .. Array Arguments .. +* DOUBLE PRECISION D( * ), DELTA( * ), WORK( * ), Z( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> This subroutine computes the square root of the I-th updated +*> eigenvalue of a positive symmetric rank-one modification to +*> a positive diagonal matrix whose entries are given as the squares +*> of the corresponding entries in the array d, and that +*> +*> 0 <= D(i) < D(j) for i < j +*> +*> and that RHO > 0. This is arranged by the calling routine, and is +*> no loss in generality. The rank-one modified system is thus +*> +*> diag( D ) * diag( D ) + RHO * Z * Z_transpose. +*> +*> where we assume the Euclidean norm of Z is 1. +*> +*> The method consists of approximating the rational functions in the +*> secular equation by simpler interpolating rational functions. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The length of all arrays. +*> \endverbatim +*> +*> \param[in] I +*> \verbatim +*> I is INTEGER +*> The index of the eigenvalue to be computed. 1 <= I <= N. +*> \endverbatim +*> +*> \param[in] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( N ) +*> The original eigenvalues. It is assumed that they are in +*> order, 0 <= D(I) < D(J) for I < J. +*> \endverbatim +*> +*> \param[in] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( N ) +*> The components of the updating vector. +*> \endverbatim +*> +*> \param[out] DELTA +*> \verbatim +*> DELTA is DOUBLE PRECISION array, dimension ( N ) +*> If N .ne. 1, DELTA contains (D(j) - sigma_I) in its j-th +*> component. If N = 1, then DELTA(1) = 1. The vector DELTA +*> contains the information necessary to construct the +*> (singular) eigenvectors. +*> \endverbatim +*> +*> \param[in] RHO +*> \verbatim +*> RHO is DOUBLE PRECISION +*> The scalar in the symmetric updating formula. +*> \endverbatim +*> +*> \param[out] SIGMA +*> \verbatim +*> SIGMA is DOUBLE PRECISION +*> The computed sigma_I, the I-th updated eigenvalue. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension ( N ) +*> If N .ne. 1, WORK contains (D(j) + sigma_I) in its j-th +*> component. If N = 1, then WORK( 1 ) = 1. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> > 0: if INFO = 1, the updating process failed. +*> \endverbatim +* +*> \par Internal Parameters: +* ========================= +*> +*> \verbatim +*> Logical variable ORGATI (origin-at-i?) is used for distinguishing +*> whether D(i) or D(i+1) is treated as the origin. +*> +*> ORGATI = .true. origin at i +*> ORGATI = .false. origin at i+1 +*> +*> Logical variable SWTCH3 (switch-for-3-poles?) is for noting +*> if we are working with THREE poles! +*> +*> MAXIT is the maximum number of iterations allowed for each +*> eigenvalue. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ren-Cang Li, Computer Science Division, University of California +*> at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASD4( N, I, D, Z, DELTA, RHO, SIGMA, WORK, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER I, INFO, N + DOUBLE PRECISION RHO, SIGMA +* .. +* .. Array Arguments .. + DOUBLE PRECISION D( * ), DELTA( * ), WORK( * ), Z( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + INTEGER MAXIT + PARAMETER ( MAXIT = 400 ) + DOUBLE PRECISION ZERO, ONE, TWO, THREE, FOUR, EIGHT, TEN + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0, TWO = 2.0D+0, + $ THREE = 3.0D+0, FOUR = 4.0D+0, EIGHT = 8.0D+0, + $ TEN = 10.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL ORGATI, SWTCH, SWTCH3, GEOMAVG + INTEGER II, IIM1, IIP1, IP1, ITER, J, NITER + DOUBLE PRECISION A, B, C, DELSQ, DELSQ2, SQ2, DPHI, DPSI, DTIIM, + $ DTIIP, DTIPSQ, DTISQ, DTNSQ, DTNSQ1, DW, EPS, + $ ERRETM, ETA, PHI, PREW, PSI, RHOINV, SGLB, + $ SGUB, TAU, TAU2, TEMP, TEMP1, TEMP2, W +* .. +* .. Local Arrays .. + DOUBLE PRECISION DD( 3 ), ZZ( 3 ) +* .. +* .. External Subroutines .. + EXTERNAL DLAED6, DLASD5 +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH + EXTERNAL DLAMCH +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN, SQRT +* .. +* .. Executable Statements .. +* +* Since this routine is called in an inner loop, we do no argument +* checking. +* +* Quick return for N=1 and 2. +* + INFO = 0 + IF( N.EQ.1 ) THEN +* +* Presumably, I=1 upon entry +* + SIGMA = SQRT( D( 1 )*D( 1 )+RHO*Z( 1 )*Z( 1 ) ) + DELTA( 1 ) = ONE + WORK( 1 ) = ONE + RETURN + END IF + IF( N.EQ.2 ) THEN + CALL DLASD5( I, D, Z, DELTA, RHO, SIGMA, WORK ) + RETURN + END IF +* +* Compute machine epsilon +* + EPS = DLAMCH( 'Epsilon' ) + RHOINV = ONE / RHO + TAU2= ZERO +* +* The case I = N +* + IF( I.EQ.N ) THEN +* +* Initialize some basic variables +* + II = N - 1 + NITER = 1 +* +* Calculate initial guess +* + TEMP = RHO / TWO +* +* If ||Z||_2 is not one, then TEMP should be set to +* RHO * ||Z||_2^2 / TWO +* + TEMP1 = TEMP / ( D( N )+SQRT( D( N )*D( N )+TEMP ) ) + DO 10 J = 1, N + WORK( J ) = D( J ) + D( N ) + TEMP1 + DELTA( J ) = ( D( J )-D( N ) ) - TEMP1 + 10 CONTINUE +* + PSI = ZERO + DO 20 J = 1, N - 2 + PSI = PSI + Z( J )*Z( J ) / ( DELTA( J )*WORK( J ) ) + 20 CONTINUE +* + C = RHOINV + PSI + W = C + Z( II )*Z( II ) / ( DELTA( II )*WORK( II ) ) + + $ Z( N )*Z( N ) / ( DELTA( N )*WORK( N ) ) +* + IF( W.LE.ZERO ) THEN + TEMP1 = SQRT( D( N )*D( N )+RHO ) + TEMP = Z( N-1 )*Z( N-1 ) / ( ( D( N-1 )+TEMP1 )* + $ ( D( N )-D( N-1 )+RHO / ( D( N )+TEMP1 ) ) ) + + $ Z( N )*Z( N ) / RHO +* +* The following TAU2 is to approximate +* SIGMA_n^2 - D( N )*D( N ) +* + IF( C.LE.TEMP ) THEN + TAU = RHO + ELSE + DELSQ = ( D( N )-D( N-1 ) )*( D( N )+D( N-1 ) ) + A = -C*DELSQ + Z( N-1 )*Z( N-1 ) + Z( N )*Z( N ) + B = Z( N )*Z( N )*DELSQ + IF( A.LT.ZERO ) THEN + TAU2 = TWO*B / ( SQRT( A*A+FOUR*B*C )-A ) + ELSE + TAU2 = ( A+SQRT( A*A+FOUR*B*C ) ) / ( TWO*C ) + END IF + TAU = TAU2 / ( D( N )+SQRT( D( N )*D( N )+TAU2 ) ) + END IF +* +* It can be proved that +* D(N)^2+RHO/2 <= SIGMA_n^2 < D(N)^2+TAU2 <= D(N)^2+RHO +* + ELSE + DELSQ = ( D( N )-D( N-1 ) )*( D( N )+D( N-1 ) ) + A = -C*DELSQ + Z( N-1 )*Z( N-1 ) + Z( N )*Z( N ) + B = Z( N )*Z( N )*DELSQ +* +* The following TAU2 is to approximate +* SIGMA_n^2 - D( N )*D( N ) +* + IF( A.LT.ZERO ) THEN + TAU2 = TWO*B / ( SQRT( A*A+FOUR*B*C )-A ) + ELSE + TAU2 = ( A+SQRT( A*A+FOUR*B*C ) ) / ( TWO*C ) + END IF + TAU = TAU2 / ( D( N )+SQRT( D( N )*D( N )+TAU2 ) ) + +* +* It can be proved that +* D(N)^2 < D(N)^2+TAU2 < SIGMA(N)^2 < D(N)^2+RHO/2 +* + END IF +* +* The following TAU is to approximate SIGMA_n - D( N ) +* +* TAU = TAU2 / ( D( N )+SQRT( D( N )*D( N )+TAU2 ) ) +* + SIGMA = D( N ) + TAU + DO 30 J = 1, N + DELTA( J ) = ( D( J )-D( N ) ) - TAU + WORK( J ) = D( J ) + D( N ) + TAU + 30 CONTINUE +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 40 J = 1, II + TEMP = Z( J ) / ( DELTA( J )*WORK( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 40 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + TEMP = Z( N ) / ( DELTA( N )*WORK( N ) ) + PHI = Z( N )*TEMP + DPHI = TEMP*TEMP + ERRETM = EIGHT*( -PHI-PSI ) + ERRETM - PHI + RHOINV +* $ + ABS( TAU2 )*( DPSI+DPHI ) +* + W = RHOINV + PHI + PSI +* +* Test for convergence +* + IF( ABS( W ).LE.EPS*ERRETM ) THEN + GO TO 240 + END IF +* +* Calculate the new step +* + NITER = NITER + 1 + DTNSQ1 = WORK( N-1 )*DELTA( N-1 ) + DTNSQ = WORK( N )*DELTA( N ) + C = W - DTNSQ1*DPSI - DTNSQ*DPHI + A = ( DTNSQ+DTNSQ1 )*W - DTNSQ*DTNSQ1*( DPSI+DPHI ) + B = DTNSQ*DTNSQ1*W + IF( C.LT.ZERO ) + $ C = ABS( C ) + IF( C.EQ.ZERO ) THEN + ETA = RHO - SIGMA*SIGMA + ELSE IF( A.GE.ZERO ) THEN + ETA = ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF +* +* Note, eta should be positive if w is negative, and +* eta should be negative otherwise. However, +* if for some reason caused by roundoff, eta*w > 0, +* we simply use one Newton step instead. This way +* will guarantee eta*w < 0. +* + IF( W*ETA.GT.ZERO ) + $ ETA = -W / ( DPSI+DPHI ) + TEMP = ETA - DTNSQ + IF( TEMP.GT.RHO ) + $ ETA = RHO + DTNSQ +* + ETA = ETA / ( SIGMA+SQRT( ETA+SIGMA*SIGMA ) ) + TAU = TAU + ETA + SIGMA = SIGMA + ETA +* + DO 50 J = 1, N + DELTA( J ) = DELTA( J ) - ETA + WORK( J ) = WORK( J ) + ETA + 50 CONTINUE +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 60 J = 1, II + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 60 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + TAU2 = WORK( N )*DELTA( N ) + TEMP = Z( N ) / TAU2 + PHI = Z( N )*TEMP + DPHI = TEMP*TEMP + ERRETM = EIGHT*( -PHI-PSI ) + ERRETM - PHI + RHOINV +* $ + ABS( TAU2 )*( DPSI+DPHI ) +* + W = RHOINV + PHI + PSI +* +* Main loop to update the values of the array DELTA +* + ITER = NITER + 1 +* + DO 90 NITER = ITER, MAXIT +* +* Test for convergence +* + IF( ABS( W ).LE.EPS*ERRETM ) THEN + GO TO 240 + END IF +* +* Calculate the new step +* + DTNSQ1 = WORK( N-1 )*DELTA( N-1 ) + DTNSQ = WORK( N )*DELTA( N ) + C = W - DTNSQ1*DPSI - DTNSQ*DPHI + A = ( DTNSQ+DTNSQ1 )*W - DTNSQ1*DTNSQ*( DPSI+DPHI ) + B = DTNSQ1*DTNSQ*W + IF( A.GE.ZERO ) THEN + ETA = ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF +* +* Note, eta should be positive if w is negative, and +* eta should be negative otherwise. However, +* if for some reason caused by roundoff, eta*w > 0, +* we simply use one Newton step instead. This way +* will guarantee eta*w < 0. +* + IF( W*ETA.GT.ZERO ) + $ ETA = -W / ( DPSI+DPHI ) + TEMP = ETA - DTNSQ + IF( TEMP.LE.ZERO ) + $ ETA = ETA / TWO +* + ETA = ETA / ( SIGMA+SQRT( ETA+SIGMA*SIGMA ) ) + TAU = TAU + ETA + SIGMA = SIGMA + ETA +* + DO 70 J = 1, N + DELTA( J ) = DELTA( J ) - ETA + WORK( J ) = WORK( J ) + ETA + 70 CONTINUE +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 80 J = 1, II + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 80 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + TAU2 = WORK( N )*DELTA( N ) + TEMP = Z( N ) / TAU2 + PHI = Z( N )*TEMP + DPHI = TEMP*TEMP + ERRETM = EIGHT*( -PHI-PSI ) + ERRETM - PHI + RHOINV +* $ + ABS( TAU2 )*( DPSI+DPHI ) +* + W = RHOINV + PHI + PSI + 90 CONTINUE +* +* Return with INFO = 1, NITER = MAXIT and not converged +* + INFO = 1 + GO TO 240 +* +* End for the case I = N +* + ELSE +* +* The case for I < N +* + NITER = 1 + IP1 = I + 1 +* +* Calculate initial guess +* + DELSQ = ( D( IP1 )-D( I ) )*( D( IP1 )+D( I ) ) + DELSQ2 = DELSQ / TWO + SQ2=SQRT( ( D( I )*D( I )+D( IP1 )*D( IP1 ) ) / TWO ) + TEMP = DELSQ2 / ( D( I )+SQ2 ) + DO 100 J = 1, N + WORK( J ) = D( J ) + D( I ) + TEMP + DELTA( J ) = ( D( J )-D( I ) ) - TEMP + 100 CONTINUE +* + PSI = ZERO + DO 110 J = 1, I - 1 + PSI = PSI + Z( J )*Z( J ) / ( WORK( J )*DELTA( J ) ) + 110 CONTINUE +* + PHI = ZERO + DO 120 J = N, I + 2, -1 + PHI = PHI + Z( J )*Z( J ) / ( WORK( J )*DELTA( J ) ) + 120 CONTINUE + C = RHOINV + PSI + PHI + W = C + Z( I )*Z( I ) / ( WORK( I )*DELTA( I ) ) + + $ Z( IP1 )*Z( IP1 ) / ( WORK( IP1 )*DELTA( IP1 ) ) +* + GEOMAVG = .FALSE. + IF( W.GT.ZERO ) THEN +* +* d(i)^2 < the ith sigma^2 < (d(i)^2+d(i+1)^2)/2 +* +* We choose d(i) as origin. +* + ORGATI = .TRUE. + II = I + SGLB = ZERO + SGUB = DELSQ2 / ( D( I )+SQ2 ) + A = C*DELSQ + Z( I )*Z( I ) + Z( IP1 )*Z( IP1 ) + B = Z( I )*Z( I )*DELSQ + IF( A.GT.ZERO ) THEN + TAU2 = TWO*B / ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) + ELSE + TAU2 = ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + END IF +* +* TAU2 now is an estimation of SIGMA^2 - D( I )^2. The +* following, however, is the corresponding estimation of +* SIGMA - D( I ). +* + TAU = TAU2 / ( D( I )+SQRT( D( I )*D( I )+TAU2 ) ) + TEMP = SQRT(EPS) + IF( (D(I).LE.TEMP*D(IP1)).AND.(ABS(Z(I)).LE.TEMP) + $ .AND.(D(I).GT.ZERO) ) THEN + TAU = MIN( TEN*D(I), SGUB ) + GEOMAVG = .TRUE. + END IF + ELSE +* +* (d(i)^2+d(i+1)^2)/2 <= the ith sigma^2 < d(i+1)^2/2 +* +* We choose d(i+1) as origin. +* + ORGATI = .FALSE. + II = IP1 + SGLB = -DELSQ2 / ( D( II )+SQ2 ) + SGUB = ZERO + A = C*DELSQ - Z( I )*Z( I ) - Z( IP1 )*Z( IP1 ) + B = Z( IP1 )*Z( IP1 )*DELSQ + IF( A.LT.ZERO ) THEN + TAU2 = TWO*B / ( A-SQRT( ABS( A*A+FOUR*B*C ) ) ) + ELSE + TAU2 = -( A+SQRT( ABS( A*A+FOUR*B*C ) ) ) / ( TWO*C ) + END IF +* +* TAU2 now is an estimation of SIGMA^2 - D( IP1 )^2. The +* following, however, is the corresponding estimation of +* SIGMA - D( IP1 ). +* + TAU = TAU2 / ( D( IP1 )+SQRT( ABS( D( IP1 )*D( IP1 )+ + $ TAU2 ) ) ) + END IF +* + SIGMA = D( II ) + TAU + DO 130 J = 1, N + WORK( J ) = D( J ) + D( II ) + TAU + DELTA( J ) = ( D( J )-D( II ) ) - TAU + 130 CONTINUE + IIM1 = II - 1 + IIP1 = II + 1 +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 150 J = 1, IIM1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 150 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + DPHI = ZERO + PHI = ZERO + DO 160 J = N, IIP1, -1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PHI = PHI + Z( J )*TEMP + DPHI = DPHI + TEMP*TEMP + ERRETM = ERRETM + PHI + 160 CONTINUE +* + W = RHOINV + PHI + PSI +* +* W is the value of the secular function with +* its ii-th element removed. +* + SWTCH3 = .FALSE. + IF( ORGATI ) THEN + IF( W.LT.ZERO ) + $ SWTCH3 = .TRUE. + ELSE + IF( W.GT.ZERO ) + $ SWTCH3 = .TRUE. + END IF + IF( II.EQ.1 .OR. II.EQ.N ) + $ SWTCH3 = .FALSE. +* + TEMP = Z( II ) / ( WORK( II )*DELTA( II ) ) + DW = DPSI + DPHI + TEMP*TEMP + TEMP = Z( II )*TEMP + W = W + TEMP + ERRETM = EIGHT*( PHI-PSI ) + ERRETM + TWO*RHOINV + $ + THREE*ABS( TEMP ) +* $ + ABS( TAU2 )*DW +* +* Test for convergence +* + IF( ABS( W ).LE.EPS*ERRETM ) THEN + GO TO 240 + END IF +* + IF( W.LE.ZERO ) THEN + SGLB = MAX( SGLB, TAU ) + ELSE + SGUB = MIN( SGUB, TAU ) + END IF +* +* Calculate the new step +* + NITER = NITER + 1 + IF( .NOT.SWTCH3 ) THEN + DTIPSQ = WORK( IP1 )*DELTA( IP1 ) + DTISQ = WORK( I )*DELTA( I ) + IF( ORGATI ) THEN + C = W - DTIPSQ*DW + DELSQ*( Z( I ) / DTISQ )**2 + ELSE + C = W - DTISQ*DW - DELSQ*( Z( IP1 ) / DTIPSQ )**2 + END IF + A = ( DTIPSQ+DTISQ )*W - DTIPSQ*DTISQ*DW + B = DTIPSQ*DTISQ*W + IF( C.EQ.ZERO ) THEN + IF( A.EQ.ZERO ) THEN + IF( ORGATI ) THEN + A = Z( I )*Z( I ) + DTIPSQ*DTIPSQ*( DPSI+DPHI ) + ELSE + A = Z( IP1 )*Z( IP1 ) + DTISQ*DTISQ*( DPSI+DPHI ) + END IF + END IF + ETA = B / A + ELSE IF( A.LE.ZERO ) THEN + ETA = ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF + ELSE +* +* Interpolation using THREE most relevant poles +* + DTIIM = WORK( IIM1 )*DELTA( IIM1 ) + DTIIP = WORK( IIP1 )*DELTA( IIP1 ) + TEMP = RHOINV + PSI + PHI + IF( ORGATI ) THEN + TEMP1 = Z( IIM1 ) / DTIIM + TEMP1 = TEMP1*TEMP1 + C = ( TEMP - DTIIP*( DPSI+DPHI ) ) - + $ ( D( IIM1 )-D( IIP1 ) )*( D( IIM1 )+D( IIP1 ) )*TEMP1 + ZZ( 1 ) = Z( IIM1 )*Z( IIM1 ) + IF( DPSI.LT.TEMP1 ) THEN + ZZ( 3 ) = DTIIP*DTIIP*DPHI + ELSE + ZZ( 3 ) = DTIIP*DTIIP*( ( DPSI-TEMP1 )+DPHI ) + END IF + ELSE + TEMP1 = Z( IIP1 ) / DTIIP + TEMP1 = TEMP1*TEMP1 + C = ( TEMP - DTIIM*( DPSI+DPHI ) ) - + $ ( D( IIP1 )-D( IIM1 ) )*( D( IIM1 )+D( IIP1 ) )*TEMP1 + IF( DPHI.LT.TEMP1 ) THEN + ZZ( 1 ) = DTIIM*DTIIM*DPSI + ELSE + ZZ( 1 ) = DTIIM*DTIIM*( DPSI+( DPHI-TEMP1 ) ) + END IF + ZZ( 3 ) = Z( IIP1 )*Z( IIP1 ) + END IF + ZZ( 2 ) = Z( II )*Z( II ) + DD( 1 ) = DTIIM + DD( 2 ) = DELTA( II )*WORK( II ) + DD( 3 ) = DTIIP + CALL DLAED6( NITER, ORGATI, C, DD, ZZ, W, ETA, INFO ) +* + IF( INFO.NE.0 ) THEN +* +* If INFO is not 0, i.e., DLAED6 failed, switch back +* to 2 pole interpolation. +* + SWTCH3 = .FALSE. + INFO = 0 + DTIPSQ = WORK( IP1 )*DELTA( IP1 ) + DTISQ = WORK( I )*DELTA( I ) + IF( ORGATI ) THEN + C = W - DTIPSQ*DW + DELSQ*( Z( I ) / DTISQ )**2 + ELSE + C = W - DTISQ*DW - DELSQ*( Z( IP1 ) / DTIPSQ )**2 + END IF + A = ( DTIPSQ+DTISQ )*W - DTIPSQ*DTISQ*DW + B = DTIPSQ*DTISQ*W + IF( C.EQ.ZERO ) THEN + IF( A.EQ.ZERO ) THEN + IF( ORGATI ) THEN + A = Z( I )*Z( I ) + DTIPSQ*DTIPSQ*( DPSI+DPHI ) + ELSE + A = Z( IP1 )*Z( IP1 ) + DTISQ*DTISQ*( DPSI+DPHI) + END IF + END IF + ETA = B / A + ELSE IF( A.LE.ZERO ) THEN + ETA = ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF + END IF + END IF +* +* Note, eta should be positive if w is negative, and +* eta should be negative otherwise. However, +* if for some reason caused by roundoff, eta*w > 0, +* we simply use one Newton step instead. This way +* will guarantee eta*w < 0. +* + IF( W*ETA.GE.ZERO ) + $ ETA = -W / DW +* + ETA = ETA / ( SIGMA+SQRT( SIGMA*SIGMA+ETA ) ) + TEMP = TAU + ETA + IF( TEMP.GT.SGUB .OR. TEMP.LT.SGLB ) THEN + IF( W.LT.ZERO ) THEN + ETA = ( SGUB-TAU ) / TWO + ELSE + ETA = ( SGLB-TAU ) / TWO + END IF + IF( GEOMAVG ) THEN + IF( W .LT. ZERO ) THEN + IF( TAU .GT. ZERO ) THEN + ETA = SQRT(SGUB*TAU)-TAU + END IF + ELSE + IF( SGLB .GT. ZERO ) THEN + ETA = SQRT(SGLB*TAU)-TAU + END IF + END IF + END IF + END IF +* + PREW = W +* + TAU = TAU + ETA + SIGMA = SIGMA + ETA +* + DO 170 J = 1, N + WORK( J ) = WORK( J ) + ETA + DELTA( J ) = DELTA( J ) - ETA + 170 CONTINUE +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 180 J = 1, IIM1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 180 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + DPHI = ZERO + PHI = ZERO + DO 190 J = N, IIP1, -1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PHI = PHI + Z( J )*TEMP + DPHI = DPHI + TEMP*TEMP + ERRETM = ERRETM + PHI + 190 CONTINUE +* + TAU2 = WORK( II )*DELTA( II ) + TEMP = Z( II ) / TAU2 + DW = DPSI + DPHI + TEMP*TEMP + TEMP = Z( II )*TEMP + W = RHOINV + PHI + PSI + TEMP + ERRETM = EIGHT*( PHI-PSI ) + ERRETM + TWO*RHOINV + $ + THREE*ABS( TEMP ) +* $ + ABS( TAU2 )*DW +* + SWTCH = .FALSE. + IF( ORGATI ) THEN + IF( -W.GT.ABS( PREW ) / TEN ) + $ SWTCH = .TRUE. + ELSE + IF( W.GT.ABS( PREW ) / TEN ) + $ SWTCH = .TRUE. + END IF +* +* Main loop to update the values of the array DELTA and WORK +* + ITER = NITER + 1 +* + DO 230 NITER = ITER, MAXIT +* +* Test for convergence +* + IF( ABS( W ).LE.EPS*ERRETM ) THEN +* $ .OR. (SGUB-SGLB).LE.EIGHT*ABS(SGUB+SGLB) ) THEN + GO TO 240 + END IF +* + IF( W.LE.ZERO ) THEN + SGLB = MAX( SGLB, TAU ) + ELSE + SGUB = MIN( SGUB, TAU ) + END IF +* +* Calculate the new step +* + IF( .NOT.SWTCH3 ) THEN + DTIPSQ = WORK( IP1 )*DELTA( IP1 ) + DTISQ = WORK( I )*DELTA( I ) + IF( .NOT.SWTCH ) THEN + IF( ORGATI ) THEN + C = W - DTIPSQ*DW + DELSQ*( Z( I ) / DTISQ )**2 + ELSE + C = W - DTISQ*DW - DELSQ*( Z( IP1 ) / DTIPSQ )**2 + END IF + ELSE + TEMP = Z( II ) / ( WORK( II )*DELTA( II ) ) + IF( ORGATI ) THEN + DPSI = DPSI + TEMP*TEMP + ELSE + DPHI = DPHI + TEMP*TEMP + END IF + C = W - DTISQ*DPSI - DTIPSQ*DPHI + END IF + A = ( DTIPSQ+DTISQ )*W - DTIPSQ*DTISQ*DW + B = DTIPSQ*DTISQ*W + IF( C.EQ.ZERO ) THEN + IF( A.EQ.ZERO ) THEN + IF( .NOT.SWTCH ) THEN + IF( ORGATI ) THEN + A = Z( I )*Z( I ) + DTIPSQ*DTIPSQ* + $ ( DPSI+DPHI ) + ELSE + A = Z( IP1 )*Z( IP1 ) + + $ DTISQ*DTISQ*( DPSI+DPHI ) + END IF + ELSE + A = DTISQ*DTISQ*DPSI + DTIPSQ*DTIPSQ*DPHI + END IF + END IF + ETA = B / A + ELSE IF( A.LE.ZERO ) THEN + ETA = ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF + ELSE +* +* Interpolation using THREE most relevant poles +* + DTIIM = WORK( IIM1 )*DELTA( IIM1 ) + DTIIP = WORK( IIP1 )*DELTA( IIP1 ) + TEMP = RHOINV + PSI + PHI + IF( SWTCH ) THEN + C = TEMP - DTIIM*DPSI - DTIIP*DPHI + ZZ( 1 ) = DTIIM*DTIIM*DPSI + ZZ( 3 ) = DTIIP*DTIIP*DPHI + ELSE + IF( ORGATI ) THEN + TEMP1 = Z( IIM1 ) / DTIIM + TEMP1 = TEMP1*TEMP1 + TEMP2 = ( D( IIM1 )-D( IIP1 ) )* + $ ( D( IIM1 )+D( IIP1 ) )*TEMP1 + C = TEMP - DTIIP*( DPSI+DPHI ) - TEMP2 + ZZ( 1 ) = Z( IIM1 )*Z( IIM1 ) + IF( DPSI.LT.TEMP1 ) THEN + ZZ( 3 ) = DTIIP*DTIIP*DPHI + ELSE + ZZ( 3 ) = DTIIP*DTIIP*( ( DPSI-TEMP1 )+DPHI ) + END IF + ELSE + TEMP1 = Z( IIP1 ) / DTIIP + TEMP1 = TEMP1*TEMP1 + TEMP2 = ( D( IIP1 )-D( IIM1 ) )* + $ ( D( IIM1 )+D( IIP1 ) )*TEMP1 + C = TEMP - DTIIM*( DPSI+DPHI ) - TEMP2 + IF( DPHI.LT.TEMP1 ) THEN + ZZ( 1 ) = DTIIM*DTIIM*DPSI + ELSE + ZZ( 1 ) = DTIIM*DTIIM*( DPSI+( DPHI-TEMP1 ) ) + END IF + ZZ( 3 ) = Z( IIP1 )*Z( IIP1 ) + END IF + END IF + DD( 1 ) = DTIIM + DD( 2 ) = DELTA( II )*WORK( II ) + DD( 3 ) = DTIIP + CALL DLAED6( NITER, ORGATI, C, DD, ZZ, W, ETA, INFO ) +* + IF( INFO.NE.0 ) THEN +* +* If INFO is not 0, i.e., DLAED6 failed, switch +* back to two pole interpolation +* + SWTCH3 = .FALSE. + INFO = 0 + DTIPSQ = WORK( IP1 )*DELTA( IP1 ) + DTISQ = WORK( I )*DELTA( I ) + IF( .NOT.SWTCH ) THEN + IF( ORGATI ) THEN + C = W - DTIPSQ*DW + DELSQ*( Z( I )/DTISQ )**2 + ELSE + C = W - DTISQ*DW - DELSQ*( Z( IP1 )/DTIPSQ )**2 + END IF + ELSE + TEMP = Z( II ) / ( WORK( II )*DELTA( II ) ) + IF( ORGATI ) THEN + DPSI = DPSI + TEMP*TEMP + ELSE + DPHI = DPHI + TEMP*TEMP + END IF + C = W - DTISQ*DPSI - DTIPSQ*DPHI + END IF + A = ( DTIPSQ+DTISQ )*W - DTIPSQ*DTISQ*DW + B = DTIPSQ*DTISQ*W + IF( C.EQ.ZERO ) THEN + IF( A.EQ.ZERO ) THEN + IF( .NOT.SWTCH ) THEN + IF( ORGATI ) THEN + A = Z( I )*Z( I ) + DTIPSQ*DTIPSQ* + $ ( DPSI+DPHI ) + ELSE + A = Z( IP1 )*Z( IP1 ) + + $ DTISQ*DTISQ*( DPSI+DPHI ) + END IF + ELSE + A = DTISQ*DTISQ*DPSI + DTIPSQ*DTIPSQ*DPHI + END IF + END IF + ETA = B / A + ELSE IF( A.LE.ZERO ) THEN + ETA = ( A-SQRT( ABS( A*A-FOUR*B*C ) ) ) / ( TWO*C ) + ELSE + ETA = TWO*B / ( A+SQRT( ABS( A*A-FOUR*B*C ) ) ) + END IF + END IF + END IF +* +* Note, eta should be positive if w is negative, and +* eta should be negative otherwise. However, +* if for some reason caused by roundoff, eta*w > 0, +* we simply use one Newton step instead. This way +* will guarantee eta*w < 0. +* + IF( W*ETA.GE.ZERO ) + $ ETA = -W / DW +* + ETA = ETA / ( SIGMA+SQRT( SIGMA*SIGMA+ETA ) ) + TEMP=TAU+ETA + IF( TEMP.GT.SGUB .OR. TEMP.LT.SGLB ) THEN + IF( W.LT.ZERO ) THEN + ETA = ( SGUB-TAU ) / TWO + ELSE + ETA = ( SGLB-TAU ) / TWO + END IF + IF( GEOMAVG ) THEN + IF( W .LT. ZERO ) THEN + IF( TAU .GT. ZERO ) THEN + ETA = SQRT(SGUB*TAU)-TAU + END IF + ELSE + IF( SGLB .GT. ZERO ) THEN + ETA = SQRT(SGLB*TAU)-TAU + END IF + END IF + END IF + END IF +* + PREW = W +* + TAU = TAU + ETA + SIGMA = SIGMA + ETA +* + DO 200 J = 1, N + WORK( J ) = WORK( J ) + ETA + DELTA( J ) = DELTA( J ) - ETA + 200 CONTINUE +* +* Evaluate PSI and the derivative DPSI +* + DPSI = ZERO + PSI = ZERO + ERRETM = ZERO + DO 210 J = 1, IIM1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PSI = PSI + Z( J )*TEMP + DPSI = DPSI + TEMP*TEMP + ERRETM = ERRETM + PSI + 210 CONTINUE + ERRETM = ABS( ERRETM ) +* +* Evaluate PHI and the derivative DPHI +* + DPHI = ZERO + PHI = ZERO + DO 220 J = N, IIP1, -1 + TEMP = Z( J ) / ( WORK( J )*DELTA( J ) ) + PHI = PHI + Z( J )*TEMP + DPHI = DPHI + TEMP*TEMP + ERRETM = ERRETM + PHI + 220 CONTINUE +* + TAU2 = WORK( II )*DELTA( II ) + TEMP = Z( II ) / TAU2 + DW = DPSI + DPHI + TEMP*TEMP + TEMP = Z( II )*TEMP + W = RHOINV + PHI + PSI + TEMP + ERRETM = EIGHT*( PHI-PSI ) + ERRETM + TWO*RHOINV + $ + THREE*ABS( TEMP ) +* $ + ABS( TAU2 )*DW +* + IF( W*PREW.GT.ZERO .AND. ABS( W ).GT.ABS( PREW ) / TEN ) + $ SWTCH = .NOT.SWTCH +* + 230 CONTINUE +* +* Return with INFO = 1, NITER = MAXIT and not converged +* + INFO = 1 +* + END IF +* + 240 CONTINUE + RETURN +* +* End of DLASD4 +* + END diff --git a/lib/linalg/dlasd5.f b/lib/linalg/dlasd5.f new file mode 100644 index 0000000000000000000000000000000000000000..4896ba6b97933679049f70b83afa1f45cb7796db --- /dev/null +++ b/lib/linalg/dlasd5.f @@ -0,0 +1,231 @@ +*> \brief \b DLASD5 computes the square root of the i-th eigenvalue of a positive symmetric rank-one modification of a 2-by-2 diagonal matrix. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASD5 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASD5( I, D, Z, DELTA, RHO, DSIGMA, WORK ) +* +* .. Scalar Arguments .. +* INTEGER I +* DOUBLE PRECISION DSIGMA, RHO +* .. +* .. Array Arguments .. +* DOUBLE PRECISION D( 2 ), DELTA( 2 ), WORK( 2 ), Z( 2 ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> This subroutine computes the square root of the I-th eigenvalue +*> of a positive symmetric rank-one modification of a 2-by-2 diagonal +*> matrix +*> +*> diag( D ) * diag( D ) + RHO * Z * transpose(Z) . +*> +*> The diagonal entries in the array D are assumed to satisfy +*> +*> 0 <= D(i) < D(j) for i < j . +*> +*> We also assume RHO > 0 and that the Euclidean norm of the vector +*> Z is one. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] I +*> \verbatim +*> I is INTEGER +*> The index of the eigenvalue to be computed. I = 1 or I = 2. +*> \endverbatim +*> +*> \param[in] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( 2 ) +*> The original eigenvalues. We assume 0 <= D(1) < D(2). +*> \endverbatim +*> +*> \param[in] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( 2 ) +*> The components of the updating vector. +*> \endverbatim +*> +*> \param[out] DELTA +*> \verbatim +*> DELTA is DOUBLE PRECISION array, dimension ( 2 ) +*> Contains (D(j) - sigma_I) in its j-th component. +*> The vector DELTA contains the information necessary +*> to construct the eigenvectors. +*> \endverbatim +*> +*> \param[in] RHO +*> \verbatim +*> RHO is DOUBLE PRECISION +*> The scalar in the symmetric updating formula. +*> \endverbatim +*> +*> \param[out] DSIGMA +*> \verbatim +*> DSIGMA is DOUBLE PRECISION +*> The computed sigma_I, the I-th updated eigenvalue. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension ( 2 ) +*> WORK contains (D(j) + sigma_I) in its j-th component. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ren-Cang Li, Computer Science Division, University of California +*> at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASD5( I, D, Z, DELTA, RHO, DSIGMA, WORK ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER I + DOUBLE PRECISION DSIGMA, RHO +* .. +* .. Array Arguments .. + DOUBLE PRECISION D( 2 ), DELTA( 2 ), WORK( 2 ), Z( 2 ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE, TWO, THREE, FOUR + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0, TWO = 2.0D+0, + $ THREE = 3.0D+0, FOUR = 4.0D+0 ) +* .. +* .. Local Scalars .. + DOUBLE PRECISION B, C, DEL, DELSQ, TAU, W +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, SQRT +* .. +* .. Executable Statements .. +* + DEL = D( 2 ) - D( 1 ) + DELSQ = DEL*( D( 2 )+D( 1 ) ) + IF( I.EQ.1 ) THEN + W = ONE + FOUR*RHO*( Z( 2 )*Z( 2 ) / ( D( 1 )+THREE*D( 2 ) )- + $ Z( 1 )*Z( 1 ) / ( THREE*D( 1 )+D( 2 ) ) ) / DEL + IF( W.GT.ZERO ) THEN + B = DELSQ + RHO*( Z( 1 )*Z( 1 )+Z( 2 )*Z( 2 ) ) + C = RHO*Z( 1 )*Z( 1 )*DELSQ +* +* B > ZERO, always +* +* The following TAU is DSIGMA * DSIGMA - D( 1 ) * D( 1 ) +* + TAU = TWO*C / ( B+SQRT( ABS( B*B-FOUR*C ) ) ) +* +* The following TAU is DSIGMA - D( 1 ) +* + TAU = TAU / ( D( 1 )+SQRT( D( 1 )*D( 1 )+TAU ) ) + DSIGMA = D( 1 ) + TAU + DELTA( 1 ) = -TAU + DELTA( 2 ) = DEL - TAU + WORK( 1 ) = TWO*D( 1 ) + TAU + WORK( 2 ) = ( D( 1 )+TAU ) + D( 2 ) +* DELTA( 1 ) = -Z( 1 ) / TAU +* DELTA( 2 ) = Z( 2 ) / ( DEL-TAU ) + ELSE + B = -DELSQ + RHO*( Z( 1 )*Z( 1 )+Z( 2 )*Z( 2 ) ) + C = RHO*Z( 2 )*Z( 2 )*DELSQ +* +* The following TAU is DSIGMA * DSIGMA - D( 2 ) * D( 2 ) +* + IF( B.GT.ZERO ) THEN + TAU = -TWO*C / ( B+SQRT( B*B+FOUR*C ) ) + ELSE + TAU = ( B-SQRT( B*B+FOUR*C ) ) / TWO + END IF +* +* The following TAU is DSIGMA - D( 2 ) +* + TAU = TAU / ( D( 2 )+SQRT( ABS( D( 2 )*D( 2 )+TAU ) ) ) + DSIGMA = D( 2 ) + TAU + DELTA( 1 ) = -( DEL+TAU ) + DELTA( 2 ) = -TAU + WORK( 1 ) = D( 1 ) + TAU + D( 2 ) + WORK( 2 ) = TWO*D( 2 ) + TAU +* DELTA( 1 ) = -Z( 1 ) / ( DEL+TAU ) +* DELTA( 2 ) = -Z( 2 ) / TAU + END IF +* TEMP = SQRT( DELTA( 1 )*DELTA( 1 )+DELTA( 2 )*DELTA( 2 ) ) +* DELTA( 1 ) = DELTA( 1 ) / TEMP +* DELTA( 2 ) = DELTA( 2 ) / TEMP + ELSE +* +* Now I=2 +* + B = -DELSQ + RHO*( Z( 1 )*Z( 1 )+Z( 2 )*Z( 2 ) ) + C = RHO*Z( 2 )*Z( 2 )*DELSQ +* +* The following TAU is DSIGMA * DSIGMA - D( 2 ) * D( 2 ) +* + IF( B.GT.ZERO ) THEN + TAU = ( B+SQRT( B*B+FOUR*C ) ) / TWO + ELSE + TAU = TWO*C / ( -B+SQRT( B*B+FOUR*C ) ) + END IF +* +* The following TAU is DSIGMA - D( 2 ) +* + TAU = TAU / ( D( 2 )+SQRT( D( 2 )*D( 2 )+TAU ) ) + DSIGMA = D( 2 ) + TAU + DELTA( 1 ) = -( DEL+TAU ) + DELTA( 2 ) = -TAU + WORK( 1 ) = D( 1 ) + TAU + D( 2 ) + WORK( 2 ) = TWO*D( 2 ) + TAU +* DELTA( 1 ) = -Z( 1 ) / ( DEL+TAU ) +* DELTA( 2 ) = -Z( 2 ) / TAU +* TEMP = SQRT( DELTA( 1 )*DELTA( 1 )+DELTA( 2 )*DELTA( 2 ) ) +* DELTA( 1 ) = DELTA( 1 ) / TEMP +* DELTA( 2 ) = DELTA( 2 ) / TEMP + END IF + RETURN +* +* End of DLASD5 +* + END diff --git a/lib/linalg/dlasd6.f b/lib/linalg/dlasd6.f new file mode 100644 index 0000000000000000000000000000000000000000..5cab78a07081eb56d7ed0a36f2194ad9e3776551 --- /dev/null +++ b/lib/linalg/dlasd6.f @@ -0,0 +1,443 @@ +*> \brief \b DLASD6 computes the SVD of an updated upper bidiagonal matrix obtained by merging two smaller ones by appending a row. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASD6 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASD6( ICOMPQ, NL, NR, SQRE, D, VF, VL, ALPHA, BETA, +* IDXQ, PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, +* LDGNUM, POLES, DIFL, DIFR, Z, K, C, S, WORK, +* IWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, +* $ NR, SQRE +* DOUBLE PRECISION ALPHA, BETA, C, S +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( LDGCOL, * ), IDXQ( * ), IWORK( * ), +* $ PERM( * ) +* DOUBLE PRECISION D( * ), DIFL( * ), DIFR( * ), +* $ GIVNUM( LDGNUM, * ), POLES( LDGNUM, * ), +* $ VF( * ), VL( * ), WORK( * ), Z( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLASD6 computes the SVD of an updated upper bidiagonal matrix B +*> obtained by merging two smaller ones by appending a row. This +*> routine is used only for the problem which requires all singular +*> values and optionally singular vector matrices in factored form. +*> B is an N-by-M matrix with N = NL + NR + 1 and M = N + SQRE. +*> A related subroutine, DLASD1, handles the case in which all singular +*> values and singular vectors of the bidiagonal matrix are desired. +*> +*> DLASD6 computes the SVD as follows: +*> +*> ( D1(in) 0 0 0 ) +*> B = U(in) * ( Z1**T a Z2**T b ) * VT(in) +*> ( 0 0 D2(in) 0 ) +*> +*> = U(out) * ( D(out) 0) * VT(out) +*> +*> where Z**T = (Z1**T a Z2**T b) = u**T VT**T, and u is a vector of dimension M +*> with ALPHA and BETA in the NL+1 and NL+2 th entries and zeros +*> elsewhere; and the entry b is empty if SQRE = 0. +*> +*> The singular values of B can be computed using D1, D2, the first +*> components of all the right singular vectors of the lower block, and +*> the last components of all the right singular vectors of the upper +*> block. These components are stored and updated in VF and VL, +*> respectively, in DLASD6. Hence U and VT are not explicitly +*> referenced. +*> +*> The singular values are stored in D. The algorithm consists of two +*> stages: +*> +*> The first stage consists of deflating the size of the problem +*> when there are multiple singular values or if there is a zero +*> in the Z vector. For each such occurrence the dimension of the +*> secular equation problem is reduced by one. This stage is +*> performed by the routine DLASD7. +*> +*> The second stage consists of calculating the updated +*> singular values. This is done by finding the roots of the +*> secular equation via the routine DLASD4 (as called by DLASD8). +*> This routine also updates VF and VL and computes the distances +*> between the updated singular values and the old singular +*> values. +*> +*> DLASD6 is called from DLASDA. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether singular vectors are to be computed in +*> factored form: +*> = 0: Compute singular values only. +*> = 1: Compute singular vectors in factored form as well. +*> \endverbatim +*> +*> \param[in] NL +*> \verbatim +*> NL is INTEGER +*> The row dimension of the upper block. NL >= 1. +*> \endverbatim +*> +*> \param[in] NR +*> \verbatim +*> NR is INTEGER +*> The row dimension of the lower block. NR >= 1. +*> \endverbatim +*> +*> \param[in] SQRE +*> \verbatim +*> SQRE is INTEGER +*> = 0: the lower block is an NR-by-NR square matrix. +*> = 1: the lower block is an NR-by-(NR+1) rectangular matrix. +*> +*> The bidiagonal matrix has row dimension N = NL + NR + 1, +*> and column dimension M = N + SQRE. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( NL+NR+1 ). +*> On entry D(1:NL,1:NL) contains the singular values of the +*> upper block, and D(NL+2:N) contains the singular values +*> of the lower block. On exit D(1:N) contains the singular +*> values of the modified matrix. +*> \endverbatim +*> +*> \param[in,out] VF +*> \verbatim +*> VF is DOUBLE PRECISION array, dimension ( M ) +*> On entry, VF(1:NL+1) contains the first components of all +*> right singular vectors of the upper block; and VF(NL+2:M) +*> contains the first components of all right singular vectors +*> of the lower block. On exit, VF contains the first components +*> of all right singular vectors of the bidiagonal matrix. +*> \endverbatim +*> +*> \param[in,out] VL +*> \verbatim +*> VL is DOUBLE PRECISION array, dimension ( M ) +*> On entry, VL(1:NL+1) contains the last components of all +*> right singular vectors of the upper block; and VL(NL+2:M) +*> contains the last components of all right singular vectors of +*> the lower block. On exit, VL contains the last components of +*> all right singular vectors of the bidiagonal matrix. +*> \endverbatim +*> +*> \param[in,out] ALPHA +*> \verbatim +*> ALPHA is DOUBLE PRECISION +*> Contains the diagonal element associated with the added row. +*> \endverbatim +*> +*> \param[in,out] BETA +*> \verbatim +*> BETA is DOUBLE PRECISION +*> Contains the off-diagonal element associated with the added +*> row. +*> \endverbatim +*> +*> \param[in,out] IDXQ +*> \verbatim +*> IDXQ is INTEGER array, dimension ( N ) +*> This contains the permutation which will reintegrate the +*> subproblem just solved back into sorted order, i.e. +*> D( IDXQ( I = 1, N ) ) will be in ascending order. +*> \endverbatim +*> +*> \param[out] PERM +*> \verbatim +*> PERM is INTEGER array, dimension ( N ) +*> The permutations (from deflation and sorting) to be applied +*> to each block. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[out] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER +*> The number of Givens rotations which took place in this +*> subproblem. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[out] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension ( LDGCOL, 2 ) +*> Each pair of numbers indicates a pair of columns to take place +*> in a Givens rotation. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[in] LDGCOL +*> \verbatim +*> LDGCOL is INTEGER +*> leading dimension of GIVCOL, must be at least N. +*> \endverbatim +*> +*> \param[out] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ) +*> Each number indicates the C or S value to be used in the +*> corresponding Givens rotation. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[in] LDGNUM +*> \verbatim +*> LDGNUM is INTEGER +*> The leading dimension of GIVNUM and POLES, must be at least N. +*> \endverbatim +*> +*> \param[out] POLES +*> \verbatim +*> POLES is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ) +*> On exit, POLES(1,*) is an array containing the new singular +*> values obtained from solving the secular equation, and +*> POLES(2,*) is an array containing the poles in the secular +*> equation. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[out] DIFL +*> \verbatim +*> DIFL is DOUBLE PRECISION array, dimension ( N ) +*> On exit, DIFL(I) is the distance between I-th updated +*> (undeflated) singular value and the I-th (undeflated) old +*> singular value. +*> \endverbatim +*> +*> \param[out] DIFR +*> \verbatim +*> DIFR is DOUBLE PRECISION array, +*> dimension ( LDDIFR, 2 ) if ICOMPQ = 1 and +*> dimension ( K ) if ICOMPQ = 0. +*> On exit, DIFR(I,1) = D(I) - DSIGMA(I+1), DIFR(K,1) is not +*> defined and will not be referenced. +*> +*> If ICOMPQ = 1, DIFR(1:K,2) is an array containing the +*> normalizing factors for the right singular vector matrix. +*> +*> See DLASD8 for details on DIFL and DIFR. +*> \endverbatim +*> +*> \param[out] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( M ) +*> The first elements of this array contain the components +*> of the deflation-adjusted updating row vector. +*> \endverbatim +*> +*> \param[out] K +*> \verbatim +*> K is INTEGER +*> Contains the dimension of the non-deflated matrix, +*> This is the order of the related secular equation. 1 <= K <=N. +*> \endverbatim +*> +*> \param[out] C +*> \verbatim +*> C is DOUBLE PRECISION +*> C contains garbage if SQRE =0 and the C-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[out] S +*> \verbatim +*> S is DOUBLE PRECISION +*> S contains garbage if SQRE =0 and the S-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension ( 4 * M ) +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension ( 3 * N ) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: if INFO = 1, a singular value did not converge +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASD6( ICOMPQ, NL, NR, SQRE, D, VF, VL, ALPHA, BETA, + $ IDXQ, PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, + $ LDGNUM, POLES, DIFL, DIFR, Z, K, C, S, WORK, + $ IWORK, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2016 +* +* .. Scalar Arguments .. + INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, + $ NR, SQRE + DOUBLE PRECISION ALPHA, BETA, C, S +* .. +* .. Array Arguments .. + INTEGER GIVCOL( LDGCOL, * ), IDXQ( * ), IWORK( * ), + $ PERM( * ) + DOUBLE PRECISION D( * ), DIFL( * ), DIFR( * ), + $ GIVNUM( LDGNUM, * ), POLES( LDGNUM, * ), + $ VF( * ), VL( * ), WORK( * ), Z( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, IDX, IDXC, IDXP, ISIGMA, IVFW, IVLW, IW, M, + $ N, N1, N2 + DOUBLE PRECISION ORGNRM +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DLAMRG, DLASCL, DLASD7, DLASD8, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + N = NL + NR + 1 + M = N + SQRE +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( NL.LT.1 ) THEN + INFO = -2 + ELSE IF( NR.LT.1 ) THEN + INFO = -3 + ELSE IF( ( SQRE.LT.0 ) .OR. ( SQRE.GT.1 ) ) THEN + INFO = -4 + ELSE IF( LDGCOL.LT.N ) THEN + INFO = -14 + ELSE IF( LDGNUM.LT.N ) THEN + INFO = -16 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLASD6', -INFO ) + RETURN + END IF +* +* The following values are for bookkeeping purposes only. They are +* integer pointers which indicate the portion of the workspace +* used by a particular array in DLASD7 and DLASD8. +* + ISIGMA = 1 + IW = ISIGMA + N + IVFW = IW + M + IVLW = IVFW + M +* + IDX = 1 + IDXC = IDX + N + IDXP = IDXC + N +* +* Scale. +* + ORGNRM = MAX( ABS( ALPHA ), ABS( BETA ) ) + D( NL+1 ) = ZERO + DO 10 I = 1, N + IF( ABS( D( I ) ).GT.ORGNRM ) THEN + ORGNRM = ABS( D( I ) ) + END IF + 10 CONTINUE + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, N, 1, D, N, INFO ) + ALPHA = ALPHA / ORGNRM + BETA = BETA / ORGNRM +* +* Sort and Deflate singular values. +* + CALL DLASD7( ICOMPQ, NL, NR, SQRE, K, D, Z, WORK( IW ), VF, + $ WORK( IVFW ), VL, WORK( IVLW ), ALPHA, BETA, + $ WORK( ISIGMA ), IWORK( IDX ), IWORK( IDXP ), IDXQ, + $ PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, C, S, + $ INFO ) +* +* Solve Secular Equation, compute DIFL, DIFR, and update VF, VL. +* + CALL DLASD8( ICOMPQ, K, D, Z, VF, VL, DIFL, DIFR, LDGNUM, + $ WORK( ISIGMA ), WORK( IW ), INFO ) +* +* Report the possible convergence failure. +* + IF( INFO.NE.0 ) THEN + RETURN + END IF +* +* Save the poles if ICOMPQ = 1. +* + IF( ICOMPQ.EQ.1 ) THEN + CALL DCOPY( K, D, 1, POLES( 1, 1 ), 1 ) + CALL DCOPY( K, WORK( ISIGMA ), 1, POLES( 1, 2 ), 1 ) + END IF +* +* Unscale. +* + CALL DLASCL( 'G', 0, 0, ONE, ORGNRM, N, 1, D, N, INFO ) +* +* Prepare the IDXQ sorting permutation. +* + N1 = K + N2 = N - K + CALL DLAMRG( N1, N2, D, 1, -1, IDXQ ) +* + RETURN +* +* End of DLASD6 +* + END diff --git a/lib/linalg/dlasd7.f b/lib/linalg/dlasd7.f new file mode 100644 index 0000000000000000000000000000000000000000..e0ddedeb577142ec443aa28f14525c3e2d22e3f8 --- /dev/null +++ b/lib/linalg/dlasd7.f @@ -0,0 +1,580 @@ +*> \brief \b DLASD7 merges the two sets of singular values together into a single sorted set. Then it tries to deflate the size of the problem. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASD7 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASD7( ICOMPQ, NL, NR, SQRE, K, D, Z, ZW, VF, VFW, VL, +* VLW, ALPHA, BETA, DSIGMA, IDX, IDXP, IDXQ, +* PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, +* C, S, INFO ) +* +* .. Scalar Arguments .. +* INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, +* $ NR, SQRE +* DOUBLE PRECISION ALPHA, BETA, C, S +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( LDGCOL, * ), IDX( * ), IDXP( * ), +* $ IDXQ( * ), PERM( * ) +* DOUBLE PRECISION D( * ), DSIGMA( * ), GIVNUM( LDGNUM, * ), +* $ VF( * ), VFW( * ), VL( * ), VLW( * ), Z( * ), +* $ ZW( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLASD7 merges the two sets of singular values together into a single +*> sorted set. Then it tries to deflate the size of the problem. There +*> are two ways in which deflation can occur: when two or more singular +*> values are close together or if there is a tiny entry in the Z +*> vector. For each such occurrence the order of the related +*> secular equation problem is reduced by one. +*> +*> DLASD7 is called from DLASD6. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether singular vectors are to be computed +*> in compact form, as follows: +*> = 0: Compute singular values only. +*> = 1: Compute singular vectors of upper +*> bidiagonal matrix in compact form. +*> \endverbatim +*> +*> \param[in] NL +*> \verbatim +*> NL is INTEGER +*> The row dimension of the upper block. NL >= 1. +*> \endverbatim +*> +*> \param[in] NR +*> \verbatim +*> NR is INTEGER +*> The row dimension of the lower block. NR >= 1. +*> \endverbatim +*> +*> \param[in] SQRE +*> \verbatim +*> SQRE is INTEGER +*> = 0: the lower block is an NR-by-NR square matrix. +*> = 1: the lower block is an NR-by-(NR+1) rectangular matrix. +*> +*> The bidiagonal matrix has +*> N = NL + NR + 1 rows and +*> M = N + SQRE >= N columns. +*> \endverbatim +*> +*> \param[out] K +*> \verbatim +*> K is INTEGER +*> Contains the dimension of the non-deflated matrix, this is +*> the order of the related secular equation. 1 <= K <=N. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( N ) +*> On entry D contains the singular values of the two submatrices +*> to be combined. On exit D contains the trailing (N-K) updated +*> singular values (those which were deflated) sorted into +*> increasing order. +*> \endverbatim +*> +*> \param[out] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( M ) +*> On exit Z contains the updating row vector in the secular +*> equation. +*> \endverbatim +*> +*> \param[out] ZW +*> \verbatim +*> ZW is DOUBLE PRECISION array, dimension ( M ) +*> Workspace for Z. +*> \endverbatim +*> +*> \param[in,out] VF +*> \verbatim +*> VF is DOUBLE PRECISION array, dimension ( M ) +*> On entry, VF(1:NL+1) contains the first components of all +*> right singular vectors of the upper block; and VF(NL+2:M) +*> contains the first components of all right singular vectors +*> of the lower block. On exit, VF contains the first components +*> of all right singular vectors of the bidiagonal matrix. +*> \endverbatim +*> +*> \param[out] VFW +*> \verbatim +*> VFW is DOUBLE PRECISION array, dimension ( M ) +*> Workspace for VF. +*> \endverbatim +*> +*> \param[in,out] VL +*> \verbatim +*> VL is DOUBLE PRECISION array, dimension ( M ) +*> On entry, VL(1:NL+1) contains the last components of all +*> right singular vectors of the upper block; and VL(NL+2:M) +*> contains the last components of all right singular vectors +*> of the lower block. On exit, VL contains the last components +*> of all right singular vectors of the bidiagonal matrix. +*> \endverbatim +*> +*> \param[out] VLW +*> \verbatim +*> VLW is DOUBLE PRECISION array, dimension ( M ) +*> Workspace for VL. +*> \endverbatim +*> +*> \param[in] ALPHA +*> \verbatim +*> ALPHA is DOUBLE PRECISION +*> Contains the diagonal element associated with the added row. +*> \endverbatim +*> +*> \param[in] BETA +*> \verbatim +*> BETA is DOUBLE PRECISION +*> Contains the off-diagonal element associated with the added +*> row. +*> \endverbatim +*> +*> \param[out] DSIGMA +*> \verbatim +*> DSIGMA is DOUBLE PRECISION array, dimension ( N ) +*> Contains a copy of the diagonal elements (K-1 singular values +*> and one zero) in the secular equation. +*> \endverbatim +*> +*> \param[out] IDX +*> \verbatim +*> IDX is INTEGER array, dimension ( N ) +*> This will contain the permutation used to sort the contents of +*> D into ascending order. +*> \endverbatim +*> +*> \param[out] IDXP +*> \verbatim +*> IDXP is INTEGER array, dimension ( N ) +*> This will contain the permutation used to place deflated +*> values of D at the end of the array. On output IDXP(2:K) +*> points to the nondeflated D-values and IDXP(K+1:N) +*> points to the deflated singular values. +*> \endverbatim +*> +*> \param[in] IDXQ +*> \verbatim +*> IDXQ is INTEGER array, dimension ( N ) +*> This contains the permutation which separately sorts the two +*> sub-problems in D into ascending order. Note that entries in +*> the first half of this permutation must first be moved one +*> position backward; and entries in the second half +*> must first have NL+1 added to their values. +*> \endverbatim +*> +*> \param[out] PERM +*> \verbatim +*> PERM is INTEGER array, dimension ( N ) +*> The permutations (from deflation and sorting) to be applied +*> to each singular block. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[out] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER +*> The number of Givens rotations which took place in this +*> subproblem. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[out] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension ( LDGCOL, 2 ) +*> Each pair of numbers indicates a pair of columns to take place +*> in a Givens rotation. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[in] LDGCOL +*> \verbatim +*> LDGCOL is INTEGER +*> The leading dimension of GIVCOL, must be at least N. +*> \endverbatim +*> +*> \param[out] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension ( LDGNUM, 2 ) +*> Each number indicates the C or S value to be used in the +*> corresponding Givens rotation. Not referenced if ICOMPQ = 0. +*> \endverbatim +*> +*> \param[in] LDGNUM +*> \verbatim +*> LDGNUM is INTEGER +*> The leading dimension of GIVNUM, must be at least N. +*> \endverbatim +*> +*> \param[out] C +*> \verbatim +*> C is DOUBLE PRECISION +*> C contains garbage if SQRE =0 and the C-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[out] S +*> \verbatim +*> S is DOUBLE PRECISION +*> S contains garbage if SQRE =0 and the S-value of a Givens +*> rotation related to the right null space if SQRE = 1. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASD7( ICOMPQ, NL, NR, SQRE, K, D, Z, ZW, VF, VFW, VL, + $ VLW, ALPHA, BETA, DSIGMA, IDX, IDXP, IDXQ, + $ PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, + $ C, S, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, + $ NR, SQRE + DOUBLE PRECISION ALPHA, BETA, C, S +* .. +* .. Array Arguments .. + INTEGER GIVCOL( LDGCOL, * ), IDX( * ), IDXP( * ), + $ IDXQ( * ), PERM( * ) + DOUBLE PRECISION D( * ), DSIGMA( * ), GIVNUM( LDGNUM, * ), + $ VF( * ), VFW( * ), VL( * ), VLW( * ), Z( * ), + $ ZW( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE, TWO, EIGHT + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0, TWO = 2.0D+0, + $ EIGHT = 8.0D+0 ) +* .. +* .. Local Scalars .. +* + INTEGER I, IDXI, IDXJ, IDXJP, J, JP, JPREV, K2, M, N, + $ NLP1, NLP2 + DOUBLE PRECISION EPS, HLFTOL, TAU, TOL, Z1 +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DLAMRG, DROT, XERBLA +* .. +* .. External Functions .. + DOUBLE PRECISION DLAMCH, DLAPY2 + EXTERNAL DLAMCH, DLAPY2 +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + N = NL + NR + 1 + M = N + SQRE +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( NL.LT.1 ) THEN + INFO = -2 + ELSE IF( NR.LT.1 ) THEN + INFO = -3 + ELSE IF( ( SQRE.LT.0 ) .OR. ( SQRE.GT.1 ) ) THEN + INFO = -4 + ELSE IF( LDGCOL.LT.N ) THEN + INFO = -22 + ELSE IF( LDGNUM.LT.N ) THEN + INFO = -24 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLASD7', -INFO ) + RETURN + END IF +* + NLP1 = NL + 1 + NLP2 = NL + 2 + IF( ICOMPQ.EQ.1 ) THEN + GIVPTR = 0 + END IF +* +* Generate the first part of the vector Z and move the singular +* values in the first part of D one position backward. +* + Z1 = ALPHA*VL( NLP1 ) + VL( NLP1 ) = ZERO + TAU = VF( NLP1 ) + DO 10 I = NL, 1, -1 + Z( I+1 ) = ALPHA*VL( I ) + VL( I ) = ZERO + VF( I+1 ) = VF( I ) + D( I+1 ) = D( I ) + IDXQ( I+1 ) = IDXQ( I ) + 1 + 10 CONTINUE + VF( 1 ) = TAU +* +* Generate the second part of the vector Z. +* + DO 20 I = NLP2, M + Z( I ) = BETA*VF( I ) + VF( I ) = ZERO + 20 CONTINUE +* +* Sort the singular values into increasing order +* + DO 30 I = NLP2, N + IDXQ( I ) = IDXQ( I ) + NLP1 + 30 CONTINUE +* +* DSIGMA, IDXC, IDXC, and ZW are used as storage space. +* + DO 40 I = 2, N + DSIGMA( I ) = D( IDXQ( I ) ) + ZW( I ) = Z( IDXQ( I ) ) + VFW( I ) = VF( IDXQ( I ) ) + VLW( I ) = VL( IDXQ( I ) ) + 40 CONTINUE +* + CALL DLAMRG( NL, NR, DSIGMA( 2 ), 1, 1, IDX( 2 ) ) +* + DO 50 I = 2, N + IDXI = 1 + IDX( I ) + D( I ) = DSIGMA( IDXI ) + Z( I ) = ZW( IDXI ) + VF( I ) = VFW( IDXI ) + VL( I ) = VLW( IDXI ) + 50 CONTINUE +* +* Calculate the allowable deflation tolerence +* + EPS = DLAMCH( 'Epsilon' ) + TOL = MAX( ABS( ALPHA ), ABS( BETA ) ) + TOL = EIGHT*EIGHT*EPS*MAX( ABS( D( N ) ), TOL ) +* +* There are 2 kinds of deflation -- first a value in the z-vector +* is small, second two (or more) singular values are very close +* together (their difference is small). +* +* If the value in the z-vector is small, we simply permute the +* array so that the corresponding singular value is moved to the +* end. +* +* If two values in the D-vector are close, we perform a two-sided +* rotation designed to make one of the corresponding z-vector +* entries zero, and then permute the array so that the deflated +* singular value is moved to the end. +* +* If there are multiple singular values then the problem deflates. +* Here the number of equal singular values are found. As each equal +* singular value is found, an elementary reflector is computed to +* rotate the corresponding singular subspace so that the +* corresponding components of Z are zero in this new basis. +* + K = 1 + K2 = N + 1 + DO 60 J = 2, N + IF( ABS( Z( J ) ).LE.TOL ) THEN +* +* Deflate due to small z component. +* + K2 = K2 - 1 + IDXP( K2 ) = J + IF( J.EQ.N ) + $ GO TO 100 + ELSE + JPREV = J + GO TO 70 + END IF + 60 CONTINUE + 70 CONTINUE + J = JPREV + 80 CONTINUE + J = J + 1 + IF( J.GT.N ) + $ GO TO 90 + IF( ABS( Z( J ) ).LE.TOL ) THEN +* +* Deflate due to small z component. +* + K2 = K2 - 1 + IDXP( K2 ) = J + ELSE +* +* Check if singular values are close enough to allow deflation. +* + IF( ABS( D( J )-D( JPREV ) ).LE.TOL ) THEN +* +* Deflation is possible. +* + S = Z( JPREV ) + C = Z( J ) +* +* Find sqrt(a**2+b**2) without overflow or +* destructive underflow. +* + TAU = DLAPY2( C, S ) + Z( J ) = TAU + Z( JPREV ) = ZERO + C = C / TAU + S = -S / TAU +* +* Record the appropriate Givens rotation +* + IF( ICOMPQ.EQ.1 ) THEN + GIVPTR = GIVPTR + 1 + IDXJP = IDXQ( IDX( JPREV )+1 ) + IDXJ = IDXQ( IDX( J )+1 ) + IF( IDXJP.LE.NLP1 ) THEN + IDXJP = IDXJP - 1 + END IF + IF( IDXJ.LE.NLP1 ) THEN + IDXJ = IDXJ - 1 + END IF + GIVCOL( GIVPTR, 2 ) = IDXJP + GIVCOL( GIVPTR, 1 ) = IDXJ + GIVNUM( GIVPTR, 2 ) = C + GIVNUM( GIVPTR, 1 ) = S + END IF + CALL DROT( 1, VF( JPREV ), 1, VF( J ), 1, C, S ) + CALL DROT( 1, VL( JPREV ), 1, VL( J ), 1, C, S ) + K2 = K2 - 1 + IDXP( K2 ) = JPREV + JPREV = J + ELSE + K = K + 1 + ZW( K ) = Z( JPREV ) + DSIGMA( K ) = D( JPREV ) + IDXP( K ) = JPREV + JPREV = J + END IF + END IF + GO TO 80 + 90 CONTINUE +* +* Record the last singular value. +* + K = K + 1 + ZW( K ) = Z( JPREV ) + DSIGMA( K ) = D( JPREV ) + IDXP( K ) = JPREV +* + 100 CONTINUE +* +* Sort the singular values into DSIGMA. The singular values which +* were not deflated go into the first K slots of DSIGMA, except +* that DSIGMA(1) is treated separately. +* + DO 110 J = 2, N + JP = IDXP( J ) + DSIGMA( J ) = D( JP ) + VFW( J ) = VF( JP ) + VLW( J ) = VL( JP ) + 110 CONTINUE + IF( ICOMPQ.EQ.1 ) THEN + DO 120 J = 2, N + JP = IDXP( J ) + PERM( J ) = IDXQ( IDX( JP )+1 ) + IF( PERM( J ).LE.NLP1 ) THEN + PERM( J ) = PERM( J ) - 1 + END IF + 120 CONTINUE + END IF +* +* The deflated singular values go back into the last N - K slots of +* D. +* + CALL DCOPY( N-K, DSIGMA( K+1 ), 1, D( K+1 ), 1 ) +* +* Determine DSIGMA(1), DSIGMA(2), Z(1), VF(1), VL(1), VF(M), and +* VL(M). +* + DSIGMA( 1 ) = ZERO + HLFTOL = TOL / TWO + IF( ABS( DSIGMA( 2 ) ).LE.HLFTOL ) + $ DSIGMA( 2 ) = HLFTOL + IF( M.GT.N ) THEN + Z( 1 ) = DLAPY2( Z1, Z( M ) ) + IF( Z( 1 ).LE.TOL ) THEN + C = ONE + S = ZERO + Z( 1 ) = TOL + ELSE + C = Z1 / Z( 1 ) + S = -Z( M ) / Z( 1 ) + END IF + CALL DROT( 1, VF( M ), 1, VF( 1 ), 1, C, S ) + CALL DROT( 1, VL( M ), 1, VL( 1 ), 1, C, S ) + ELSE + IF( ABS( Z1 ).LE.TOL ) THEN + Z( 1 ) = TOL + ELSE + Z( 1 ) = Z1 + END IF + END IF +* +* Restore Z, VF, and VL. +* + CALL DCOPY( K-1, ZW( 2 ), 1, Z( 2 ), 1 ) + CALL DCOPY( N-1, VFW( 2 ), 1, VF( 2 ), 1 ) + CALL DCOPY( N-1, VLW( 2 ), 1, VL( 2 ), 1 ) +* + RETURN +* +* End of DLASD7 +* + END diff --git a/lib/linalg/dlasd8.f b/lib/linalg/dlasd8.f new file mode 100644 index 0000000000000000000000000000000000000000..fc5c48c5285b246d1ff2c1d073fc931f76505204 --- /dev/null +++ b/lib/linalg/dlasd8.f @@ -0,0 +1,342 @@ +*> \brief \b DLASD8 finds the square roots of the roots of the secular equation, and stores, for each element in D, the distance to its two nearest poles. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASD8 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASD8( ICOMPQ, K, D, Z, VF, VL, DIFL, DIFR, LDDIFR, +* DSIGMA, WORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER ICOMPQ, INFO, K, LDDIFR +* .. +* .. Array Arguments .. +* DOUBLE PRECISION D( * ), DIFL( * ), DIFR( LDDIFR, * ), +* $ DSIGMA( * ), VF( * ), VL( * ), WORK( * ), +* $ Z( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLASD8 finds the square roots of the roots of the secular equation, +*> as defined by the values in DSIGMA and Z. It makes the appropriate +*> calls to DLASD4, and stores, for each element in D, the distance +*> to its two nearest poles (elements in DSIGMA). It also updates +*> the arrays VF and VL, the first and last components of all the +*> right singular vectors of the original bidiagonal matrix. +*> +*> DLASD8 is called from DLASD6. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether singular vectors are to be computed in +*> factored form in the calling routine: +*> = 0: Compute singular values only. +*> = 1: Compute singular vectors in factored form as well. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> The number of terms in the rational function to be solved +*> by DLASD4. K >= 1. +*> \endverbatim +*> +*> \param[out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( K ) +*> On output, D contains the updated singular values. +*> \endverbatim +*> +*> \param[in,out] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension ( K ) +*> On entry, the first K elements of this array contain the +*> components of the deflation-adjusted updating row vector. +*> On exit, Z is updated. +*> \endverbatim +*> +*> \param[in,out] VF +*> \verbatim +*> VF is DOUBLE PRECISION array, dimension ( K ) +*> On entry, VF contains information passed through DBEDE8. +*> On exit, VF contains the first K components of the first +*> components of all right singular vectors of the bidiagonal +*> matrix. +*> \endverbatim +*> +*> \param[in,out] VL +*> \verbatim +*> VL is DOUBLE PRECISION array, dimension ( K ) +*> On entry, VL contains information passed through DBEDE8. +*> On exit, VL contains the first K components of the last +*> components of all right singular vectors of the bidiagonal +*> matrix. +*> \endverbatim +*> +*> \param[out] DIFL +*> \verbatim +*> DIFL is DOUBLE PRECISION array, dimension ( K ) +*> On exit, DIFL(I) = D(I) - DSIGMA(I). +*> \endverbatim +*> +*> \param[out] DIFR +*> \verbatim +*> DIFR is DOUBLE PRECISION array, +*> dimension ( LDDIFR, 2 ) if ICOMPQ = 1 and +*> dimension ( K ) if ICOMPQ = 0. +*> On exit, DIFR(I,1) = D(I) - DSIGMA(I+1), DIFR(K,1) is not +*> defined and will not be referenced. +*> +*> If ICOMPQ = 1, DIFR(1:K,2) is an array containing the +*> normalizing factors for the right singular vector matrix. +*> \endverbatim +*> +*> \param[in] LDDIFR +*> \verbatim +*> LDDIFR is INTEGER +*> The leading dimension of DIFR, must be at least K. +*> \endverbatim +*> +*> \param[in,out] DSIGMA +*> \verbatim +*> DSIGMA is DOUBLE PRECISION array, dimension ( K ) +*> On entry, the first K elements of this array contain the old +*> roots of the deflated updating problem. These are the poles +*> of the secular equation. +*> On exit, the elements of DSIGMA may be very slightly altered +*> in value. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension (3*K) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: if INFO = 1, a singular value did not converge +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2017 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASD8( ICOMPQ, K, D, Z, VF, VL, DIFL, DIFR, LDDIFR, + $ DSIGMA, WORK, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2017 +* +* .. Scalar Arguments .. + INTEGER ICOMPQ, INFO, K, LDDIFR +* .. +* .. Array Arguments .. + DOUBLE PRECISION D( * ), DIFL( * ), DIFR( LDDIFR, * ), + $ DSIGMA( * ), VF( * ), VL( * ), WORK( * ), + $ Z( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE + PARAMETER ( ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, IWK1, IWK2, IWK2I, IWK3, IWK3I, J + DOUBLE PRECISION DIFLJ, DIFRJ, DJ, DSIGJ, DSIGJP, RHO, TEMP +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DLASCL, DLASD4, DLASET, XERBLA +* .. +* .. External Functions .. + DOUBLE PRECISION DDOT, DLAMC3, DNRM2 + EXTERNAL DDOT, DLAMC3, DNRM2 +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, SIGN, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( K.LT.1 ) THEN + INFO = -2 + ELSE IF( LDDIFR.LT.K ) THEN + INFO = -9 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLASD8', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( K.EQ.1 ) THEN + D( 1 ) = ABS( Z( 1 ) ) + DIFL( 1 ) = D( 1 ) + IF( ICOMPQ.EQ.1 ) THEN + DIFL( 2 ) = ONE + DIFR( 1, 2 ) = ONE + END IF + RETURN + END IF +* +* Modify values DSIGMA(i) to make sure all DSIGMA(i)-DSIGMA(j) can +* be computed with high relative accuracy (barring over/underflow). +* This is a problem on machines without a guard digit in +* add/subtract (Cray XMP, Cray YMP, Cray C 90 and Cray 2). +* The following code replaces DSIGMA(I) by 2*DSIGMA(I)-DSIGMA(I), +* which on any of these machines zeros out the bottommost +* bit of DSIGMA(I) if it is 1; this makes the subsequent +* subtractions DSIGMA(I)-DSIGMA(J) unproblematic when cancellation +* occurs. On binary machines with a guard digit (almost all +* machines) it does not change DSIGMA(I) at all. On hexadecimal +* and decimal machines with a guard digit, it slightly +* changes the bottommost bits of DSIGMA(I). It does not account +* for hexadecimal or decimal machines without guard digits +* (we know of none). We use a subroutine call to compute +* 2*DLAMBDA(I) to prevent optimizing compilers from eliminating +* this code. +* + DO 10 I = 1, K + DSIGMA( I ) = DLAMC3( DSIGMA( I ), DSIGMA( I ) ) - DSIGMA( I ) + 10 CONTINUE +* +* Book keeping. +* + IWK1 = 1 + IWK2 = IWK1 + K + IWK3 = IWK2 + K + IWK2I = IWK2 - 1 + IWK3I = IWK3 - 1 +* +* Normalize Z. +* + RHO = DNRM2( K, Z, 1 ) + CALL DLASCL( 'G', 0, 0, RHO, ONE, K, 1, Z, K, INFO ) + RHO = RHO*RHO +* +* Initialize WORK(IWK3). +* + CALL DLASET( 'A', K, 1, ONE, ONE, WORK( IWK3 ), K ) +* +* Compute the updated singular values, the arrays DIFL, DIFR, +* and the updated Z. +* + DO 40 J = 1, K + CALL DLASD4( K, J, DSIGMA, Z, WORK( IWK1 ), RHO, D( J ), + $ WORK( IWK2 ), INFO ) +* +* If the root finder fails, report the convergence failure. +* + IF( INFO.NE.0 ) THEN + RETURN + END IF + WORK( IWK3I+J ) = WORK( IWK3I+J )*WORK( J )*WORK( IWK2I+J ) + DIFL( J ) = -WORK( J ) + DIFR( J, 1 ) = -WORK( J+1 ) + DO 20 I = 1, J - 1 + WORK( IWK3I+I ) = WORK( IWK3I+I )*WORK( I )* + $ WORK( IWK2I+I ) / ( DSIGMA( I )- + $ DSIGMA( J ) ) / ( DSIGMA( I )+ + $ DSIGMA( J ) ) + 20 CONTINUE + DO 30 I = J + 1, K + WORK( IWK3I+I ) = WORK( IWK3I+I )*WORK( I )* + $ WORK( IWK2I+I ) / ( DSIGMA( I )- + $ DSIGMA( J ) ) / ( DSIGMA( I )+ + $ DSIGMA( J ) ) + 30 CONTINUE + 40 CONTINUE +* +* Compute updated Z. +* + DO 50 I = 1, K + Z( I ) = SIGN( SQRT( ABS( WORK( IWK3I+I ) ) ), Z( I ) ) + 50 CONTINUE +* +* Update VF and VL. +* + DO 80 J = 1, K + DIFLJ = DIFL( J ) + DJ = D( J ) + DSIGJ = -DSIGMA( J ) + IF( J.LT.K ) THEN + DIFRJ = -DIFR( J, 1 ) + DSIGJP = -DSIGMA( J+1 ) + END IF + WORK( J ) = -Z( J ) / DIFLJ / ( DSIGMA( J )+DJ ) + DO 60 I = 1, J - 1 + WORK( I ) = Z( I ) / ( DLAMC3( DSIGMA( I ), DSIGJ )-DIFLJ ) + $ / ( DSIGMA( I )+DJ ) + 60 CONTINUE + DO 70 I = J + 1, K + WORK( I ) = Z( I ) / ( DLAMC3( DSIGMA( I ), DSIGJP )+DIFRJ ) + $ / ( DSIGMA( I )+DJ ) + 70 CONTINUE + TEMP = DNRM2( K, WORK, 1 ) + WORK( IWK2I+J ) = DDOT( K, WORK, 1, VF, 1 ) / TEMP + WORK( IWK3I+J ) = DDOT( K, WORK, 1, VL, 1 ) / TEMP + IF( ICOMPQ.EQ.1 ) THEN + DIFR( J, 2 ) = TEMP + END IF + 80 CONTINUE +* + CALL DCOPY( K, WORK( IWK2 ), 1, VF, 1 ) + CALL DCOPY( K, WORK( IWK3 ), 1, VL, 1 ) +* + RETURN +* +* End of DLASD8 +* + END + diff --git a/lib/linalg/dlasda.f b/lib/linalg/dlasda.f new file mode 100644 index 0000000000000000000000000000000000000000..f41a108b804b730140a94532ee53dc69a601910f --- /dev/null +++ b/lib/linalg/dlasda.f @@ -0,0 +1,514 @@ +*> \brief \b DLASDA computes the singular value decomposition (SVD) of a real upper bidiagonal matrix with diagonal d and off-diagonal e. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASDA + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASDA( ICOMPQ, SMLSIZ, N, SQRE, D, E, U, LDU, VT, K, +* DIFL, DIFR, Z, POLES, GIVPTR, GIVCOL, LDGCOL, +* PERM, GIVNUM, C, S, WORK, IWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER ICOMPQ, INFO, LDGCOL, LDU, N, SMLSIZ, SQRE +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( LDGCOL, * ), GIVPTR( * ), IWORK( * ), +* $ K( * ), PERM( LDGCOL, * ) +* DOUBLE PRECISION C( * ), D( * ), DIFL( LDU, * ), DIFR( LDU, * ), +* $ E( * ), GIVNUM( LDU, * ), POLES( LDU, * ), +* $ S( * ), U( LDU, * ), VT( LDU, * ), WORK( * ), +* $ Z( LDU, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> Using a divide and conquer approach, DLASDA computes the singular +*> value decomposition (SVD) of a real upper bidiagonal N-by-M matrix +*> B with diagonal D and offdiagonal E, where M = N + SQRE. The +*> algorithm computes the singular values in the SVD B = U * S * VT. +*> The orthogonal matrices U and VT are optionally computed in +*> compact form. +*> +*> A related subroutine, DLASD0, computes the singular values and +*> the singular vectors in explicit form. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ICOMPQ +*> \verbatim +*> ICOMPQ is INTEGER +*> Specifies whether singular vectors are to be computed +*> in compact form, as follows +*> = 0: Compute singular values only. +*> = 1: Compute singular vectors of upper bidiagonal +*> matrix in compact form. +*> \endverbatim +*> +*> \param[in] SMLSIZ +*> \verbatim +*> SMLSIZ is INTEGER +*> The maximum size of the subproblems at the bottom of the +*> computation tree. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The row dimension of the upper bidiagonal matrix. This is +*> also the dimension of the main diagonal array D. +*> \endverbatim +*> +*> \param[in] SQRE +*> \verbatim +*> SQRE is INTEGER +*> Specifies the column dimension of the bidiagonal matrix. +*> = 0: The bidiagonal matrix has column dimension M = N; +*> = 1: The bidiagonal matrix has column dimension M = N + 1. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension ( N ) +*> On entry D contains the main diagonal of the bidiagonal +*> matrix. On exit D, if INFO = 0, contains its singular values. +*> \endverbatim +*> +*> \param[in] E +*> \verbatim +*> E is DOUBLE PRECISION array, dimension ( M-1 ) +*> Contains the subdiagonal entries of the bidiagonal matrix. +*> On exit, E has been destroyed. +*> \endverbatim +*> +*> \param[out] U +*> \verbatim +*> U is DOUBLE PRECISION array, +*> dimension ( LDU, SMLSIZ ) if ICOMPQ = 1, and not referenced +*> if ICOMPQ = 0. If ICOMPQ = 1, on exit, U contains the left +*> singular vector matrices of all subproblems at the bottom +*> level. +*> \endverbatim +*> +*> \param[in] LDU +*> \verbatim +*> LDU is INTEGER, LDU = > N. +*> The leading dimension of arrays U, VT, DIFL, DIFR, POLES, +*> GIVNUM, and Z. +*> \endverbatim +*> +*> \param[out] VT +*> \verbatim +*> VT is DOUBLE PRECISION array, +*> dimension ( LDU, SMLSIZ+1 ) if ICOMPQ = 1, and not referenced +*> if ICOMPQ = 0. If ICOMPQ = 1, on exit, VT**T contains the right +*> singular vector matrices of all subproblems at the bottom +*> level. +*> \endverbatim +*> +*> \param[out] K +*> \verbatim +*> K is INTEGER array, +*> dimension ( N ) if ICOMPQ = 1 and dimension 1 if ICOMPQ = 0. +*> If ICOMPQ = 1, on exit, K(I) is the dimension of the I-th +*> secular equation on the computation tree. +*> \endverbatim +*> +*> \param[out] DIFL +*> \verbatim +*> DIFL is DOUBLE PRECISION array, dimension ( LDU, NLVL ), +*> where NLVL = floor(log_2 (N/SMLSIZ))). +*> \endverbatim +*> +*> \param[out] DIFR +*> \verbatim +*> DIFR is DOUBLE PRECISION array, +*> dimension ( LDU, 2 * NLVL ) if ICOMPQ = 1 and +*> dimension ( N ) if ICOMPQ = 0. +*> If ICOMPQ = 1, on exit, DIFL(1:N, I) and DIFR(1:N, 2 * I - 1) +*> record distances between singular values on the I-th +*> level and singular values on the (I -1)-th level, and +*> DIFR(1:N, 2 * I ) contains the normalizing factors for +*> the right singular vector matrix. See DLASD8 for details. +*> \endverbatim +*> +*> \param[out] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, +*> dimension ( LDU, NLVL ) if ICOMPQ = 1 and +*> dimension ( N ) if ICOMPQ = 0. +*> The first K elements of Z(1, I) contain the components of +*> the deflation-adjusted updating row vector for subproblems +*> on the I-th level. +*> \endverbatim +*> +*> \param[out] POLES +*> \verbatim +*> POLES is DOUBLE PRECISION array, +*> dimension ( LDU, 2 * NLVL ) if ICOMPQ = 1, and not referenced +*> if ICOMPQ = 0. If ICOMPQ = 1, on exit, POLES(1, 2*I - 1) and +*> POLES(1, 2*I) contain the new and old singular values +*> involved in the secular equations on the I-th level. +*> \endverbatim +*> +*> \param[out] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER array, +*> dimension ( N ) if ICOMPQ = 1, and not referenced if +*> ICOMPQ = 0. If ICOMPQ = 1, on exit, GIVPTR( I ) records +*> the number of Givens rotations performed on the I-th +*> problem on the computation tree. +*> \endverbatim +*> +*> \param[out] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, +*> dimension ( LDGCOL, 2 * NLVL ) if ICOMPQ = 1, and not +*> referenced if ICOMPQ = 0. If ICOMPQ = 1, on exit, for each I, +*> GIVCOL(1, 2 *I - 1) and GIVCOL(1, 2 *I) record the locations +*> of Givens rotations performed on the I-th level on the +*> computation tree. +*> \endverbatim +*> +*> \param[in] LDGCOL +*> \verbatim +*> LDGCOL is INTEGER, LDGCOL = > N. +*> The leading dimension of arrays GIVCOL and PERM. +*> \endverbatim +*> +*> \param[out] PERM +*> \verbatim +*> PERM is INTEGER array, +*> dimension ( LDGCOL, NLVL ) if ICOMPQ = 1, and not referenced +*> if ICOMPQ = 0. If ICOMPQ = 1, on exit, PERM(1, I) records +*> permutations done on the I-th level of the computation tree. +*> \endverbatim +*> +*> \param[out] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, +*> dimension ( LDU, 2 * NLVL ) if ICOMPQ = 1, and not +*> referenced if ICOMPQ = 0. If ICOMPQ = 1, on exit, for each I, +*> GIVNUM(1, 2 *I - 1) and GIVNUM(1, 2 *I) record the C- and S- +*> values of Givens rotations performed on the I-th level on +*> the computation tree. +*> \endverbatim +*> +*> \param[out] C +*> \verbatim +*> C is DOUBLE PRECISION array, +*> dimension ( N ) if ICOMPQ = 1, and dimension 1 if ICOMPQ = 0. +*> If ICOMPQ = 1 and the I-th subproblem is not square, on exit, +*> C( I ) contains the C-value of a Givens rotation related to +*> the right null space of the I-th subproblem. +*> \endverbatim +*> +*> \param[out] S +*> \verbatim +*> S is DOUBLE PRECISION array, dimension ( N ) if +*> ICOMPQ = 1, and dimension 1 if ICOMPQ = 0. If ICOMPQ = 1 +*> and the I-th subproblem is not square, on exit, S( I ) +*> contains the S-value of a Givens rotation related to +*> the right null space of the I-th subproblem. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension +*> (6 * N + (SMLSIZ + 1)*(SMLSIZ + 1)). +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (7*N) +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: if INFO = 1, a singular value did not converge +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2017 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASDA( ICOMPQ, SMLSIZ, N, SQRE, D, E, U, LDU, VT, K, + $ DIFL, DIFR, Z, POLES, GIVPTR, GIVCOL, LDGCOL, + $ PERM, GIVNUM, C, S, WORK, IWORK, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2017 +* +* .. Scalar Arguments .. + INTEGER ICOMPQ, INFO, LDGCOL, LDU, N, SMLSIZ, SQRE +* .. +* .. Array Arguments .. + INTEGER GIVCOL( LDGCOL, * ), GIVPTR( * ), IWORK( * ), + $ K( * ), PERM( LDGCOL, * ) + DOUBLE PRECISION C( * ), D( * ), DIFL( LDU, * ), DIFR( LDU, * ), + $ E( * ), GIVNUM( LDU, * ), POLES( LDU, * ), + $ S( * ), U( LDU, * ), VT( LDU, * ), WORK( * ), + $ Z( LDU, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE + PARAMETER ( ZERO = 0.0D+0, ONE = 1.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, I1, IC, IDXQ, IDXQI, IM1, INODE, ITEMP, IWK, + $ J, LF, LL, LVL, LVL2, M, NCC, ND, NDB1, NDIML, + $ NDIMR, NL, NLF, NLP1, NLVL, NR, NRF, NRP1, NRU, + $ NWORK1, NWORK2, SMLSZP, SQREI, VF, VFI, VL, VLI + DOUBLE PRECISION ALPHA, BETA +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DLASD6, DLASDQ, DLASDT, DLASET, XERBLA +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* + IF( ( ICOMPQ.LT.0 ) .OR. ( ICOMPQ.GT.1 ) ) THEN + INFO = -1 + ELSE IF( SMLSIZ.LT.3 ) THEN + INFO = -2 + ELSE IF( N.LT.0 ) THEN + INFO = -3 + ELSE IF( ( SQRE.LT.0 ) .OR. ( SQRE.GT.1 ) ) THEN + INFO = -4 + ELSE IF( LDU.LT.( N+SQRE ) ) THEN + INFO = -8 + ELSE IF( LDGCOL.LT.N ) THEN + INFO = -17 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLASDA', -INFO ) + RETURN + END IF +* + M = N + SQRE +* +* If the input matrix is too small, call DLASDQ to find the SVD. +* + IF( N.LE.SMLSIZ ) THEN + IF( ICOMPQ.EQ.0 ) THEN + CALL DLASDQ( 'U', SQRE, N, 0, 0, 0, D, E, VT, LDU, U, LDU, + $ U, LDU, WORK, INFO ) + ELSE + CALL DLASDQ( 'U', SQRE, N, M, N, 0, D, E, VT, LDU, U, LDU, + $ U, LDU, WORK, INFO ) + END IF + RETURN + END IF +* +* Book-keeping and set up the computation tree. +* + INODE = 1 + NDIML = INODE + N + NDIMR = NDIML + N + IDXQ = NDIMR + N + IWK = IDXQ + N +* + NCC = 0 + NRU = 0 +* + SMLSZP = SMLSIZ + 1 + VF = 1 + VL = VF + M + NWORK1 = VL + M + NWORK2 = NWORK1 + SMLSZP*SMLSZP +* + CALL DLASDT( N, NLVL, ND, IWORK( INODE ), IWORK( NDIML ), + $ IWORK( NDIMR ), SMLSIZ ) +* +* for the nodes on bottom level of the tree, solve +* their subproblems by DLASDQ. +* + NDB1 = ( ND+1 ) / 2 + DO 30 I = NDB1, ND +* +* IC : center row of each node +* NL : number of rows of left subproblem +* NR : number of rows of right subproblem +* NLF: starting row of the left subproblem +* NRF: starting row of the right subproblem +* + I1 = I - 1 + IC = IWORK( INODE+I1 ) + NL = IWORK( NDIML+I1 ) + NLP1 = NL + 1 + NR = IWORK( NDIMR+I1 ) + NLF = IC - NL + NRF = IC + 1 + IDXQI = IDXQ + NLF - 2 + VFI = VF + NLF - 1 + VLI = VL + NLF - 1 + SQREI = 1 + IF( ICOMPQ.EQ.0 ) THEN + CALL DLASET( 'A', NLP1, NLP1, ZERO, ONE, WORK( NWORK1 ), + $ SMLSZP ) + CALL DLASDQ( 'U', SQREI, NL, NLP1, NRU, NCC, D( NLF ), + $ E( NLF ), WORK( NWORK1 ), SMLSZP, + $ WORK( NWORK2 ), NL, WORK( NWORK2 ), NL, + $ WORK( NWORK2 ), INFO ) + ITEMP = NWORK1 + NL*SMLSZP + CALL DCOPY( NLP1, WORK( NWORK1 ), 1, WORK( VFI ), 1 ) + CALL DCOPY( NLP1, WORK( ITEMP ), 1, WORK( VLI ), 1 ) + ELSE + CALL DLASET( 'A', NL, NL, ZERO, ONE, U( NLF, 1 ), LDU ) + CALL DLASET( 'A', NLP1, NLP1, ZERO, ONE, VT( NLF, 1 ), LDU ) + CALL DLASDQ( 'U', SQREI, NL, NLP1, NL, NCC, D( NLF ), + $ E( NLF ), VT( NLF, 1 ), LDU, U( NLF, 1 ), LDU, + $ U( NLF, 1 ), LDU, WORK( NWORK1 ), INFO ) + CALL DCOPY( NLP1, VT( NLF, 1 ), 1, WORK( VFI ), 1 ) + CALL DCOPY( NLP1, VT( NLF, NLP1 ), 1, WORK( VLI ), 1 ) + END IF + IF( INFO.NE.0 ) THEN + RETURN + END IF + DO 10 J = 1, NL + IWORK( IDXQI+J ) = J + 10 CONTINUE + IF( ( I.EQ.ND ) .AND. ( SQRE.EQ.0 ) ) THEN + SQREI = 0 + ELSE + SQREI = 1 + END IF + IDXQI = IDXQI + NLP1 + VFI = VFI + NLP1 + VLI = VLI + NLP1 + NRP1 = NR + SQREI + IF( ICOMPQ.EQ.0 ) THEN + CALL DLASET( 'A', NRP1, NRP1, ZERO, ONE, WORK( NWORK1 ), + $ SMLSZP ) + CALL DLASDQ( 'U', SQREI, NR, NRP1, NRU, NCC, D( NRF ), + $ E( NRF ), WORK( NWORK1 ), SMLSZP, + $ WORK( NWORK2 ), NR, WORK( NWORK2 ), NR, + $ WORK( NWORK2 ), INFO ) + ITEMP = NWORK1 + ( NRP1-1 )*SMLSZP + CALL DCOPY( NRP1, WORK( NWORK1 ), 1, WORK( VFI ), 1 ) + CALL DCOPY( NRP1, WORK( ITEMP ), 1, WORK( VLI ), 1 ) + ELSE + CALL DLASET( 'A', NR, NR, ZERO, ONE, U( NRF, 1 ), LDU ) + CALL DLASET( 'A', NRP1, NRP1, ZERO, ONE, VT( NRF, 1 ), LDU ) + CALL DLASDQ( 'U', SQREI, NR, NRP1, NR, NCC, D( NRF ), + $ E( NRF ), VT( NRF, 1 ), LDU, U( NRF, 1 ), LDU, + $ U( NRF, 1 ), LDU, WORK( NWORK1 ), INFO ) + CALL DCOPY( NRP1, VT( NRF, 1 ), 1, WORK( VFI ), 1 ) + CALL DCOPY( NRP1, VT( NRF, NRP1 ), 1, WORK( VLI ), 1 ) + END IF + IF( INFO.NE.0 ) THEN + RETURN + END IF + DO 20 J = 1, NR + IWORK( IDXQI+J ) = J + 20 CONTINUE + 30 CONTINUE +* +* Now conquer each subproblem bottom-up. +* + J = 2**NLVL + DO 50 LVL = NLVL, 1, -1 + LVL2 = LVL*2 - 1 +* +* Find the first node LF and last node LL on +* the current level LVL. +* + IF( LVL.EQ.1 ) THEN + LF = 1 + LL = 1 + ELSE + LF = 2**( LVL-1 ) + LL = 2*LF - 1 + END IF + DO 40 I = LF, LL + IM1 = I - 1 + IC = IWORK( INODE+IM1 ) + NL = IWORK( NDIML+IM1 ) + NR = IWORK( NDIMR+IM1 ) + NLF = IC - NL + NRF = IC + 1 + IF( I.EQ.LL ) THEN + SQREI = SQRE + ELSE + SQREI = 1 + END IF + VFI = VF + NLF - 1 + VLI = VL + NLF - 1 + IDXQI = IDXQ + NLF - 1 + ALPHA = D( IC ) + BETA = E( IC ) + IF( ICOMPQ.EQ.0 ) THEN + CALL DLASD6( ICOMPQ, NL, NR, SQREI, D( NLF ), + $ WORK( VFI ), WORK( VLI ), ALPHA, BETA, + $ IWORK( IDXQI ), PERM, GIVPTR( 1 ), GIVCOL, + $ LDGCOL, GIVNUM, LDU, POLES, DIFL, DIFR, Z, + $ K( 1 ), C( 1 ), S( 1 ), WORK( NWORK1 ), + $ IWORK( IWK ), INFO ) + ELSE + J = J - 1 + CALL DLASD6( ICOMPQ, NL, NR, SQREI, D( NLF ), + $ WORK( VFI ), WORK( VLI ), ALPHA, BETA, + $ IWORK( IDXQI ), PERM( NLF, LVL ), + $ GIVPTR( J ), GIVCOL( NLF, LVL2 ), LDGCOL, + $ GIVNUM( NLF, LVL2 ), LDU, + $ POLES( NLF, LVL2 ), DIFL( NLF, LVL ), + $ DIFR( NLF, LVL2 ), Z( NLF, LVL ), K( J ), + $ C( J ), S( J ), WORK( NWORK1 ), + $ IWORK( IWK ), INFO ) + END IF + IF( INFO.NE.0 ) THEN + RETURN + END IF + 40 CONTINUE + 50 CONTINUE +* + RETURN +* +* End of DLASDA +* + END diff --git a/lib/linalg/dlasdq.f b/lib/linalg/dlasdq.f new file mode 100644 index 0000000000000000000000000000000000000000..e7d3575a9897afcd64e7d3d76781223873faa99d --- /dev/null +++ b/lib/linalg/dlasdq.f @@ -0,0 +1,413 @@ +*> \brief \b DLASDQ computes the SVD of a real bidiagonal matrix with diagonal d and off-diagonal e. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASDQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASDQ( UPLO, SQRE, N, NCVT, NRU, NCC, D, E, VT, LDVT, +* U, LDU, C, LDC, WORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER INFO, LDC, LDU, LDVT, N, NCC, NCVT, NRU, SQRE +* .. +* .. Array Arguments .. +* DOUBLE PRECISION C( LDC, * ), D( * ), E( * ), U( LDU, * ), +* $ VT( LDVT, * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLASDQ computes the singular value decomposition (SVD) of a real +*> (upper or lower) bidiagonal matrix with diagonal D and offdiagonal +*> E, accumulating the transformations if desired. Letting B denote +*> the input bidiagonal matrix, the algorithm computes orthogonal +*> matrices Q and P such that B = Q * S * P**T (P**T denotes the transpose +*> of P). The singular values S are overwritten on D. +*> +*> The input matrix U is changed to U * Q if desired. +*> The input matrix VT is changed to P**T * VT if desired. +*> The input matrix C is changed to Q**T * C if desired. +*> +*> See "Computing Small Singular Values of Bidiagonal Matrices With +*> Guaranteed High Relative Accuracy," by J. Demmel and W. Kahan, +*> LAPACK Working Note #3, for a detailed description of the algorithm. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> On entry, UPLO specifies whether the input bidiagonal matrix +*> is upper or lower bidiagonal, and whether it is square are +*> not. +*> UPLO = 'U' or 'u' B is upper bidiagonal. +*> UPLO = 'L' or 'l' B is lower bidiagonal. +*> \endverbatim +*> +*> \param[in] SQRE +*> \verbatim +*> SQRE is INTEGER +*> = 0: then the input matrix is N-by-N. +*> = 1: then the input matrix is N-by-(N+1) if UPLU = 'U' and +*> (N+1)-by-N if UPLU = 'L'. +*> +*> The bidiagonal matrix has +*> N = NL + NR + 1 rows and +*> M = N + SQRE >= N columns. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> On entry, N specifies the number of rows and columns +*> in the matrix. N must be at least 0. +*> \endverbatim +*> +*> \param[in] NCVT +*> \verbatim +*> NCVT is INTEGER +*> On entry, NCVT specifies the number of columns of +*> the matrix VT. NCVT must be at least 0. +*> \endverbatim +*> +*> \param[in] NRU +*> \verbatim +*> NRU is INTEGER +*> On entry, NRU specifies the number of rows of +*> the matrix U. NRU must be at least 0. +*> \endverbatim +*> +*> \param[in] NCC +*> \verbatim +*> NCC is INTEGER +*> On entry, NCC specifies the number of columns of +*> the matrix C. NCC must be at least 0. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry, D contains the diagonal entries of the +*> bidiagonal matrix whose SVD is desired. On normal exit, +*> D contains the singular values in ascending order. +*> \endverbatim +*> +*> \param[in,out] E +*> \verbatim +*> E is DOUBLE PRECISION array. +*> dimension is (N-1) if SQRE = 0 and N if SQRE = 1. +*> On entry, the entries of E contain the offdiagonal entries +*> of the bidiagonal matrix whose SVD is desired. On normal +*> exit, E will contain 0. If the algorithm does not converge, +*> D and E will contain the diagonal and superdiagonal entries +*> of a bidiagonal matrix orthogonally equivalent to the one +*> given as input. +*> \endverbatim +*> +*> \param[in,out] VT +*> \verbatim +*> VT is DOUBLE PRECISION array, dimension (LDVT, NCVT) +*> On entry, contains a matrix which on exit has been +*> premultiplied by P**T, dimension N-by-NCVT if SQRE = 0 +*> and (N+1)-by-NCVT if SQRE = 1 (not referenced if NCVT=0). +*> \endverbatim +*> +*> \param[in] LDVT +*> \verbatim +*> LDVT is INTEGER +*> On entry, LDVT specifies the leading dimension of VT as +*> declared in the calling (sub) program. LDVT must be at +*> least 1. If NCVT is nonzero LDVT must also be at least N. +*> \endverbatim +*> +*> \param[in,out] U +*> \verbatim +*> U is DOUBLE PRECISION array, dimension (LDU, N) +*> On entry, contains a matrix which on exit has been +*> postmultiplied by Q, dimension NRU-by-N if SQRE = 0 +*> and NRU-by-(N+1) if SQRE = 1 (not referenced if NRU=0). +*> \endverbatim +*> +*> \param[in] LDU +*> \verbatim +*> LDU is INTEGER +*> On entry, LDU specifies the leading dimension of U as +*> declared in the calling (sub) program. LDU must be at +*> least max( 1, NRU ) . +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is DOUBLE PRECISION array, dimension (LDC, NCC) +*> On entry, contains an N-by-NCC matrix which on exit +*> has been premultiplied by Q**T dimension N-by-NCC if SQRE = 0 +*> and (N+1)-by-NCC if SQRE = 1 (not referenced if NCC=0). +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> On entry, LDC specifies the leading dimension of C as +*> declared in the calling (sub) program. LDC must be at +*> least 1. If NCC is nonzero, LDC must also be at least N. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is DOUBLE PRECISION array, dimension (4*N) +*> Workspace. Only referenced if one of NCVT, NRU, or NCC is +*> nonzero, and if N is at least 2. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> On exit, a value of 0 indicates a successful exit. +*> If INFO < 0, argument number -INFO is illegal. +*> If INFO > 0, the algorithm did not converge, and INFO +*> specifies how many superdiagonals did not converge. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASDQ( UPLO, SQRE, N, NCVT, NRU, NCC, D, E, VT, LDVT, + $ U, LDU, C, LDC, WORK, INFO ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2016 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDC, LDU, LDVT, N, NCC, NCVT, NRU, SQRE +* .. +* .. Array Arguments .. + DOUBLE PRECISION C( LDC, * ), D( * ), E( * ), U( LDU, * ), + $ VT( LDVT, * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO + PARAMETER ( ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL ROTATE + INTEGER I, ISUB, IUPLO, J, NP1, SQRE1 + DOUBLE PRECISION CS, R, SMIN, SN +* .. +* .. External Subroutines .. + EXTERNAL DBDSQR, DLARTG, DLASR, DSWAP, XERBLA +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + IUPLO = 0 + IF( LSAME( UPLO, 'U' ) ) + $ IUPLO = 1 + IF( LSAME( UPLO, 'L' ) ) + $ IUPLO = 2 + IF( IUPLO.EQ.0 ) THEN + INFO = -1 + ELSE IF( ( SQRE.LT.0 ) .OR. ( SQRE.GT.1 ) ) THEN + INFO = -2 + ELSE IF( N.LT.0 ) THEN + INFO = -3 + ELSE IF( NCVT.LT.0 ) THEN + INFO = -4 + ELSE IF( NRU.LT.0 ) THEN + INFO = -5 + ELSE IF( NCC.LT.0 ) THEN + INFO = -6 + ELSE IF( ( NCVT.EQ.0 .AND. LDVT.LT.1 ) .OR. + $ ( NCVT.GT.0 .AND. LDVT.LT.MAX( 1, N ) ) ) THEN + INFO = -10 + ELSE IF( LDU.LT.MAX( 1, NRU ) ) THEN + INFO = -12 + ELSE IF( ( NCC.EQ.0 .AND. LDC.LT.1 ) .OR. + $ ( NCC.GT.0 .AND. LDC.LT.MAX( 1, N ) ) ) THEN + INFO = -14 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DLASDQ', -INFO ) + RETURN + END IF + IF( N.EQ.0 ) + $ RETURN +* +* ROTATE is true if any singular vectors desired, false otherwise +* + ROTATE = ( NCVT.GT.0 ) .OR. ( NRU.GT.0 ) .OR. ( NCC.GT.0 ) + NP1 = N + 1 + SQRE1 = SQRE +* +* If matrix non-square upper bidiagonal, rotate to be lower +* bidiagonal. The rotations are on the right. +* + IF( ( IUPLO.EQ.1 ) .AND. ( SQRE1.EQ.1 ) ) THEN + DO 10 I = 1, N - 1 + CALL DLARTG( D( I ), E( I ), CS, SN, R ) + D( I ) = R + E( I ) = SN*D( I+1 ) + D( I+1 ) = CS*D( I+1 ) + IF( ROTATE ) THEN + WORK( I ) = CS + WORK( N+I ) = SN + END IF + 10 CONTINUE + CALL DLARTG( D( N ), E( N ), CS, SN, R ) + D( N ) = R + E( N ) = ZERO + IF( ROTATE ) THEN + WORK( N ) = CS + WORK( N+N ) = SN + END IF + IUPLO = 2 + SQRE1 = 0 +* +* Update singular vectors if desired. +* + IF( NCVT.GT.0 ) + $ CALL DLASR( 'L', 'V', 'F', NP1, NCVT, WORK( 1 ), + $ WORK( NP1 ), VT, LDVT ) + END IF +* +* If matrix lower bidiagonal, rotate to be upper bidiagonal +* by applying Givens rotations on the left. +* + IF( IUPLO.EQ.2 ) THEN + DO 20 I = 1, N - 1 + CALL DLARTG( D( I ), E( I ), CS, SN, R ) + D( I ) = R + E( I ) = SN*D( I+1 ) + D( I+1 ) = CS*D( I+1 ) + IF( ROTATE ) THEN + WORK( I ) = CS + WORK( N+I ) = SN + END IF + 20 CONTINUE +* +* If matrix (N+1)-by-N lower bidiagonal, one additional +* rotation is needed. +* + IF( SQRE1.EQ.1 ) THEN + CALL DLARTG( D( N ), E( N ), CS, SN, R ) + D( N ) = R + IF( ROTATE ) THEN + WORK( N ) = CS + WORK( N+N ) = SN + END IF + END IF +* +* Update singular vectors if desired. +* + IF( NRU.GT.0 ) THEN + IF( SQRE1.EQ.0 ) THEN + CALL DLASR( 'R', 'V', 'F', NRU, N, WORK( 1 ), + $ WORK( NP1 ), U, LDU ) + ELSE + CALL DLASR( 'R', 'V', 'F', NRU, NP1, WORK( 1 ), + $ WORK( NP1 ), U, LDU ) + END IF + END IF + IF( NCC.GT.0 ) THEN + IF( SQRE1.EQ.0 ) THEN + CALL DLASR( 'L', 'V', 'F', N, NCC, WORK( 1 ), + $ WORK( NP1 ), C, LDC ) + ELSE + CALL DLASR( 'L', 'V', 'F', NP1, NCC, WORK( 1 ), + $ WORK( NP1 ), C, LDC ) + END IF + END IF + END IF +* +* Call DBDSQR to compute the SVD of the reduced real +* N-by-N upper bidiagonal matrix. +* + CALL DBDSQR( 'U', N, NCVT, NRU, NCC, D, E, VT, LDVT, U, LDU, C, + $ LDC, WORK, INFO ) +* +* Sort the singular values into ascending order (insertion sort on +* singular values, but only one transposition per singular vector) +* + DO 40 I = 1, N +* +* Scan for smallest D(I). +* + ISUB = I + SMIN = D( I ) + DO 30 J = I + 1, N + IF( D( J ).LT.SMIN ) THEN + ISUB = J + SMIN = D( J ) + END IF + 30 CONTINUE + IF( ISUB.NE.I ) THEN +* +* Swap singular values and vectors. +* + D( ISUB ) = D( I ) + D( I ) = SMIN + IF( NCVT.GT.0 ) + $ CALL DSWAP( NCVT, VT( ISUB, 1 ), LDVT, VT( I, 1 ), LDVT ) + IF( NRU.GT.0 ) + $ CALL DSWAP( NRU, U( 1, ISUB ), 1, U( 1, I ), 1 ) + IF( NCC.GT.0 ) + $ CALL DSWAP( NCC, C( ISUB, 1 ), LDC, C( I, 1 ), LDC ) + END IF + 40 CONTINUE +* + RETURN +* +* End of DLASDQ +* + END diff --git a/lib/linalg/dlasdt.f b/lib/linalg/dlasdt.f new file mode 100644 index 0000000000000000000000000000000000000000..37da2d035e91a3d4ef9ace7396dc2de5511091af --- /dev/null +++ b/lib/linalg/dlasdt.f @@ -0,0 +1,172 @@ +*> \brief \b DLASDT creates a tree of subproblems for bidiagonal divide and conquer. Used by sbdsdc. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download DLASDT + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE DLASDT( N, LVL, ND, INODE, NDIML, NDIMR, MSUB ) +* +* .. Scalar Arguments .. +* INTEGER LVL, MSUB, N, ND +* .. +* .. Array Arguments .. +* INTEGER INODE( * ), NDIML( * ), NDIMR( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DLASDT creates a tree of subproblems for bidiagonal divide and +*> conquer. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> On entry, the number of diagonal elements of the +*> bidiagonal matrix. +*> \endverbatim +*> +*> \param[out] LVL +*> \verbatim +*> LVL is INTEGER +*> On exit, the number of levels on the computation tree. +*> \endverbatim +*> +*> \param[out] ND +*> \verbatim +*> ND is INTEGER +*> On exit, the number of nodes on the tree. +*> \endverbatim +*> +*> \param[out] INODE +*> \verbatim +*> INODE is INTEGER array, dimension ( N ) +*> On exit, centers of subproblems. +*> \endverbatim +*> +*> \param[out] NDIML +*> \verbatim +*> NDIML is INTEGER array, dimension ( N ) +*> On exit, row dimensions of left children. +*> \endverbatim +*> +*> \param[out] NDIMR +*> \verbatim +*> NDIMR is INTEGER array, dimension ( N ) +*> On exit, row dimensions of right children. +*> \endverbatim +*> +*> \param[in] MSUB +*> \verbatim +*> MSUB is INTEGER +*> On entry, the maximum row dimension each subproblem at the +*> bottom of the tree can be of. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup OTHERauxiliary +* +*> \par Contributors: +* ================== +*> +*> Ming Gu and Huan Ren, Computer Science Division, University of +*> California at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE DLASDT( N, LVL, ND, INODE, NDIML, NDIMR, MSUB ) +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + INTEGER LVL, MSUB, N, ND +* .. +* .. Array Arguments .. + INTEGER INODE( * ), NDIML( * ), NDIMR( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION TWO + PARAMETER ( TWO = 2.0D+0 ) +* .. +* .. Local Scalars .. + INTEGER I, IL, IR, LLST, MAXN, NCRNT, NLVL + DOUBLE PRECISION TEMP +* .. +* .. Intrinsic Functions .. + INTRINSIC DBLE, INT, LOG, MAX +* .. +* .. Executable Statements .. +* +* Find the number of levels on the tree. +* + MAXN = MAX( 1, N ) + TEMP = LOG( DBLE( MAXN ) / DBLE( MSUB+1 ) ) / LOG( TWO ) + LVL = INT( TEMP ) + 1 +* + I = N / 2 + INODE( 1 ) = I + 1 + NDIML( 1 ) = I + NDIMR( 1 ) = N - I - 1 + IL = 0 + IR = 1 + LLST = 1 + DO 20 NLVL = 1, LVL - 1 +* +* Constructing the tree at (NLVL+1)-st level. The number of +* nodes created on this level is LLST * 2. +* + DO 10 I = 0, LLST - 1 + IL = IL + 2 + IR = IR + 2 + NCRNT = LLST + I + NDIML( IL ) = NDIML( NCRNT ) / 2 + NDIMR( IL ) = NDIML( NCRNT ) - NDIML( IL ) - 1 + INODE( IL ) = INODE( NCRNT ) - NDIMR( IL ) - 1 + NDIML( IR ) = NDIMR( NCRNT ) / 2 + NDIMR( IR ) = NDIMR( NCRNT ) - NDIML( IR ) - 1 + INODE( IR ) = INODE( NCRNT ) + NDIML( IR ) + 1 + 10 CONTINUE + LLST = LLST*2 + 20 CONTINUE + ND = LLST*2 - 1 +* + RETURN +* +* End of DLASDT +* + END diff --git a/lib/linalg/dlaset.f b/lib/linalg/dlaset.f index 1ce34662ab7cd468118ab53ac559bc146339ac0c..3a0c469a3ca48571881328e7b3379c1e089aec80 100644 --- a/lib/linalg/dlaset.f +++ b/lib/linalg/dlaset.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASET + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASET + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER LDA, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -77,7 +77,7 @@ *> The constant to which the diagonal elements are to be set. *> \endverbatim *> -*> \param[in,out] A +*> \param[out] A *> \verbatim *> A is DOUBLE PRECISION array, dimension (LDA,N) *> On exit, the leading m-by-n submatrix of A is set as follows: @@ -98,22 +98,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlasq1.f b/lib/linalg/dlasq1.f index d12fb7a5fd45e3be2bdc8a98e6cd40c7f7f65f02..468676eebd3b88ec09d524263d2d6dd6b47fbc17 100644 --- a/lib/linalg/dlasq1.f +++ b/lib/linalg/dlasq1.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ1 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ1 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASQ1( N, D, E, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, N * .. * .. Array Arguments .. * DOUBLE PRECISION D( * ), E( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -89,29 +89,29 @@ *> represent a matrix with the same singular values *> which the calling subroutine could use to finish the *> computation, or even feed back into DLASQ1 -*> = 3, termination criterion of outer while loop not met +*> = 3, termination criterion of outer while loop not met *> (program created more than N unreduced blocks) *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASQ1( N, D, E, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N @@ -144,7 +144,7 @@ * INFO = 0 IF( N.LT.0 ) THEN - INFO = -2 + INFO = -1 CALL XERBLA( 'DLASQ1', -INFO ) RETURN ELSE IF( N.EQ.0 ) THEN @@ -189,7 +189,7 @@ CALL DCOPY( N-1, E, 1, WORK( 2 ), 2 ) CALL DLASCL( 'G', 0, 0, SIGMX, SCALE, 2*N-1, 1, WORK, 2*N-1, $ IINFO ) -* +* * Compute the q's and e's. * DO 30 I = 1, 2*N - 1 diff --git a/lib/linalg/dlasq2.f b/lib/linalg/dlasq2.f index df1690d020d282c25d12d575f94a22ccef3cd3a6..68d9228704e64b4495ede050666f2b837ad4117e 100644 --- a/lib/linalg/dlasq2.f +++ b/lib/linalg/dlasq2.f @@ -2,38 +2,38 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASQ2( N, Z, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, N * .. * .. Array Arguments .. * DOUBLE PRECISION Z( * ) * .. -* +* * *> \par Purpose: * ============= *> *> \verbatim *> -*> DLASQ2 computes all the eigenvalues of the symmetric positive +*> DLASQ2 computes all the eigenvalues of the symmetric positive *> definite tridiagonal matrix associated with the qd array Z to high *> relative accuracy are computed to high relative accuracy, in the *> absence of denormalization, underflow and overflow. @@ -83,19 +83,19 @@ *> = 2, current block of Z not diagonalized after 100*N *> iterations (in inner while loop). On exit Z holds *> a qd array with the same eigenvalues as the given Z. -*> = 3, termination criterion of outer while loop not met +*> = 3, termination criterion of outer while loop not met *> (program created more than N unreduced blocks) *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -112,10 +112,10 @@ * ===================================================================== SUBROUTINE DLASQ2( N, Z, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N @@ -136,7 +136,7 @@ * .. Local Scalars .. LOGICAL IEEE INTEGER I0, I1, I4, IINFO, IPN4, ITER, IWHILA, IWHILB, - $ K, KMIN, N0, N1, NBIG, NDIV, NFAIL, PP, SPLT, + $ K, KMIN, N0, N1, NBIG, NDIV, NFAIL, PP, SPLT, $ TTYPE DOUBLE PRECISION D, DEE, DEEMIN, DESIG, DMIN, DMIN1, DMIN2, DN, $ DN1, DN2, E, EMAX, EMIN, EPS, G, OLDEMN, QMAX, @@ -155,7 +155,7 @@ INTRINSIC ABS, DBLE, MAX, MIN, SQRT * .. * .. Executable Statements .. -* +* * Test the input arguments. * (in case DLASQ2 is not called by DLASQ1) * @@ -195,7 +195,7 @@ END IF Z( 5 ) = Z( 1 ) + Z( 2 ) + Z( 3 ) IF( Z( 2 ).GT.Z( 3 )*TOL2 ) THEN - T = HALF*( ( Z( 1 )-Z( 3 ) )+Z( 2 ) ) + T = HALF*( ( Z( 1 )-Z( 3 ) )+Z( 2 ) ) S = Z( 3 )*( Z( 2 ) / T ) IF( S.LE.T ) THEN S = Z( 3 )*( Z( 2 ) / ( T*( ONE+SQRT( ONE+S / T ) ) ) ) @@ -264,19 +264,19 @@ Z( 2*N-1 ) = ZERO RETURN END IF -* +* * Check whether the machine is IEEE conformable. -* +* IEEE = ILAENV( 10, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 .AND. - $ ILAENV( 11, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 -* + $ ILAENV( 11, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 +* * Rearrange data for locality: Z=(q1,qq1,e1,ee1,q2,qq2,e2,ee2,...). * DO 30 K = 2*N, 2, -2 - Z( 2*K ) = ZERO - Z( 2*K-1 ) = Z( K ) - Z( 2*K-2 ) = ZERO - Z( 2*K-3 ) = Z( K-1 ) + Z( 2*K ) = ZERO + Z( 2*K-1 ) = Z( K ) + Z( 2*K-2 ) = ZERO + Z( 2*K-3 ) = Z( K-1 ) 30 CONTINUE * I0 = 1 @@ -333,7 +333,7 @@ D = Z( I4+1 )*( D / Z( I4-2*PP-2 ) ) END IF EMIN = MIN( EMIN, Z( I4-2*PP ) ) - 60 CONTINUE + 60 CONTINUE Z( 4*N0-PP-2 ) = D * * Now find qmax. @@ -364,14 +364,14 @@ NDIV = 2*( N0-I0 ) * DO 160 IWHILA = 1, N + 1 - IF( N0.LT.1 ) + IF( N0.LT.1 ) $ GO TO 170 * -* While array unfinished do +* While array unfinished do * * E(N0) holds the value of SIGMA when submatrix in I0:N0 * splits from the rest of the array, but is negated. -* +* DESIG = ZERO IF( N0.EQ.N ) THEN SIGMA = ZERO @@ -386,7 +386,7 @@ * Find last unreduced submatrix's top index I0, find QMAX and * EMIN. Find Gershgorin-type bound if Q's much greater than E's. * - EMAX = ZERO + EMAX = ZERO IF( N0.GT.I0 ) THEN EMIN = ABS( Z( 4*N0-5 ) ) ELSE @@ -404,7 +404,7 @@ QMAX = MAX( QMAX, Z( I4-7 )+Z( I4-5 ) ) EMIN = MIN( EMIN, Z( I4-5 ) ) 90 CONTINUE - I4 = 4 + I4 = 4 * 100 CONTINUE I0 = I4 / 4 @@ -421,7 +421,7 @@ KMIN = ( I4+3 )/4 END IF 110 CONTINUE - IF( (KMIN-I0)*2.LT.N0-KMIN .AND. + IF( (KMIN-I0)*2.LT.N0-KMIN .AND. $ DEEMIN.LE.HALF*Z(4*N0-3) ) THEN IPN4 = 4*( I0+N0 ) PP = 2 @@ -446,15 +446,15 @@ * DMIN = -MAX( ZERO, QMIN-TWO*SQRT( QMIN )*SQRT( EMAX ) ) * -* Now I0:N0 is unreduced. +* Now I0:N0 is unreduced. * PP = 0 for ping, PP = 1 for pong. * PP = 2 indicates that flipping was applied to the Z array and -* and that the tests for deflation upon entry in DLASQ3 +* and that the tests for deflation upon entry in DLASQ3 * should not be performed. * NBIG = 100*( N0-I0+1 ) DO 140 IWHILB = 1, NBIG - IF( I0.GT.N0 ) + IF( I0.GT.N0 ) $ GO TO 150 * * While submatrix unfinished take a good dqds step. @@ -497,8 +497,8 @@ 140 CONTINUE * INFO = 2 -* -* Maximum number of iterations exceeded, restore the shift +* +* Maximum number of iterations exceeded, restore the shift * SIGMA and place the new d's and e's in a qd array. * This might need to be done for several blocks * @@ -549,16 +549,16 @@ INFO = 3 RETURN * -* end IWHILA +* end IWHILA * 170 CONTINUE -* +* * Move q's to the front. -* +* DO 180 K = 2, N Z( K ) = Z( 4*K-3 ) 180 CONTINUE -* +* * Sort and compute sum of eigenvalues. * CALL DLASRT( 'D', N, Z, IINFO ) @@ -570,7 +570,7 @@ * * Store trace, sum(eigenvalues) and information on performance. * - Z( 2*N+1 ) = TRACE + Z( 2*N+1 ) = TRACE Z( 2*N+2 ) = E Z( 2*N+3 ) = DBLE( ITER ) Z( 2*N+4 ) = DBLE( NDIV ) / DBLE( N**2 ) diff --git a/lib/linalg/dlasq3.f b/lib/linalg/dlasq3.f index d49d1c59398a71f8beccf9932434fe2e477a8527..c095bdbbb58b2f15a926618d258dd379141d58c6 100644 --- a/lib/linalg/dlasq3.f +++ b/lib/linalg/dlasq3.f @@ -2,18 +2,18 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ3 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ3 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== @@ -21,7 +21,7 @@ * SUBROUTINE DLASQ3( I0, N0, Z, PP, DMIN, SIGMA, DESIG, QMAX, NFAIL, * ITER, NDIV, IEEE, TTYPE, DMIN1, DMIN2, DN, DN1, * DN2, G, TAU ) -* +* * .. Scalar Arguments .. * LOGICAL IEEE * INTEGER I0, ITER, N0, NDIV, NFAIL, PP @@ -31,7 +31,7 @@ * .. Array Arguments .. * DOUBLE PRECISION Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -58,9 +58,9 @@ *> Last index. *> \endverbatim *> -*> \param[in] Z +*> \param[in,out] Z *> \verbatim -*> Z is DOUBLE PRECISION array, dimension ( 4*N ) +*> Z is DOUBLE PRECISION array, dimension ( 4*N0 ) *> Z holds the qd array. *> \endverbatim *> @@ -68,8 +68,8 @@ *> \verbatim *> PP is INTEGER *> PP=0 for ping, PP=1 for pong. -*> PP=2 indicates that flipping was applied to the Z array -*> and that the initial tests for deflation should not be +*> PP=2 indicates that flipping was applied to the Z array +*> and that the initial tests for deflation should not be *> performed. *> \endverbatim *> @@ -97,22 +97,22 @@ *> Maximum value of q. *> \endverbatim *> -*> \param[out] NFAIL +*> \param[in,out] NFAIL *> \verbatim *> NFAIL is INTEGER -*> Number of times shift was too big. +*> Increment NFAIL by 1 each time the shift was too big. *> \endverbatim *> -*> \param[out] ITER +*> \param[in,out] ITER *> \verbatim *> ITER is INTEGER -*> Number of iterations. +*> Increment ITER by 1 for each iteration. *> \endverbatim *> -*> \param[out] NDIV +*> \param[in,out] NDIV *> \verbatim *> NDIV is INTEGER -*> Number of divisions. +*> Increment NDIV by 1 for each division. *> \endverbatim *> *> \param[in] IEEE @@ -168,12 +168,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * @@ -182,10 +182,10 @@ $ ITER, NDIV, IEEE, TTYPE, DMIN1, DMIN2, DN, DN1, $ DN2, G, TAU ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. LOGICAL IEEE @@ -286,7 +286,7 @@ GO TO 10 * 50 CONTINUE - IF( PP.EQ.2 ) + IF( PP.EQ.2 ) $ PP = 0 * * Reverse the qd-array, if warranted. @@ -345,7 +345,7 @@ * GO TO 90 * - ELSE IF( DMIN.LT.ZERO .AND. DMIN1.GT.ZERO .AND. + ELSE IF( DMIN.LT.ZERO .AND. DMIN1.GT.ZERO .AND. $ Z( 4*( N0-1 )-PP ).LT.TOL*( SIGMA+DN1 ) .AND. $ ABS( DN ).LT.TOL*SIGMA ) THEN * @@ -389,7 +389,7 @@ GO TO 70 END IF ELSE -* +* * Possible underflow. Play it safe. * GO TO 80 diff --git a/lib/linalg/dlasq4.f b/lib/linalg/dlasq4.f index 97d9bdeba31a930364553d60ffba192f91f01df7..d4ddbbc7b2e9b8d7383be615becb7c6fdb0a37a0 100644 --- a/lib/linalg/dlasq4.f +++ b/lib/linalg/dlasq4.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ4 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ4 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASQ4( I0, N0, Z, PP, N0IN, DMIN, DMIN1, DMIN2, DN, * DN1, DN2, TAU, TTYPE, G ) -* +* * .. Scalar Arguments .. * INTEGER I0, N0, N0IN, PP, TTYPE * DOUBLE PRECISION DMIN, DMIN1, DMIN2, DN, DN1, DN2, G, TAU @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -56,7 +56,7 @@ *> *> \param[in] Z *> \verbatim -*> Z is DOUBLE PRECISION array, dimension ( 4*N ) +*> Z is DOUBLE PRECISION array, dimension ( 4*N0 ) *> Z holds the qd array. *> \endverbatim *> @@ -122,7 +122,7 @@ *> *> \param[in,out] G *> \verbatim -*> G is REAL +*> G is DOUBLE PRECISION *> G is passed as an argument in order to save its value between *> calls to DLASQ4. *> \endverbatim @@ -130,12 +130,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * @@ -151,10 +151,10 @@ SUBROUTINE DLASQ4( I0, N0, Z, PP, N0IN, DMIN, DMIN1, DMIN2, DN, $ DN1, DN2, TAU, TTYPE, G ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. INTEGER I0, N0, N0IN, PP, TTYPE @@ -192,7 +192,7 @@ TTYPE = -1 RETURN END IF -* +* NN = 4*N0 + PP IF( N0IN.EQ.N0 ) THEN * @@ -240,7 +240,6 @@ NP = NN - 9 ELSE NP = NN - 2*PP - B2 = Z( NP-2 ) GAM = DN1 IF( Z( NP-4 ) .GT. Z( NP-2 ) ) $ RETURN @@ -262,7 +261,7 @@ $ RETURN B2 = B2*( Z( I4 ) / Z( I4-2 ) ) A2 = A2 + B2 - IF( HUNDRD*MAX( B2, B1 ).LT.A2 .OR. CNST1.LT.A2 ) + IF( HUNDRD*MAX( B2, B1 ).LT.A2 .OR. CNST1.LT.A2 ) $ GO TO 20 10 CONTINUE 20 CONTINUE @@ -303,7 +302,7 @@ $ RETURN B2 = B2*( Z( I4 ) / Z( I4-2 ) ) A2 = A2 + B2 - IF( HUNDRD*MAX( B2, B1 ).LT.A2 .OR. CNST1.LT.A2 ) + IF( HUNDRD*MAX( B2, B1 ).LT.A2 .OR. CNST1.LT.A2 ) $ GO TO 40 30 CONTINUE 40 CONTINUE @@ -331,7 +330,7 @@ * * One eigenvalue just deflated. Use DMIN1, DN1 for DMIN and DN. * - IF( DMIN1.EQ.DN1 .AND. DMIN2.EQ.DN2 ) THEN + IF( DMIN1.EQ.DN1 .AND. DMIN2.EQ.DN2 ) THEN * * Cases 7 and 8. * @@ -349,7 +348,7 @@ $ RETURN B1 = B1*( Z( I4 ) / Z( I4-2 ) ) B2 = B2 + B1 - IF( HUNDRD*MAX( B1, A2 ).LT.B2 ) + IF( HUNDRD*MAX( B1, A2 ).LT.B2 ) $ GO TO 60 50 CONTINUE 60 CONTINUE @@ -358,7 +357,7 @@ GAP2 = HALF*DMIN2 - A2 IF( GAP2.GT.ZERO .AND. GAP2.GT.B2*A2 ) THEN S = MAX( S, A2*( ONE-CNST2*A2*( B2 / GAP2 )*B2 ) ) - ELSE + ELSE S = MAX( S, A2*( ONE-CNST2*B2 ) ) TTYPE = -8 END IF @@ -378,7 +377,7 @@ * * Cases 10 and 11. * - IF( DMIN2.EQ.DN2 .AND. TWO*Z( NN-5 ).LT.Z( NN-7 ) ) THEN + IF( DMIN2.EQ.DN2 .AND. TWO*Z( NN-5 ).LT.Z( NN-7 ) ) THEN TTYPE = -10 S = THIRD*DMIN2 IF( Z( NN-5 ).GT.Z( NN-7 ) ) @@ -402,7 +401,7 @@ $ SQRT( Z( NN-11 ) )*SQRT( Z( NN-9 ) ) - A2 IF( GAP2.GT.ZERO .AND. GAP2.GT.B2*A2 ) THEN S = MAX( S, A2*( ONE-CNST2*A2*( B2 / GAP2 )*B2 ) ) - ELSE + ELSE S = MAX( S, A2*( ONE-CNST2*B2 ) ) END IF ELSE @@ -413,7 +412,7 @@ * * Case 12, more than two eigenvalues deflated. No information. * - S = ZERO + S = ZERO TTYPE = -12 END IF * diff --git a/lib/linalg/dlasq5.f b/lib/linalg/dlasq5.f index cdd8cf1ae3d2cc05f29c7f4e5c3df1cb82a3889f..3812c879fa2df1d2017b6d40c36c79d4452c34f3 100644 --- a/lib/linalg/dlasq5.f +++ b/lib/linalg/dlasq5.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ5 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ5 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASQ5( I0, N0, Z, PP, TAU, SIGMA, DMIN, DMIN1, DMIN2, DN, * DNM1, DNM2, IEEE, EPS ) -* +* * .. Scalar Arguments .. * LOGICAL IEEE * INTEGER I0, N0, PP @@ -29,7 +29,7 @@ * .. Array Arguments .. * DOUBLE PRECISION Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -121,7 +121,7 @@ *> IEEE is LOGICAL *> Flag for IEEE or non IEEE arithmetic. *> \endverbatim -* +*> *> \param[in] EPS *> \verbatim *> EPS is DOUBLE PRECISION @@ -131,12 +131,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * *> \ingroup auxOTHERcomputational * @@ -144,10 +144,10 @@ SUBROUTINE DLASQ5( I0, N0, Z, PP, TAU, SIGMA, DMIN, DMIN1, DMIN2, $ DN, DNM1, DNM2, IEEE, EPS ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. LOGICAL IEEE @@ -181,7 +181,7 @@ IF( TAU.LT.DTHRESH*HALF ) TAU = ZERO IF( TAU.NE.ZERO ) THEN J4 = 4*I0 + PP - 3 - EMIN = Z( J4+4 ) + EMIN = Z( J4+4 ) D = Z( J4 ) - TAU DMIN = D DMIN1 = -Z( J4 ) @@ -192,7 +192,7 @@ * IF( PP.EQ.0 ) THEN DO 10 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-2 ) = D + Z( J4-1 ) + Z( J4-2 ) = D + Z( J4-1 ) TEMP = Z( J4+1 ) / Z( J4-2 ) D = D*TEMP - TAU DMIN = MIN( DMIN, D ) @@ -201,7 +201,7 @@ 10 CONTINUE ELSE DO 20 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-3 ) = D + Z( J4 ) + Z( J4-3 ) = D + Z( J4 ) TEMP = Z( J4+2 ) / Z( J4-3 ) D = D*TEMP - TAU DMIN = MIN( DMIN, D ) @@ -210,7 +210,7 @@ 20 CONTINUE END IF * -* Unroll last two steps. +* Unroll last two steps. * DNM2 = D DMIN2 = DMIN @@ -235,10 +235,10 @@ * IF( PP.EQ.0 ) THEN DO 30 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-2 ) = D + Z( J4-1 ) + Z( J4-2 ) = D + Z( J4-1 ) IF( D.LT.ZERO ) THEN RETURN - ELSE + ELSE Z( J4 ) = Z( J4+1 )*( Z( J4-1 ) / Z( J4-2 ) ) D = Z( J4+1 )*( D / Z( J4-2 ) ) - TAU END IF @@ -247,10 +247,10 @@ 30 CONTINUE ELSE DO 40 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-3 ) = D + Z( J4 ) + Z( J4-3 ) = D + Z( J4 ) IF( D.LT.ZERO ) THEN RETURN - ELSE + ELSE Z( J4-1 ) = Z( J4+2 )*( Z( J4 ) / Z( J4-3 ) ) D = Z( J4+2 )*( D / Z( J4-3 ) ) - TAU END IF @@ -259,7 +259,7 @@ 40 CONTINUE END IF * -* Unroll last two steps. +* Unroll last two steps. * DNM2 = D DMIN2 = DMIN @@ -290,17 +290,17 @@ ELSE * This is the version that sets d's to zero if they are small enough J4 = 4*I0 + PP - 3 - EMIN = Z( J4+4 ) + EMIN = Z( J4+4 ) D = Z( J4 ) - TAU DMIN = D DMIN1 = -Z( J4 ) IF( IEEE ) THEN -* +* * Code for IEEE arithmetic. -* +* IF( PP.EQ.0 ) THEN DO 50 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-2 ) = D + Z( J4-1 ) + Z( J4-2 ) = D + Z( J4-1 ) TEMP = Z( J4+1 ) / Z( J4-2 ) D = D*TEMP - TAU IF( D.LT.DTHRESH ) D = ZERO @@ -310,7 +310,7 @@ 50 CONTINUE ELSE DO 60 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-3 ) = D + Z( J4 ) + Z( J4-3 ) = D + Z( J4 ) TEMP = Z( J4+2 ) / Z( J4-3 ) D = D*TEMP - TAU IF( D.LT.DTHRESH ) D = ZERO @@ -319,9 +319,9 @@ EMIN = MIN( Z( J4-1 ), EMIN ) 60 CONTINUE END IF -* -* Unroll last two steps. -* +* +* Unroll last two steps. +* DNM2 = D DMIN2 = DMIN J4 = 4*( N0-2 ) - PP @@ -330,7 +330,7 @@ Z( J4 ) = Z( J4P2+2 )*( Z( J4P2 ) / Z( J4-2 ) ) DNM1 = Z( J4P2+2 )*( DNM2 / Z( J4-2 ) ) - TAU DMIN = MIN( DMIN, DNM1 ) -* +* DMIN1 = DMIN J4 = J4 + 4 J4P2 = J4 + 2*PP - 1 @@ -338,17 +338,17 @@ Z( J4 ) = Z( J4P2+2 )*( Z( J4P2 ) / Z( J4-2 ) ) DN = Z( J4P2+2 )*( DNM1 / Z( J4-2 ) ) - TAU DMIN = MIN( DMIN, DN ) -* +* ELSE -* +* * Code for non IEEE arithmetic. -* +* IF( PP.EQ.0 ) THEN DO 70 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-2 ) = D + Z( J4-1 ) + Z( J4-2 ) = D + Z( J4-1 ) IF( D.LT.ZERO ) THEN RETURN - ELSE + ELSE Z( J4 ) = Z( J4+1 )*( Z( J4-1 ) / Z( J4-2 ) ) D = Z( J4+1 )*( D / Z( J4-2 ) ) - TAU END IF @@ -358,10 +358,10 @@ 70 CONTINUE ELSE DO 80 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-3 ) = D + Z( J4 ) + Z( J4-3 ) = D + Z( J4 ) IF( D.LT.ZERO ) THEN RETURN - ELSE + ELSE Z( J4-1 ) = Z( J4+2 )*( Z( J4 ) / Z( J4-3 ) ) D = Z( J4+2 )*( D / Z( J4-3 ) ) - TAU END IF @@ -370,9 +370,9 @@ EMIN = MIN( EMIN, Z( J4-1 ) ) 80 CONTINUE END IF -* -* Unroll last two steps. -* +* +* Unroll last two steps. +* DNM2 = D DMIN2 = DMIN J4 = 4*( N0-2 ) - PP @@ -385,7 +385,7 @@ DNM1 = Z( J4P2+2 )*( DNM2 / Z( J4-2 ) ) - TAU END IF DMIN = MIN( DMIN, DNM1 ) -* +* DMIN1 = DMIN J4 = J4 + 4 J4P2 = J4 + 2*PP - 1 @@ -397,10 +397,10 @@ DN = Z( J4P2+2 )*( DNM1 / Z( J4-2 ) ) - TAU END IF DMIN = MIN( DMIN, DN ) -* +* END IF END IF -* +* Z( J4+2 ) = DN Z( 4*N0-PP ) = EMIN RETURN diff --git a/lib/linalg/dlasq6.f b/lib/linalg/dlasq6.f index 3c8661bbba264994a35b8131aba2e93b348b6ee2..d871386bdbdbe09b244e17455136a1b9fa568c1f 100644 --- a/lib/linalg/dlasq6.f +++ b/lib/linalg/dlasq6.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASQ6 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASQ6 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASQ6( I0, N0, Z, PP, DMIN, DMIN1, DMIN2, DN, * DNM1, DNM2 ) -* +* * .. Scalar Arguments .. * INTEGER I0, N0, PP * DOUBLE PRECISION DMIN, DMIN1, DMIN2, DN, DNM1, DNM2 @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION Z( * ) * .. -* +* * *> \par Purpose: * ============= @@ -106,12 +106,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * @@ -119,10 +119,10 @@ SUBROUTINE DLASQ6( I0, N0, Z, PP, DMIN, DMIN1, DMIN2, DN, $ DNM1, DNM2 ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER I0, N0, PP @@ -156,13 +156,13 @@ * SAFMIN = DLAMCH( 'Safe minimum' ) J4 = 4*I0 + PP - 3 - EMIN = Z( J4+4 ) + EMIN = Z( J4+4 ) D = Z( J4 ) DMIN = D * IF( PP.EQ.0 ) THEN DO 10 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-2 ) = D + Z( J4-1 ) + Z( J4-2 ) = D + Z( J4-1 ) IF( Z( J4-2 ).EQ.ZERO ) THEN Z( J4 ) = ZERO D = Z( J4+1 ) @@ -173,7 +173,7 @@ TEMP = Z( J4+1 ) / Z( J4-2 ) Z( J4 ) = Z( J4-1 )*TEMP D = D*TEMP - ELSE + ELSE Z( J4 ) = Z( J4+1 )*( Z( J4-1 ) / Z( J4-2 ) ) D = Z( J4+1 )*( D / Z( J4-2 ) ) END IF @@ -182,7 +182,7 @@ 10 CONTINUE ELSE DO 20 J4 = 4*I0, 4*( N0-3 ), 4 - Z( J4-3 ) = D + Z( J4 ) + Z( J4-3 ) = D + Z( J4 ) IF( Z( J4-3 ).EQ.ZERO ) THEN Z( J4-1 ) = ZERO D = Z( J4+2 ) @@ -193,7 +193,7 @@ TEMP = Z( J4+2 ) / Z( J4-3 ) Z( J4-1 ) = Z( J4 )*TEMP D = D*TEMP - ELSE + ELSE Z( J4-1 ) = Z( J4+2 )*( Z( J4 ) / Z( J4-3 ) ) D = Z( J4+2 )*( D / Z( J4-3 ) ) END IF @@ -202,7 +202,7 @@ 20 CONTINUE END IF * -* Unroll last two steps. +* Unroll last two steps. * DNM2 = D DMIN2 = DMIN diff --git a/lib/linalg/dlasr.f b/lib/linalg/dlasr.f index 645d03b3d87a6e1c1067bf28db973d2a4f9d2994..6059c6293aa7ed169d61b573fb4a487dfd6bd24c 100644 --- a/lib/linalg/dlasr.f +++ b/lib/linalg/dlasr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, PIVOT, SIDE * INTEGER LDA, M, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( * ), S( * ) * .. -* +* * *> \par Purpose: * ============= @@ -36,35 +36,35 @@ *> *> DLASR applies a sequence of plane rotations to a real matrix A, *> from either the left or the right. -*> +*> *> When SIDE = 'L', the transformation takes the form -*> +*> *> A := P*A -*> +*> *> and when SIDE = 'R', the transformation takes the form -*> +*> *> A := A*P**T -*> +*> *> where P is an orthogonal matrix consisting of a sequence of z plane *> rotations, with z = M when SIDE = 'L' and z = N when SIDE = 'R', *> and P**T is the transpose of P. -*> +*> *> When DIRECT = 'F' (Forward sequence), then -*> +*> *> P = P(z-1) * ... * P(2) * P(1) -*> +*> *> and when DIRECT = 'B' (Backward sequence), then -*> +*> *> P = P(1) * P(2) * ... * P(z-1) -*> +*> *> where P(k) is a plane rotation matrix defined by the 2-by-2 rotation -*> +*> *> R(k) = ( c(k) s(k) ) *> = ( -s(k) c(k) ). -*> +*> *> When PIVOT = 'V' (Variable pivot), the rotation is performed *> for the plane (k,k+1), i.e., P(k) has the form -*> +*> *> P(k) = ( 1 ) *> ( ... ) *> ( 1 ) @@ -73,13 +73,13 @@ *> ( 1 ) *> ( ... ) *> ( 1 ) -*> +*> *> where R(k) appears as a rank-2 modification to the identity matrix in *> rows and columns k and k+1. -*> +*> *> When PIVOT = 'T' (Top pivot), the rotation is performed for the *> plane (1,k+1), so P(k) has the form -*> +*> *> P(k) = ( c(k) s(k) ) *> ( 1 ) *> ( ... ) @@ -88,12 +88,12 @@ *> ( 1 ) *> ( ... ) *> ( 1 ) -*> +*> *> where R(k) appears in rows and columns 1 and k+1. -*> +*> *> Similarly, when PIVOT = 'B' (Bottom pivot), the rotation is *> performed for the plane (k,z), giving P(k) the form -*> +*> *> P(k) = ( 1 ) *> ( ... ) *> ( 1 ) @@ -102,7 +102,7 @@ *> ( ... ) *> ( 1 ) *> ( -s(k) c(k) ) -*> +*> *> where R(k) appears in rows and columns k and z. The rotations are *> performed without ever forming P(k) explicitly. *> \endverbatim @@ -187,22 +187,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, PIVOT, SIDE diff --git a/lib/linalg/dlasrt.f b/lib/linalg/dlasrt.f index f5d0e6cd1a8ceb180ec14fbf9293ab55ac4b6f94..4705311d78325b7d0b6188f324e29c64cc7eb5e2 100644 --- a/lib/linalg/dlasrt.f +++ b/lib/linalg/dlasrt.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASRT + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASRT + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASRT( ID, N, D, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER ID * INTEGER INFO, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( * ) * .. -* +* * *> \par Purpose: * ============= @@ -76,22 +76,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASRT( ID, N, D, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. CHARACTER ID @@ -123,7 +123,7 @@ * .. * .. Executable Statements .. * -* Test the input paramters. +* Test the input parameters. * INFO = 0 DIR = -1 diff --git a/lib/linalg/dlassq.f b/lib/linalg/dlassq.f index c7c4087e808e5e8588037b640d96541b85dac338..885395e3c970eec247d8b84a3f5c6c80558efed9 100644 --- a/lib/linalg/dlassq.f +++ b/lib/linalg/dlassq.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASSQ + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASSQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASSQ( N, X, INCX, SCALE, SUMSQ ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * DOUBLE PRECISION SCALE, SUMSQ @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -91,22 +91,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASSQ( N, X, INCX, SCALE, SUMSQ ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/dlasv2.f b/lib/linalg/dlasv2.f index 96aaa1e45c77b75f9c7617c599cd45e29d9545d4..9371d6d3b2df1cf5d30cc85af8a3e6e3bcb14e3a 100644 --- a/lib/linalg/dlasv2.f +++ b/lib/linalg/dlasv2.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASV2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASV2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASV2( F, G, H, SSMIN, SSMAX, SNR, CSR, SNL, CSL ) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION CSL, CSR, F, G, H, SNL, SNR, SSMAX, SSMIN * .. -* +* * *> \par Purpose: * ============= @@ -102,14 +102,14 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -138,10 +138,10 @@ * ===================================================================== SUBROUTINE DLASV2( F, G, H, SSMIN, SSMAX, SNR, CSR, SNL, CSL ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION CSL, CSR, F, G, H, SNL, SNR, SSMAX, SSMIN diff --git a/lib/linalg/dlaswp.f b/lib/linalg/dlaswp.f index 937e12b2f02fbf2ce911beee1964d276b0d361fa..202fd8df1bac9cf8d84ea31f78f4ececbf7f79ad 100644 --- a/lib/linalg/dlaswp.f +++ b/lib/linalg/dlaswp.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLASWP + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLASWP + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLASWP( N, A, LDA, K1, K2, IPIV, INCX ) -* +* * .. Scalar Arguments .. * INTEGER INCX, K1, K2, LDA, N * .. @@ -27,7 +27,7 @@ * INTEGER IPIV( * ) * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -71,34 +71,35 @@ *> \param[in] K2 *> \verbatim *> K2 is INTEGER -*> The last element of IPIV for which a row interchange will -*> be done. +*> (K2-K1+1) is the number of elements of IPIV for which a row +*> interchange will be done. *> \endverbatim *> *> \param[in] IPIV *> \verbatim -*> IPIV is INTEGER array, dimension (K2*abs(INCX)) -*> The vector of pivot indices. Only the elements in positions -*> K1 through K2 of IPIV are accessed. -*> IPIV(K) = L implies rows K and L are to be interchanged. +*> IPIV is INTEGER array, dimension (K1+(K2-K1)*abs(INCX)) +*> The vector of pivot indices. Only the elements in positions +*> K1 through K1+(K2-K1)*abs(INCX) of IPIV are accessed. +*> IPIV(K1+(K-K1)*abs(INCX)) = L implies rows K and L are to be +*> interchanged. *> \endverbatim *> *> \param[in] INCX *> \verbatim *> INCX is INTEGER -*> The increment between successive values of IPIV. If IPIV +*> The increment between successive values of IPIV. If INCX *> is negative, the pivots are applied in reverse order. *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2017 * *> \ingroup doubleOTHERauxiliary * @@ -114,10 +115,10 @@ * ===================================================================== SUBROUTINE DLASWP( N, A, LDA, K1, K2, IPIV, INCX ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2017 * * .. Scalar Arguments .. INTEGER INCX, K1, K2, LDA, N @@ -135,7 +136,8 @@ * .. * .. Executable Statements .. * -* Interchange row I with row IPIV(I) for each of rows K1 through K2. +* Interchange row I with row IPIV(K1+(I-K1)*abs(INCX)) for each of rows +* K1 through K2. * IF( INCX.GT.0 ) THEN IX0 = K1 @@ -143,7 +145,7 @@ I2 = K2 INC = 1 ELSE IF( INCX.LT.0 ) THEN - IX0 = 1 + ( 1-K2 )*INCX + IX0 = K1 + ( K1-K2 )*INCX I1 = K2 I2 = K1 INC = -1 diff --git a/lib/linalg/dlatrd.f b/lib/linalg/dlatrd.f index 69ec0018be6c28fb1244e26172968765fee18de1..a1df43e48a5381a50b7a115f6d317415e0850e69 100644 --- a/lib/linalg/dlatrd.f +++ b/lib/linalg/dlatrd.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLATRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLATRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER LDA, LDW, N, NB @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), E( * ), TAU( * ), W( LDW, * ) * .. -* +* * *> \par Purpose: * ============= @@ -134,12 +134,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * @@ -198,10 +198,10 @@ * ===================================================================== SUBROUTINE DLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlatrs.f b/lib/linalg/dlatrs.f index b34795eb1579a205de813af80f9d86f1e4afe443..5ad5f66c55dfb227d89592fde75b8aa9f5a93033 100644 --- a/lib/linalg/dlatrs.f +++ b/lib/linalg/dlatrs.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DLATRS + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DLATRS + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DLATRS( UPLO, TRANS, DIAG, NORMIN, N, A, LDA, X, SCALE, * CNORM, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER DIAG, NORMIN, TRANS, UPLO * INTEGER INFO, LDA, N @@ -29,7 +29,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), CNORM( * ), X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -153,12 +153,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * @@ -238,10 +238,10 @@ SUBROUTINE DLATRS( UPLO, TRANS, DIAG, NORMIN, N, A, LDA, X, SCALE, $ CNORM, INFO ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, NORMIN, TRANS, UPLO diff --git a/lib/linalg/dnrm2.f b/lib/linalg/dnrm2.f index 5ea257a2004bc8adc91ccf51112bc50e7d8cc2fa..30552e1d1dc252c2673438152706be549f208b7c 100644 --- a/lib/linalg/dnrm2.f +++ b/lib/linalg/dnrm2.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DNRM2(N,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * .. * .. Array Arguments .. * DOUBLE PRECISION X(*) * .. -* +* * *> \par Purpose: * ============= @@ -29,15 +29,35 @@ *> DNRM2 := sqrt( x'*x ) *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] X +*> \verbatim +*> X is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -54,10 +74,10 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DNRM2(N,X,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/dorg2l.f b/lib/linalg/dorg2l.f index b95fa50fc52e0b4da682052cd46e400b6ad2bcee..36ff4e5d4b281c3f51ded4ae3f8b573dc2aab1c7 100644 --- a/lib/linalg/dorg2l.f +++ b/lib/linalg/dorg2l.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORG2L + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORG2L + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORG2L( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORG2L( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorg2r.f b/lib/linalg/dorg2r.f index 86df6dddc7fce64bb161b4b4451ff6365e0b3464..4b71011a9ff65aaf9c4cc5cd0aea36143b8115b8 100644 --- a/lib/linalg/dorg2r.f +++ b/lib/linalg/dorg2r.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORG2R + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORG2R + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORG2R( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORG2R( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorgbr.f b/lib/linalg/dorgbr.f index ddfa7262a0654872ec3e9f85e4e98455938f303f..cfebda5abdbb8303a07a7d26bea47b1b11e269f2 100644 --- a/lib/linalg/dorgbr.f +++ b/lib/linalg/dorgbr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGBR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGBR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGBR( VECT, M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER VECT * INTEGER INFO, K, LDA, LWORK, M, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -145,10 +145,10 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * *> \date April 2012 * @@ -157,7 +157,7 @@ * ===================================================================== SUBROUTINE DORGBR( VECT, M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.1) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- * April 2012 @@ -182,8 +182,7 @@ * .. * .. External Functions .. LOGICAL LSAME - INTEGER ILAENV - EXTERNAL LSAME, ILAENV + EXTERNAL LSAME * .. * .. External Subroutines .. EXTERNAL DORGLQ, DORGQR, XERBLA diff --git a/lib/linalg/dorgl2.f b/lib/linalg/dorgl2.f index 3e8398b73f872c1b8301900cf302a7d3383d49ce..5d8985d7589f104d067a4cabd0ae797f142b76ba 100644 --- a/lib/linalg/dorgl2.f +++ b/lib/linalg/dorgl2.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGL2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGL2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGL2( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -101,22 +101,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGL2( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorglq.f b/lib/linalg/dorglq.f index 88aec15005ca7a708534a0ff7469224902d40f84..912b5de84ed345ac1845e87d2668eabf75bdaead 100644 --- a/lib/linalg/dorglq.f +++ b/lib/linalg/dorglq.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGLQ + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGLQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGLQ( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, LWORK, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -115,22 +115,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGLQ( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgql.f b/lib/linalg/dorgql.f index ca4698d799dbb9ef7568a696210891aaece4ad10..ea12be91b11112fe1489629001f9a91572e48871 100644 --- a/lib/linalg/dorgql.f +++ b/lib/linalg/dorgql.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGQL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGQL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, LWORK, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,22 +116,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgqr.f b/lib/linalg/dorgqr.f index 404ab184e655145c301fda51efa7a4c2f5c1f0fc..628eeacba702afe0b43b0b93ad7064274c0ecbcb 100644 --- a/lib/linalg/dorgqr.f +++ b/lib/linalg/dorgqr.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, LWORK, M, N * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,22 +116,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgtr.f b/lib/linalg/dorgtr.f index 06a7b6cc1cdc5bd335ce9e50777a006ebfab3c06..72623eac06d1876429075783549b24c8011fb4cd 100644 --- a/lib/linalg/dorgtr.f +++ b/lib/linalg/dorgtr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORGTR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORGTR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, LWORK, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -111,22 +111,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dorm2l.f b/lib/linalg/dorm2l.f index 3ff25869a7524b58a6bd6fb6b6a437c8110060e0..1014cb2378398fd77d0c9c022e82faf2097e4701 100644 --- a/lib/linalg/dorm2l.f +++ b/lib/linalg/dorm2l.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORM2L + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORM2L + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -146,12 +146,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -159,10 +159,10 @@ SUBROUTINE DORM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dorm2r.f b/lib/linalg/dorm2r.f index b13f12d53cb4bd14a5ca28333f2b5073cd1a720f..632b70e740caa5d70026bda87b0cc7953af8567f 100644 --- a/lib/linalg/dorm2r.f +++ b/lib/linalg/dorm2r.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORM2R + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORM2R + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -146,12 +146,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -159,10 +159,10 @@ SUBROUTINE DORM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dormbr.f b/lib/linalg/dormbr.f index 7a0d9b9038527296cd528b5edf62cd3cdaa2c239..f035d0ae66fa2f9574bfe4ffc85e0865b9b8ea32 100644 --- a/lib/linalg/dormbr.f +++ b/lib/linalg/dormbr.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORMBR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORMBR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORMBR( VECT, SIDE, TRANS, M, N, K, A, LDA, TAU, C, * LDC, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS, VECT * INTEGER INFO, K, LDA, LDC, LWORK, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -182,12 +182,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -195,10 +195,10 @@ SUBROUTINE DORMBR( VECT, SIDE, TRANS, M, N, K, A, LDA, TAU, C, $ LDC, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS, VECT diff --git a/lib/linalg/dorml2.f b/lib/linalg/dorml2.f index 9ae2396e12da7f83e9aa095f7e21ed1d9b6556a9..2c55c7f1fd380a03a831773bf01747dbdd5c25d3 100644 --- a/lib/linalg/dorml2.f +++ b/lib/linalg/dorml2.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORML2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORML2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORML2( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -146,12 +146,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -159,10 +159,10 @@ SUBROUTINE DORML2( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dormlq.f b/lib/linalg/dormlq.f index ebbd4d26e2cb3e9dce593896a9d72f272d829d12..bb5469d273bbb38697c0d67eb78f09102896b6bb 100644 --- a/lib/linalg/dormlq.f +++ b/lib/linalg/dormlq.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORMLQ + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORMLQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORMLQ( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, LWORK, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -136,9 +136,7 @@ *> The dimension of the array WORK. *> If SIDE = 'L', LWORK >= max(1,N); *> if SIDE = 'R', LWORK >= max(1,M). -*> For optimum performance LWORK >= N*NB if SIDE = 'L', and -*> LWORK >= M*NB if SIDE = 'R', where NB is the optimal -*> blocksize. +*> For good performance, LWORK should generally be larger. *> *> If LWORK = -1, then a workspace query is assumed; the routine *> only calculates the optimal size of the WORK array, returns @@ -156,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -169,10 +167,10 @@ SUBROUTINE DORMLQ( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -185,18 +183,16 @@ * ===================================================================== * * .. Parameters .. - INTEGER NBMAX, LDT - PARAMETER ( NBMAX = 64, LDT = NBMAX+1 ) + INTEGER NBMAX, LDT, TSIZE + PARAMETER ( NBMAX = 64, LDT = NBMAX+1, + $ TSIZE = LDT*NBMAX ) * .. * .. Local Scalars .. LOGICAL LEFT, LQUERY, NOTRAN CHARACTER TRANST - INTEGER I, I1, I2, I3, IB, IC, IINFO, IWS, JC, LDWORK, + INTEGER I, I1, I2, I3, IB, IC, IINFO, IWT, JC, LDWORK, $ LWKOPT, MI, NB, NBMIN, NI, NQ, NW * .. -* .. Local Arrays .. - DOUBLE PRECISION T( LDT, NBMAX ) -* .. * .. External Functions .. LOGICAL LSAME INTEGER ILAENV @@ -246,12 +242,11 @@ * IF( INFO.EQ.0 ) THEN * -* Determine the block size. NB may be at most NBMAX, where NBMAX -* is used to define the local array T. +* Compute the workspace requirements * NB = MIN( NBMAX, ILAENV( 1, 'DORMLQ', SIDE // TRANS, M, N, K, $ -1 ) ) - LWKOPT = MAX( 1, NW )*NB + LWKOPT = MAX( 1, NW )*NB + TSIZE WORK( 1 ) = LWKOPT END IF * @@ -272,14 +267,11 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IWS = NW*NB - IF( LWORK.LT.IWS ) THEN - NB = LWORK / LDWORK + IF( LWORK.LT.NW*NB+TSIZE ) THEN + NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMLQ', SIDE // TRANS, M, N, K, $ -1 ) ) END IF - ELSE - IWS = NW END IF * IF( NB.LT.NBMIN .OR. NB.GE.K ) THEN @@ -292,6 +284,7 @@ * * Use blocked code * + IWT = 1 + NW*NB IF( ( LEFT .AND. NOTRAN ) .OR. $ ( .NOT.LEFT .AND. .NOT.NOTRAN ) ) THEN I1 = 1 @@ -324,7 +317,7 @@ * H = H(i) H(i+1) . . . H(i+ib-1) * CALL DLARFT( 'Forward', 'Rowwise', NQ-I+1, IB, A( I, I ), - $ LDA, TAU( I ), T, LDT ) + $ LDA, TAU( I ), WORK( IWT ), LDT ) IF( LEFT ) THEN * * H or H**T is applied to C(i:m,1:n) @@ -342,8 +335,8 @@ * Apply H or H**T * CALL DLARFB( SIDE, TRANST, 'Forward', 'Rowwise', MI, NI, IB, - $ A( I, I ), LDA, T, LDT, C( IC, JC ), LDC, WORK, - $ LDWORK ) + $ A( I, I ), LDA, WORK( IWT ), LDT, + $ C( IC, JC ), LDC, WORK, LDWORK ) 10 CONTINUE END IF WORK( 1 ) = LWKOPT diff --git a/lib/linalg/dormql.f b/lib/linalg/dormql.f index 96c6f1958ed492c358454180e27e3e70d047b3ac..7d2b5d6c32bb618c026a305de7bca5d28a2cfd09 100644 --- a/lib/linalg/dormql.f +++ b/lib/linalg/dormql.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORMQL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORMQL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORMQL( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, LWORK, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -136,9 +136,7 @@ *> The dimension of the array WORK. *> If SIDE = 'L', LWORK >= max(1,N); *> if SIDE = 'R', LWORK >= max(1,M). -*> For optimum performance LWORK >= N*NB if SIDE = 'L', and -*> LWORK >= M*NB if SIDE = 'R', where NB is the optimal -*> blocksize. +*> For good performance, LWORK should generally be larger. *> *> If LWORK = -1, then a workspace query is assumed; the routine *> only calculates the optimal size of the WORK array, returns @@ -156,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -169,10 +167,10 @@ SUBROUTINE DORMQL( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -185,17 +183,15 @@ * ===================================================================== * * .. Parameters .. - INTEGER NBMAX, LDT - PARAMETER ( NBMAX = 64, LDT = NBMAX+1 ) + INTEGER NBMAX, LDT, TSIZE + PARAMETER ( NBMAX = 64, LDT = NBMAX+1, + $ TSIZE = LDT*NBMAX ) * .. * .. Local Scalars .. LOGICAL LEFT, LQUERY, NOTRAN - INTEGER I, I1, I2, I3, IB, IINFO, IWS, LDWORK, LWKOPT, + INTEGER I, I1, I2, I3, IB, IINFO, IWT, LDWORK, LWKOPT, $ MI, NB, NBMIN, NI, NQ, NW * .. -* .. Local Arrays .. - DOUBLE PRECISION T( LDT, NBMAX ) -* .. * .. External Functions .. LOGICAL LSAME INTEGER ILAENV @@ -239,25 +235,22 @@ INFO = -7 ELSE IF( LDC.LT.MAX( 1, M ) ) THEN INFO = -10 + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN + INFO = -12 END IF * IF( INFO.EQ.0 ) THEN +* +* Compute the workspace requirements +* IF( M.EQ.0 .OR. N.EQ.0 ) THEN LWKOPT = 1 ELSE -* -* Determine the block size. NB may be at most NBMAX, where -* NBMAX is used to define the local array T. -* NB = MIN( NBMAX, ILAENV( 1, 'DORMQL', SIDE // TRANS, M, N, $ K, -1 ) ) - LWKOPT = NW*NB + LWKOPT = NW*NB + TSIZE END IF WORK( 1 ) = LWKOPT -* - IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN - INFO = -12 - END IF END IF * IF( INFO.NE.0 ) THEN @@ -276,14 +269,11 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IWS = NW*NB - IF( LWORK.LT.IWS ) THEN - NB = LWORK / LDWORK + IF( LWORK.LT.NW*NB+TSIZE ) THEN + NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMQL', SIDE // TRANS, M, N, K, $ -1 ) ) END IF - ELSE - IWS = NW END IF * IF( NB.LT.NBMIN .OR. NB.GE.K ) THEN @@ -296,6 +286,7 @@ * * Use blocked code * + IWT = 1 + NW*NB IF( ( LEFT .AND. NOTRAN ) .OR. $ ( .NOT.LEFT .AND. .NOT.NOTRAN ) ) THEN I1 = 1 @@ -320,7 +311,7 @@ * H = H(i+ib-1) . . . H(i+1) H(i) * CALL DLARFT( 'Backward', 'Columnwise', NQ-K+I+IB-1, IB, - $ A( 1, I ), LDA, TAU( I ), T, LDT ) + $ A( 1, I ), LDA, TAU( I ), WORK( IWT ), LDT ) IF( LEFT ) THEN * * H or H**T is applied to C(1:m-k+i+ib-1,1:n) @@ -336,8 +327,8 @@ * Apply H or H**T * CALL DLARFB( SIDE, TRANS, 'Backward', 'Columnwise', MI, NI, - $ IB, A( 1, I ), LDA, T, LDT, C, LDC, WORK, - $ LDWORK ) + $ IB, A( 1, I ), LDA, WORK( IWT ), LDT, C, LDC, + $ WORK, LDWORK ) 10 CONTINUE END IF WORK( 1 ) = LWKOPT diff --git a/lib/linalg/dormqr.f b/lib/linalg/dormqr.f index c0767ecf61e2f07f4e7974df3f8a48b7fec5a4bf..7f2ebb9ace5f6116df657954cdd0591916376f91 100644 --- a/lib/linalg/dormqr.f +++ b/lib/linalg/dormqr.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORMQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORMQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORMQR( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, * WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS * INTEGER INFO, K, LDA, LDC, LWORK, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -136,9 +136,7 @@ *> The dimension of the array WORK. *> If SIDE = 'L', LWORK >= max(1,N); *> if SIDE = 'R', LWORK >= max(1,M). -*> For optimum performance LWORK >= N*NB if SIDE = 'L', and -*> LWORK >= M*NB if SIDE = 'R', where NB is the optimal -*> blocksize. +*> For good performance, LWORK should generally be larger. *> *> If LWORK = -1, then a workspace query is assumed; the routine *> only calculates the optimal size of the WORK array, returns @@ -156,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -169,10 +167,10 @@ SUBROUTINE DORMQR( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -185,17 +183,15 @@ * ===================================================================== * * .. Parameters .. - INTEGER NBMAX, LDT - PARAMETER ( NBMAX = 64, LDT = NBMAX+1 ) + INTEGER NBMAX, LDT, TSIZE + PARAMETER ( NBMAX = 64, LDT = NBMAX+1, + $ TSIZE = LDT*NBMAX ) * .. * .. Local Scalars .. LOGICAL LEFT, LQUERY, NOTRAN - INTEGER I, I1, I2, I3, IB, IC, IINFO, IWS, JC, LDWORK, + INTEGER I, I1, I2, I3, IB, IC, IINFO, IWT, JC, LDWORK, $ LWKOPT, MI, NB, NBMIN, NI, NQ, NW * .. -* .. Local Arrays .. - DOUBLE PRECISION T( LDT, NBMAX ) -* .. * .. External Functions .. LOGICAL LSAME INTEGER ILAENV @@ -245,12 +241,11 @@ * IF( INFO.EQ.0 ) THEN * -* Determine the block size. NB may be at most NBMAX, where NBMAX -* is used to define the local array T. +* Compute the workspace requirements * NB = MIN( NBMAX, ILAENV( 1, 'DORMQR', SIDE // TRANS, M, N, K, $ -1 ) ) - LWKOPT = MAX( 1, NW )*NB + LWKOPT = MAX( 1, NW )*NB + TSIZE WORK( 1 ) = LWKOPT END IF * @@ -271,14 +266,11 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IWS = NW*NB - IF( LWORK.LT.IWS ) THEN - NB = LWORK / LDWORK + IF( LWORK.LT.NW*NB+TSIZE ) THEN + NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMQR', SIDE // TRANS, M, N, K, $ -1 ) ) END IF - ELSE - IWS = NW END IF * IF( NB.LT.NBMIN .OR. NB.GE.K ) THEN @@ -291,6 +283,7 @@ * * Use blocked code * + IWT = 1 + NW*NB IF( ( LEFT .AND. .NOT.NOTRAN ) .OR. $ ( .NOT.LEFT .AND. NOTRAN ) ) THEN I1 = 1 @@ -317,7 +310,7 @@ * H = H(i) H(i+1) . . . H(i+ib-1) * CALL DLARFT( 'Forward', 'Columnwise', NQ-I+1, IB, A( I, I ), - $ LDA, TAU( I ), T, LDT ) + $ LDA, TAU( I ), WORK( IWT ), LDT ) IF( LEFT ) THEN * * H or H**T is applied to C(i:m,1:n) @@ -335,8 +328,8 @@ * Apply H or H**T * CALL DLARFB( SIDE, TRANS, 'Forward', 'Columnwise', MI, NI, - $ IB, A( I, I ), LDA, T, LDT, C( IC, JC ), LDC, - $ WORK, LDWORK ) + $ IB, A( I, I ), LDA, WORK( IWT ), LDT, + $ C( IC, JC ), LDC, WORK, LDWORK ) 10 CONTINUE END IF WORK( 1 ) = LWKOPT diff --git a/lib/linalg/dormtr.f b/lib/linalg/dormtr.f index 00fff4dda2a6546fccd1cfcb792956268813568d..d2443c1dac51b6957a34bcc3342e695578969f8b 100644 --- a/lib/linalg/dormtr.f +++ b/lib/linalg/dormtr.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DORMTR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DORMTR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DORMTR( SIDE, UPLO, TRANS, M, N, A, LDA, TAU, C, LDC, * WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE, TRANS, UPLO * INTEGER INFO, LDA, LDC, LWORK, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -158,12 +158,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * @@ -171,10 +171,10 @@ SUBROUTINE DORMTR( SIDE, UPLO, TRANS, M, N, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS, UPLO diff --git a/lib/linalg/dpotf2.f b/lib/linalg/dpotf2.f index 6003e19b055ca2075781ebdabde72d0723d9c1ac..1fb60a903b42cae801ac8ca984b09c45140d392b 100644 --- a/lib/linalg/dpotf2.f +++ b/lib/linalg/dpotf2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DPOTF2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DPOTF2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DPOTF2( UPLO, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -97,22 +97,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doublePOcomputational * * ===================================================================== SUBROUTINE DPOTF2( UPLO, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dpotrf.f b/lib/linalg/dpotrf.f index 3457230b56724e0d8adb350fb34ba634a4a63d53..1fa75a465424f69d9df88f695c41fb79efe79729 100644 --- a/lib/linalg/dpotrf.f +++ b/lib/linalg/dpotrf.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DPOTRF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DPOTRF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DPOTRF( UPLO, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -95,22 +95,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doublePOcomputational * * ===================================================================== SUBROUTINE DPOTRF( UPLO, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -136,7 +136,7 @@ EXTERNAL LSAME, ILAENV * .. * .. External Subroutines .. - EXTERNAL DGEMM, DPOTF2, DSYRK, DTRSM, XERBLA + EXTERNAL DGEMM, DPOTRF2, DSYRK, DTRSM, XERBLA * .. * .. Intrinsic Functions .. INTRINSIC MAX, MIN @@ -171,7 +171,7 @@ * * Use unblocked code. * - CALL DPOTF2( UPLO, N, A, LDA, INFO ) + CALL DPOTRF2( UPLO, N, A, LDA, INFO ) ELSE * * Use blocked code. @@ -188,7 +188,7 @@ JB = MIN( NB, N-J+1 ) CALL DSYRK( 'Upper', 'Transpose', JB, J-1, -ONE, $ A( 1, J ), LDA, ONE, A( J, J ), LDA ) - CALL DPOTF2( 'Upper', JB, A( J, J ), LDA, INFO ) + CALL DPOTRF2( 'Upper', JB, A( J, J ), LDA, INFO ) IF( INFO.NE.0 ) $ GO TO 30 IF( J+JB.LE.N ) THEN @@ -216,7 +216,7 @@ JB = MIN( NB, N-J+1 ) CALL DSYRK( 'Lower', 'No transpose', JB, J-1, -ONE, $ A( J, 1 ), LDA, ONE, A( J, J ), LDA ) - CALL DPOTF2( 'Lower', JB, A( J, J ), LDA, INFO ) + CALL DPOTRF2( 'Lower', JB, A( J, J ), LDA, INFO ) IF( INFO.NE.0 ) $ GO TO 30 IF( J+JB.LE.N ) THEN diff --git a/lib/linalg/dpotrf2.f b/lib/linalg/dpotrf2.f new file mode 100644 index 0000000000000000000000000000000000000000..0d419c4f008595bc8e86d8e128a789d138d1b25d --- /dev/null +++ b/lib/linalg/dpotrf2.f @@ -0,0 +1,237 @@ +*> \brief \b DPOTRF2 +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +* Definition: +* =========== +* +* RECURSIVE SUBROUTINE DPOTRF2( UPLO, N, A, LDA, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER INFO, LDA, N +* .. +* .. Array Arguments .. +* REAL A( LDA, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> DPOTRF2 computes the Cholesky factorization of a real symmetric +*> positive definite matrix A using the recursive algorithm. +*> +*> The factorization has the form +*> A = U**T * U, if UPLO = 'U', or +*> A = L * L**T, if UPLO = 'L', +*> where U is an upper triangular matrix and L is lower triangular. +*> +*> This is the recursive version of the algorithm. It divides +*> the matrix into four submatrices: +*> +*> [ A11 | A12 ] where A11 is n1 by n1 and A22 is n2 by n2 +*> A = [ -----|----- ] with n1 = n/2 +*> [ A21 | A22 ] n2 = n-n1 +*> +*> The subroutine calls itself to factor A11. Update and scale A21 +*> or A12, update A22 then calls itself to factor A22. +*> +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': Upper triangle of A is stored; +*> = 'L': Lower triangle of A is stored. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The order of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is DOUBLE PRECISION array, dimension (LDA,N) +*> On entry, the symmetric matrix A. If UPLO = 'U', the leading +*> N-by-N upper triangular part of A contains the upper +*> triangular part of the matrix A, and the strictly lower +*> triangular part of A is not referenced. If UPLO = 'L', the +*> leading N-by-N lower triangular part of A contains the lower +*> triangular part of the matrix A, and the strictly upper +*> triangular part of A is not referenced. +*> +*> On exit, if INFO = 0, the factor U or L from the Cholesky +*> factorization A = U**T*U or A = L*L**T. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,N). +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> > 0: if INFO = i, the leading minor of order i is not +*> positive definite, and the factorization could not be +*> completed. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date December 2016 +* +*> \ingroup doublePOcomputational +* +* ===================================================================== + RECURSIVE SUBROUTINE DPOTRF2( UPLO, N, A, LDA, INFO ) +* +* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* December 2016 +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER INFO, LDA, N +* .. +* .. Array Arguments .. + DOUBLE PRECISION A( LDA, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D+0, ZERO = 0.0D+0 ) +* .. +* .. Local Scalars .. + LOGICAL UPPER + INTEGER N1, N2, IINFO +* .. +* .. External Functions .. + LOGICAL LSAME, DISNAN + EXTERNAL LSAME, DISNAN +* .. +* .. External Subroutines .. + EXTERNAL DSYRK, DTRSM, XERBLA +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters +* + INFO = 0 + UPPER = LSAME( UPLO, 'U' ) + IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -4 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'DPOTRF2', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* N=1 case +* + IF( N.EQ.1 ) THEN +* +* Test for non-positive-definiteness +* + IF( A( 1, 1 ).LE.ZERO.OR.DISNAN( A( 1, 1 ) ) ) THEN + INFO = 1 + RETURN + END IF +* +* Factor +* + A( 1, 1 ) = SQRT( A( 1, 1 ) ) +* +* Use recursive code +* + ELSE + N1 = N/2 + N2 = N-N1 +* +* Factor A11 +* + CALL DPOTRF2( UPLO, N1, A( 1, 1 ), LDA, IINFO ) + IF ( IINFO.NE.0 ) THEN + INFO = IINFO + RETURN + END IF +* +* Compute the Cholesky factorization A = U**T*U +* + IF( UPPER ) THEN +* +* Update and scale A12 +* + CALL DTRSM( 'L', 'U', 'T', 'N', N1, N2, ONE, + $ A( 1, 1 ), LDA, A( 1, N1+1 ), LDA ) +* +* Update and factor A22 +* + CALL DSYRK( UPLO, 'T', N2, N1, -ONE, A( 1, N1+1 ), LDA, + $ ONE, A( N1+1, N1+1 ), LDA ) + CALL DPOTRF2( UPLO, N2, A( N1+1, N1+1 ), LDA, IINFO ) + IF ( IINFO.NE.0 ) THEN + INFO = IINFO + N1 + RETURN + END IF +* +* Compute the Cholesky factorization A = L*L**T +* + ELSE +* +* Update and scale A21 +* + CALL DTRSM( 'R', 'L', 'T', 'N', N2, N1, ONE, + $ A( 1, 1 ), LDA, A( N1+1, 1 ), LDA ) +* +* Update and factor A22 +* + CALL DSYRK( UPLO, 'N', N2, N1, -ONE, A( N1+1, 1 ), LDA, + $ ONE, A( N1+1, N1+1 ), LDA ) + CALL DPOTRF2( UPLO, N2, A( N1+1, N1+1 ), LDA, IINFO ) + IF ( IINFO.NE.0 ) THEN + INFO = IINFO + N1 + RETURN + END IF + END IF + END IF + RETURN +* +* End of DPOTRF2 +* + END diff --git a/lib/linalg/drot.f b/lib/linalg/drot.f index 1615ef6a875c9f44d8c4a399dc7ed784283b0669..0d33ea76c859d424e6d7208498415ba811c22b39 100644 --- a/lib/linalg/drot.f +++ b/lib/linalg/drot.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DROT(N,DX,INCX,DY,INCY,C,S) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION C,S * INTEGER INCX,INCY,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION DX(*),DY(*) * .. -* +* * *> \par Purpose: * ============= @@ -27,15 +27,56 @@ *> DROT applies a plane rotation. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in,out] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +*> +*> \param[in,out] DY +*> \verbatim +*> DY is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of DY +*> \endverbatim +*> +*> \param[in] C +*> \verbatim +*> C is DOUBLE PRECISION +*> \endverbatim +*> +*> \param[in] S +*> \verbatim +*> S is DOUBLE PRECISION +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -51,10 +92,10 @@ * ===================================================================== SUBROUTINE DROT(N,DX,INCX,DY,INCY,C,S) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION C,S diff --git a/lib/linalg/drscl.f b/lib/linalg/drscl.f index 21ba19c11afd8b42b1dda66b1b8e378d3df9a6de..92511436801917b86c7c32ba8012c57b4a971867 100644 --- a/lib/linalg/drscl.f +++ b/lib/linalg/drscl.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DRSCL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DRSCL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DRSCL( N, SA, SX, INCX ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * DOUBLE PRECISION SA @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION SX( * ) * .. -* +* * *> \par Purpose: * ============= @@ -72,22 +72,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DRSCL( N, SA, SX, INCX ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/dscal.f b/lib/linalg/dscal.f index 3337de8e63c498715f5d9e90284dab9c6607a170..e0a92de6ba652a525c356439326bf3f2813d287a 100644 --- a/lib/linalg/dscal.f +++ b/lib/linalg/dscal.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSCAL(N,DA,DX,INCX) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION DA * INTEGER INCX,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION DX(*) * .. -* +* * *> \par Purpose: * ============= @@ -25,18 +25,44 @@ *> \verbatim *> *> DSCAL scales a vector by a constant. -*> uses unrolled loops for increment equal to one. +*> uses unrolled loops for increment equal to 1. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DA +*> \verbatim +*> DA is DOUBLE PRECISION +*> On entry, DA specifies the scalar alpha. +*> \endverbatim +*> +*> \param[in,out] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -53,10 +79,10 @@ * ===================================================================== SUBROUTINE DSCAL(N,DA,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA diff --git a/lib/linalg/dstedc.f b/lib/linalg/dstedc.f index b59e1c3bbd56de572cfb3e7ce6bbcf759a14c3df..61b44bc06b5180fe7c12cd02c384291756a4ae66 100644 --- a/lib/linalg/dstedc.f +++ b/lib/linalg/dstedc.f @@ -1,26 +1,26 @@ -*> \brief \b DSTEBZ +*> \brief \b DSTEDC * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSTEDC + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSTEDC + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSTEDC( COMPZ, N, D, E, Z, LDZ, WORK, LWORK, IWORK, * LIWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER COMPZ * INTEGER INFO, LDZ, LIWORK, LWORK, N @@ -29,7 +29,7 @@ * INTEGER IWORK( * ) * DOUBLE PRECISION D( * ), E( * ), WORK( * ), Z( LDZ, * ) * .. -* +* * *> \par Purpose: * ============= @@ -105,8 +105,7 @@ *> *> \param[out] WORK *> \verbatim -*> WORK is DOUBLE PRECISION array, -*> dimension (LWORK) +*> WORK is DOUBLE PRECISION array, dimension (MAX(1,LWORK)) *> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. *> \endverbatim *> @@ -169,12 +168,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date June 2017 * *> \ingroup auxOTHERcomputational * @@ -189,10 +188,10 @@ SUBROUTINE DSTEDC( COMPZ, N, D, E, Z, LDZ, WORK, LWORK, IWORK, $ LIWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* June 2017 * * .. Scalar Arguments .. CHARACTER COMPZ @@ -443,38 +442,32 @@ * * endwhile * -* If the problem split any number of times, then the eigenvalues -* will not be properly ordered. Here we permute the eigenvalues -* (and the associated eigenvectors) into ascending order. -* - IF( M.NE.N ) THEN - IF( ICOMPZ.EQ.0 ) THEN + IF( ICOMPZ.EQ.0 ) THEN * -* Use Quick Sort +* Use Quick Sort * - CALL DLASRT( 'I', N, D, INFO ) + CALL DLASRT( 'I', N, D, INFO ) * - ELSE + ELSE * -* Use Selection Sort to minimize swaps of eigenvectors -* - DO 40 II = 2, N - I = II - 1 - K = I - P = D( I ) - DO 30 J = II, N - IF( D( J ).LT.P ) THEN - K = J - P = D( J ) - END IF - 30 CONTINUE - IF( K.NE.I ) THEN - D( K ) = D( I ) - D( I ) = P - CALL DSWAP( N, Z( 1, I ), 1, Z( 1, K ), 1 ) - END IF - 40 CONTINUE - END IF +* Use Selection Sort to minimize swaps of eigenvectors +* + DO 40 II = 2, N + I = II - 1 + K = I + P = D( I ) + DO 30 J = II, N + IF( D( J ).LT.P ) THEN + K = J + P = D( J ) + END IF + 30 CONTINUE + IF( K.NE.I ) THEN + D( K ) = D( I ) + D( I ) = P + CALL DSWAP( N, Z( 1, I ), 1, Z( 1, K ), 1 ) + END IF + 40 CONTINUE END IF END IF * diff --git a/lib/linalg/dsteqr.f b/lib/linalg/dsteqr.f index 9e165bb6bbeb523e05e0859d67cbfb60eab7c779..c34a548984aeaf252dd29040ccf33a2616d84b10 100644 --- a/lib/linalg/dsteqr.f +++ b/lib/linalg/dsteqr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSTEQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSTEQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER COMPZ * INTEGER INFO, LDZ, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION D( * ), E( * ), WORK( * ), Z( LDZ, * ) * .. -* +* * *> \par Purpose: * ============= @@ -119,22 +119,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER COMPZ diff --git a/lib/linalg/dsterf.f b/lib/linalg/dsterf.f index b93cc13dd6ada6eb41882a143898eb7ebf8fe4c2..3401894819aee18d6ab0742c7b7327e25efc2a7c 100644 --- a/lib/linalg/dsterf.f +++ b/lib/linalg/dsterf.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSTERF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSTERF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSTERF( N, D, E, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, N * .. * .. Array Arguments .. * DOUBLE PRECISION D( * ), E( * ) * .. -* +* * *> \par Purpose: * ============= @@ -74,22 +74,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DSTERF( N, D, E, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N @@ -190,7 +190,7 @@ ANORM = DLANST( 'M', LEND-L+1, D( L ), E( L ) ) ISCALE = 0 IF( ANORM.EQ.ZERO ) - $ GO TO 10 + $ GO TO 10 IF( (ANORM.GT.SSFMAX) ) THEN ISCALE = 1 CALL DLASCL( 'G', 0, 0, ANORM, SSFMAX, LEND-L+1, 1, D( L ), N, diff --git a/lib/linalg/dswap.f b/lib/linalg/dswap.f index e567bd93ec3e5078dcfc86a19dcf6e1e0cdf37e3..94dfea3bb919eb115fea75777a27403da3ac8af6 100644 --- a/lib/linalg/dswap.f +++ b/lib/linalg/dswap.f @@ -2,40 +2,71 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSWAP(N,DX,INCX,DY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * DOUBLE PRECISION DX(*),DY(*) * .. -* +* * *> \par Purpose: * ============= *> *> \verbatim *> -*> interchanges two vectors. -*> uses unrolled loops for increments equal one. +*> DSWAP interchanges two vectors. +*> uses unrolled loops for increments equal to 1. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in,out] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of DX +*> \endverbatim +*> +*> \param[in,out] DY +*> \verbatim +*> DY is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of DY *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -51,10 +82,10 @@ * ===================================================================== SUBROUTINE DSWAP(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N diff --git a/lib/linalg/dsyev.f b/lib/linalg/dsyev.f index 64b39ed84783e6eaa8df5220437c433ad3153afe..ee8c479abea1995ba16bd3a3930db3ab5205a906 100644 --- a/lib/linalg/dsyev.f +++ b/lib/linalg/dsyev.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYEV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYEV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBZ, UPLO * INTEGER INFO, LDA, LWORK, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), W( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -120,22 +120,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleSYeigen * * ===================================================================== SUBROUTINE DSYEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, INFO ) * -* -- LAPACK driver routine (version 3.4.0) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsyevd.f b/lib/linalg/dsyevd.f index 3c9545ac31a5f85ee054d46d8be9eeea2e66079e..2db67846dc309fcb81380c7ccedf53b9197b6eaa 100644 --- a/lib/linalg/dsyevd.f +++ b/lib/linalg/dsyevd.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYEVD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYEVD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, IWORK, * LIWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBZ, UPLO * INTEGER INFO, LDA, LIWORK, LWORK, N @@ -29,7 +29,7 @@ * INTEGER IWORK( * ) * DOUBLE PRECISION A( LDA, * ), W( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -162,12 +162,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleSYeigen * @@ -185,10 +185,10 @@ SUBROUTINE DSYEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, IWORK, $ LIWORK, INFO ) * -* -- LAPACK driver routine (version 3.4.2) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsygs2.f b/lib/linalg/dsygs2.f index 644dcfff1b79223dbd5e27830c943de7b906450f..a54955c01e3cec4e3a20165fc3d469470804dd4c 100644 --- a/lib/linalg/dsygs2.f +++ b/lib/linalg/dsygs2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYGS2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYGS2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYGS2( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, ITYPE, LDA, LDB, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), B( LDB, * ) * .. -* +* * *> \par Purpose: * ============= @@ -115,22 +115,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleSYcomputational * * ===================================================================== SUBROUTINE DSYGS2( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsygst.f b/lib/linalg/dsygst.f index f1d5311c9afdee54560f1ce71f0b613228a952bb..5055acdf1de62b512f2ab294e06a7e3dff27d21d 100644 --- a/lib/linalg/dsygst.f +++ b/lib/linalg/dsygst.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYGST + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYGST + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYGST( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, ITYPE, LDA, LDB, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), B( LDB, * ) * .. -* +* * *> \par Purpose: * ============= @@ -115,22 +115,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleSYcomputational * * ===================================================================== SUBROUTINE DSYGST( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsygv.f b/lib/linalg/dsygv.f index e55631851869147a167a53aeeda1f72247794f1a..651abc5c7b18b7265c0fbf7ae26329c3cf892ba7 100644 --- a/lib/linalg/dsygv.f +++ b/lib/linalg/dsygv.f @@ -1,26 +1,26 @@ -*> \brief \b DSYGST +*> \brief \b DSYGV * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYGV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYGV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYGV( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, * LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBZ, UPLO * INTEGER INFO, ITYPE, LDA, LDB, LWORK, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), B( LDB, * ), W( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -162,12 +162,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleSYeigen * @@ -175,10 +175,10 @@ SUBROUTINE DSYGV( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, $ LWORK, INFO ) * -* -- LAPACK driver routine (version 3.4.0) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsygvd.f b/lib/linalg/dsygvd.f index 171aa175ff11fdf0ae813221c348b0fd6e5be28e..29c78283a703986f750bd5b6ddaa3bfa82722af6 100644 --- a/lib/linalg/dsygvd.f +++ b/lib/linalg/dsygvd.f @@ -1,26 +1,26 @@ -*> \brief \b DSYGST +*> \brief \b DSYGVD * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYGVD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYGVD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYGVD( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, * LWORK, IWORK, LIWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBZ, UPLO * INTEGER INFO, ITYPE, LDA, LDB, LIWORK, LWORK, N @@ -29,7 +29,7 @@ * INTEGER IWORK( * ) * DOUBLE PRECISION A( LDA, * ), B( LDB, * ), W( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -198,12 +198,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleSYeigen * @@ -227,10 +227,10 @@ SUBROUTINE DSYGVD( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, $ LWORK, IWORK, LIWORK, INFO ) * -* -- LAPACK driver routine (version 3.4.0) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsymm.f b/lib/linalg/dsymm.f index ee8df4df4b2a616c861a859c79e8ba13f35d92a2..622d2469f15a6ee192a8e0ae458e614d69ec976e 100644 --- a/lib/linalg/dsymm.f +++ b/lib/linalg/dsymm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSYMM(SIDE,UPLO,M,N,ALPHA,A,LDA,B,LDB,BETA,C,LDC) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER LDA,LDB,LDC,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),B(LDB,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -87,7 +87,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, ka ), where ka is +*> A is DOUBLE PRECISION array, dimension ( LDA, ka ), where ka is *> m when SIDE = 'L' or 'l' and is n otherwise. *> Before entry with SIDE = 'L' or 'l', the m by m part of *> the array A must contain the symmetric matrix, such that @@ -122,7 +122,7 @@ *> *> \param[in] B *> \verbatim -*> B is DOUBLE PRECISION array of DIMENSION ( LDB, n ). +*> B is DOUBLE PRECISION array, dimension ( LDB, N ) *> Before entry, the leading m by n part of the array B must *> contain the matrix B. *> \endverbatim @@ -144,7 +144,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is DOUBLE PRECISION array of DIMENSION ( LDC, n ). +*> C is DOUBLE PRECISION array, dimension ( LDC, N ) *> Before entry, the leading m by n part of the array C must *> contain the matrix C, except when beta is zero, in which *> case C need not be set on entry. @@ -163,12 +163,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -189,10 +189,10 @@ * ===================================================================== SUBROUTINE DSYMM(SIDE,UPLO,M,N,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA diff --git a/lib/linalg/dsymv.f b/lib/linalg/dsymv.f index 552202383471a392774ccd6a6b37be9096755080..4bf973f10a443cc7629c594279dfc6260387d333 100644 --- a/lib/linalg/dsymv.f +++ b/lib/linalg/dsymv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSYMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER INCX,INCY,LDA,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -65,7 +65,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular part of the symmetric matrix and the strictly @@ -86,7 +86,7 @@ *> *> \param[in] X *> \verbatim -*> X is DOUBLE PRECISION array of dimension at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. @@ -108,7 +108,7 @@ *> *> \param[in,out] Y *> \verbatim -*> Y is DOUBLE PRECISION array of dimension at least +*> Y is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. On exit, Y is overwritten by the updated @@ -125,12 +125,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level2 * @@ -152,10 +152,10 @@ * ===================================================================== SUBROUTINE DSYMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA diff --git a/lib/linalg/dsyr2.f b/lib/linalg/dsyr2.f index 05e148105cb1ac3c3764d73ea0da67d76c3e27fa..8970c4dcfd932a247a7384dca53225dfd8f7e235 100644 --- a/lib/linalg/dsyr2.f +++ b/lib/linalg/dsyr2.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSYR2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA * INTEGER INCX,INCY,LDA,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -65,7 +65,7 @@ *> *> \param[in] X *> \verbatim -*> X is DOUBLE PRECISION array of dimension at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. @@ -80,7 +80,7 @@ *> *> \param[in] Y *> \verbatim -*> Y is DOUBLE PRECISION array of dimension at least +*> Y is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. @@ -95,7 +95,7 @@ *> *> \param[in,out] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular part of the symmetric matrix and the strictly @@ -121,12 +121,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level2 * @@ -147,10 +147,10 @@ * ===================================================================== SUBROUTINE DSYR2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA diff --git a/lib/linalg/dsyr2k.f b/lib/linalg/dsyr2k.f index 2dde293eae5d72a6e321140b567d23e5df19970f..f3a5940c7f7f88b311ff751787cdafbcf30b6271 100644 --- a/lib/linalg/dsyr2k.f +++ b/lib/linalg/dsyr2k.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSYR2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER K,LDA,LDB,LDC,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),B(LDB,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -95,7 +95,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, ka ), where ka is +*> A is DOUBLE PRECISION array, dimension ( LDA, ka ), where ka is *> k when TRANS = 'N' or 'n', and is n otherwise. *> Before entry with TRANS = 'N' or 'n', the leading n by k *> part of the array A must contain the matrix A, otherwise @@ -114,7 +114,7 @@ *> *> \param[in] B *> \verbatim -*> B is DOUBLE PRECISION array of DIMENSION ( LDB, kb ), where kb is +*> B is DOUBLE PRECISION array, dimension ( LDB, kb ), where kb is *> k when TRANS = 'N' or 'n', and is n otherwise. *> Before entry with TRANS = 'N' or 'n', the leading n by k *> part of the array B must contain the matrix B, otherwise @@ -139,7 +139,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is DOUBLE PRECISION array of DIMENSION ( LDC, n ). +*> C is DOUBLE PRECISION array, dimension ( LDC, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array C must contain the upper *> triangular part of the symmetric matrix and the strictly @@ -165,12 +165,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -192,10 +192,10 @@ * ===================================================================== SUBROUTINE DSYR2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA diff --git a/lib/linalg/dsyrk.f b/lib/linalg/dsyrk.f index d91c3369f620c8ade13017920d3c690a6319f62c..4be4d8d3c4f53148d6b9371a39d5aed996c979e1 100644 --- a/lib/linalg/dsyrk.f +++ b/lib/linalg/dsyrk.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DSYRK(UPLO,TRANS,N,K,ALPHA,A,LDA,BETA,C,LDC) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA,BETA * INTEGER K,LDA,LDC,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -92,7 +92,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, ka ), where ka is +*> A is DOUBLE PRECISION array, dimension ( LDA, ka ), where ka is *> k when TRANS = 'N' or 'n', and is n otherwise. *> Before entry with TRANS = 'N' or 'n', the leading n by k *> part of the array A must contain the matrix A, otherwise @@ -117,7 +117,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is DOUBLE PRECISION array of DIMENSION ( LDC, n ). +*> C is DOUBLE PRECISION array, dimension ( LDC, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array C must contain the upper *> triangular part of the symmetric matrix and the strictly @@ -143,12 +143,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -169,10 +169,10 @@ * ===================================================================== SUBROUTINE DSYRK(UPLO,TRANS,N,K,ALPHA,A,LDA,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA diff --git a/lib/linalg/dsytd2.f b/lib/linalg/dsytd2.f index a238f9ab3b830d267555ff8966ffb31cf5b568ca..6fb4d5507e7b204620438880003cb8c86a4a7f7f 100644 --- a/lib/linalg/dsytd2.f +++ b/lib/linalg/dsytd2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYTD2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYTD2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYTD2( UPLO, N, A, LDA, D, E, TAU, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ), D( * ), E( * ), TAU( * ) * .. -* +* * *> \par Purpose: * ============= @@ -115,12 +115,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleSYcomputational * @@ -173,10 +173,10 @@ * ===================================================================== SUBROUTINE DSYTD2( UPLO, N, A, LDA, D, E, TAU, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsytrd.f b/lib/linalg/dsytrd.f index b268f4c1e4d7ef46cc73c91f1f8c050995661711..d330b241fa27cdba2eba435cc4f4c28e1cb84b03 100644 --- a/lib/linalg/dsytrd.f +++ b/lib/linalg/dsytrd.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DSYTRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DSYTRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DSYTRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, LWORK, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION A( LDA, * ), D( * ), E( * ), TAU( * ), * $ WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -134,12 +134,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleSYcomputational * @@ -192,10 +192,10 @@ * ===================================================================== SUBROUTINE DSYTRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dtrmm.f b/lib/linalg/dtrmm.f index cbd5ce7034a4444656c21b2169cd4ba7e66f909e..0241c4d1465bb3ea05dca4de1a5dade03f32ed54 100644 --- a/lib/linalg/dtrmm.f +++ b/lib/linalg/dtrmm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA * INTEGER LDA,LDB,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),B(LDB,*) * .. -* +* * *> \par Purpose: * ============= @@ -109,7 +109,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, k ), where k is m +*> A is DOUBLE PRECISION array, dimension ( LDA, k ), where k is m *> when SIDE = 'L' or 'l' and is n when SIDE = 'R' or 'r'. *> Before entry with UPLO = 'U' or 'u', the leading k by k *> upper triangular part of the array A must contain the upper @@ -134,7 +134,7 @@ *> *> \param[in,out] B *> \verbatim -*> B is DOUBLE PRECISION array of DIMENSION ( LDB, n ). +*> B is DOUBLE PRECISION array, dimension ( LDB, N ) *> Before entry, the leading m by n part of the array B must *> contain the matrix B, and on exit is overwritten by the *> transformed matrix. @@ -151,12 +151,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -177,10 +177,10 @@ * ===================================================================== SUBROUTINE DTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA diff --git a/lib/linalg/dtrmv.f b/lib/linalg/dtrmv.f index 71459fe7c87bb9ba7ea18063c81b9825a483f3f6..11c12ac724468ff59b017fd6afd995496781e85f 100644 --- a/lib/linalg/dtrmv.f +++ b/lib/linalg/dtrmv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,LDA,N * CHARACTER DIAG,TRANS,UPLO @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -80,7 +80,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular matrix and the strictly lower triangular part of @@ -103,11 +103,11 @@ *> *> \param[in,out] X *> \verbatim -*> X is DOUBLE PRECISION array of dimension at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. On exit, X is overwritten with the -*> tranformed vector x. +*> transformed vector x. *> \endverbatim *> *> \param[in] INCX @@ -120,12 +120,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level2 * @@ -147,10 +147,10 @@ * ===================================================================== SUBROUTINE DTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N diff --git a/lib/linalg/dtrsm.f b/lib/linalg/dtrsm.f index 065df9a15332106e98b0ab5179e74c369bf1f6cd..5a92bcafd09557e07ddbe19124551b2bc46cbe6a 100644 --- a/lib/linalg/dtrsm.f +++ b/lib/linalg/dtrsm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DTRSM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA * INTEGER LDA,LDB,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),B(LDB,*) * .. -* +* * *> \par Purpose: * ============= @@ -111,8 +111,8 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, k ), -*> where k is m when SIDE = 'L' or 'l' +*> A is DOUBLE PRECISION array, dimension ( LDA, k ), +*> where k is m when SIDE = 'L' or 'l' *> and k is n when SIDE = 'R' or 'r'. *> Before entry with UPLO = 'U' or 'u', the leading k by k *> upper triangular part of the array A must contain the upper @@ -137,7 +137,7 @@ *> *> \param[in,out] B *> \verbatim -*> B is DOUBLE PRECISION array of DIMENSION ( LDB, n ). +*> B is DOUBLE PRECISION array, dimension ( LDB, N ) *> Before entry, the leading m by n part of the array B must *> contain the right-hand side matrix B, and on exit is *> overwritten by the solution matrix X. @@ -154,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level3 * @@ -181,10 +181,10 @@ * ===================================================================== SUBROUTINE DTRSM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA diff --git a/lib/linalg/dtrsv.f b/lib/linalg/dtrsv.f index e54303a93a0d88f44f0c37aee57e08668defd813..331f1d431180edfae8258a714b1a65e7775ca9f2 100644 --- a/lib/linalg/dtrsv.f +++ b/lib/linalg/dtrsv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE DTRSV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,LDA,N * CHARACTER DIAG,TRANS,UPLO @@ -17,7 +17,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A(LDA,*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -83,7 +83,7 @@ *> *> \param[in] A *> \verbatim -*> A is DOUBLE PRECISION array of DIMENSION ( LDA, n ). +*> A is DOUBLE PRECISION array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular matrix and the strictly lower triangular part of @@ -106,7 +106,7 @@ *> *> \param[in,out] X *> \verbatim -*> X is DOUBLE PRECISION array of dimension at least +*> X is DOUBLE PRECISION array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element right-hand side vector b. On exit, X is overwritten @@ -131,22 +131,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * * ===================================================================== SUBROUTINE DTRSV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N diff --git a/lib/linalg/dtrti2.f b/lib/linalg/dtrti2.f index edf1b5b003ad42458cb3308b0706eb064daa60d0..0a9d5b696ccc5240475067b68ad9768ce6e3b09f 100644 --- a/lib/linalg/dtrti2.f +++ b/lib/linalg/dtrti2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DTRTI2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DTRTI2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DTRTI2( UPLO, DIAG, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER DIAG, UPLO * INTEGER INFO, LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -98,22 +98,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DTRTI2( UPLO, DIAG, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/dtrtri.f b/lib/linalg/dtrtri.f index 5d27ca56af1e081a39598e6006cc18ade457d6a3..d34b40bcc00b0d6d647d3a863a6302e662c27b2a 100644 --- a/lib/linalg/dtrtri.f +++ b/lib/linalg/dtrtri.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download DTRTRI + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download DTRTRI + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE DTRTRI( UPLO, DIAG, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER DIAG, UPLO * INTEGER INFO, LDA, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -97,22 +97,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DTRTRI( UPLO, DIAG, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/dznrm2.f b/lib/linalg/dznrm2.f index b5713a2bfaf0b92dd3e27e8a007eb91130c2195a..e5a71d98f6709b81f8d2484822c196810285f0ee 100644 --- a/lib/linalg/dznrm2.f +++ b/lib/linalg/dznrm2.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * DOUBLE PRECISION FUNCTION DZNRM2(N,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * .. * .. Array Arguments .. * COMPLEX*16 X(*) * .. -* +* * *> \par Purpose: * ============= @@ -29,15 +29,36 @@ *> DZNRM2 := sqrt( x**H*x ) *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] X +*> \verbatim +*> X is COMPLEX*16 array, dimension (N) +*> complex vector with N elements +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of X +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup double_blas_level1 * @@ -54,10 +75,10 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DZNRM2(N,X,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/idamax.f b/lib/linalg/idamax.f index 4233fcc27350e97319f56818bee1031df0c7a94c..17041680a40c8953314a32a7a164b220a8900f26 100644 --- a/lib/linalg/idamax.f +++ b/lib/linalg/idamax.f @@ -2,39 +2,59 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * INTEGER FUNCTION IDAMAX(N,DX,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * .. * .. Array Arguments .. * DOUBLE PRECISION DX(*) * .. -* +* * *> \par Purpose: * ============= *> *> \verbatim *> -*> IDAMAX finds the index of element having max. absolute value. +*> IDAMAX finds the index of the first element having maximum absolute value. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DX +*> \verbatim +*> DX is DOUBLE PRECISION array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of SX *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup aux_blas * @@ -51,10 +71,10 @@ * ===================================================================== INTEGER FUNCTION IDAMAX(N,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/ieeeck.f b/lib/linalg/ieeeck.f index 132e436770774827878009d82d957052816cf2ae..2655958b4a2d94179e9691f9c9fe696e9bdef134 100644 --- a/lib/linalg/ieeeck.f +++ b/lib/linalg/ieeeck.f @@ -2,29 +2,29 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download IEEECK + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download IEEECK + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION IEEECK( ISPEC, ZERO, ONE ) -* +* * .. Scalar Arguments .. * INTEGER ISPEC * REAL ONE, ZERO * .. -* +* * *> \par Purpose: * ============= @@ -70,22 +70,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION IEEECK( ISPEC, ZERO, ONE ) * -* -- LAPACK auxiliary routine (version 3.4.0) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER ISPEC diff --git a/lib/linalg/iladlc.f b/lib/linalg/iladlc.f index b56387d320f716ea3c41cad85303de8baf21ca6a..c6476113d1550202c781f019651ab7643f4f0cc5 100644 --- a/lib/linalg/iladlc.f +++ b/lib/linalg/iladlc.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ILADLC + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ILADLC + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION ILADLC( M, N, A, LDA ) -* +* * .. Scalar Arguments .. * INTEGER M, N, LDA * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -66,22 +66,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILADLC( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/iladlr.f b/lib/linalg/iladlr.f index fe155af075fb9f1eb7ac989d8ea329855e033f88..e8951d86cc288494faa54879b96ea50f187b0207 100644 --- a/lib/linalg/iladlr.f +++ b/lib/linalg/iladlr.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ILADLR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ILADLR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION ILADLR( M, N, A, LDA ) -* +* * .. Scalar Arguments .. * INTEGER M, N, LDA * .. * .. Array Arguments .. * DOUBLE PRECISION A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -66,22 +66,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILADLR( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/ilaenv.f b/lib/linalg/ilaenv.f index 867464de357e36fd1b19db47f80c1b40d47262ac..2be05815179215335f31713eae454135e97fdde3 100644 --- a/lib/linalg/ilaenv.f +++ b/lib/linalg/ilaenv.f @@ -2,29 +2,29 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ILAENV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ILAENV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION ILAENV( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) -* +* * .. Scalar Arguments .. * CHARACTER*( * ) NAME, OPTS * INTEGER ISPEC, N1, N2, N3, N4 * .. -* +* * *> \par Purpose: * ============= @@ -82,7 +82,7 @@ *> =10: ieee NaN arithmetic can be trusted not to trap *> =11: infinity arithmetic can be trusted not to trap *> 12 <= ISPEC <= 16: -*> xHSEQR or one of its subroutines, +*> xHSEQR or related subroutines, *> see IPARMQ for detailed explanation *> \endverbatim *> @@ -127,14 +127,14 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -162,10 +162,10 @@ * ===================================================================== INTEGER FUNCTION ILAENV( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) * -* -- LAPACK auxiliary routine (version 3.4.0) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER*( * ) NAME, OPTS @@ -183,13 +183,14 @@ INTRINSIC CHAR, ICHAR, INT, MIN, REAL * .. * .. External Functions .. - INTEGER IEEECK, IPARMQ - EXTERNAL IEEECK, IPARMQ + INTEGER IEEECK, IPARMQ, IPARAM2STAGE + EXTERNAL IEEECK, IPARMQ, IPARAM2STAGE * .. * .. Executable Statements .. * GO TO ( 10, 10, 10, 80, 90, 100, 110, 120, - $ 130, 140, 150, 160, 160, 160, 160, 160 )ISPEC + $ 130, 140, 150, 160, 160, 160, 160, 160, + $ 170, 170, 170, 170, 170 )ISPEC * * Invalid value for ISPEC * @@ -283,6 +284,52 @@ ELSE NB = 32 END IF + ELSE IF( C3.EQ.'QR ') THEN + IF( N3 .EQ. 1) THEN + IF( SNAME ) THEN +* M*N + IF ((N1*N2.LE.131072).OR.(N1.LE.8192)) THEN + NB = N1 + ELSE + NB = 32768/N2 + END IF + ELSE + IF ((N1*N2.LE.131072).OR.(N1.LE.8192)) THEN + NB = N1 + ELSE + NB = 32768/N2 + END IF + END IF + ELSE + IF( SNAME ) THEN + NB = 1 + ELSE + NB = 1 + END IF + END IF + ELSE IF( C3.EQ.'LQ ') THEN + IF( N3 .EQ. 2) THEN + IF( SNAME ) THEN +* M*N + IF ((N1*N2.LE.131072).OR.(N1.LE.8192)) THEN + NB = N1 + ELSE + NB = 32768/N2 + END IF + ELSE + IF ((N1*N2.LE.131072).OR.(N1.LE.8192)) THEN + NB = N1 + ELSE + NB = 32768/N2 + END IF + END IF + ELSE + IF( SNAME ) THEN + NB = 1 + ELSE + NB = 1 + END IF + END IF ELSE IF( C3.EQ.'HRD' ) THEN IF( SNAME ) THEN NB = 32 @@ -397,6 +444,12 @@ ELSE NB = 64 END IF + ELSE IF ( C3.EQ.'EVC' ) THEN + IF( SNAME ) THEN + NB = 64 + ELSE + NB = 64 + END IF END IF ELSE IF( C2.EQ.'LA' ) THEN IF( C3.EQ.'UUM' ) THEN @@ -410,6 +463,15 @@ IF( C3.EQ.'EBZ' ) THEN NB = 1 END IF + ELSE IF( C2.EQ.'GG' ) THEN + NB = 32 + IF( C3.EQ.'HD3' ) THEN + IF( SNAME ) THEN + NB = 32 + ELSE + NB = 32 + END IF + END IF END IF ILAENV = NB RETURN @@ -488,6 +550,11 @@ NBMIN = 2 END IF END IF + ELSE IF( C2.EQ.'GG' ) THEN + NBMIN = 2 + IF( C3.EQ.'HD3' ) THEN + NBMIN = 2 + END IF END IF ILAENV = NBMIN RETURN @@ -542,6 +609,11 @@ NX = 128 END IF END IF + ELSE IF( C2.EQ.'GG' ) THEN + NX = 128 + IF( C3.EQ.'HD3' ) THEN + NX = 128 + END IF END IF ILAENV = NX RETURN @@ -614,10 +686,17 @@ * 160 CONTINUE * -* 12 <= ISPEC <= 16: xHSEQR or one of its subroutines. +* 12 <= ISPEC <= 16: xHSEQR or related subroutines. * ILAENV = IPARMQ( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) RETURN +* + 170 CONTINUE +* +* 17 <= ISPEC <= 21: 2stage eigenvalues and SVD or related subroutines. +* + ILAENV = IPARAM2STAGE( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) + RETURN * * End of ILAENV * diff --git a/lib/linalg/ilazlc.f b/lib/linalg/ilazlc.f index 718b277dfa6596e95fcbe37972f5af9d1fb79fb3..07dfc93e31af02affe9c3f3ed601d1a144b6dfc2 100644 --- a/lib/linalg/ilazlc.f +++ b/lib/linalg/ilazlc.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ILAZLC + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ILAZLC + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION ILAZLC( M, N, A, LDA ) -* +* * .. Scalar Arguments .. * INTEGER M, N, LDA * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -66,22 +66,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILAZLC( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/ilazlr.f b/lib/linalg/ilazlr.f index 44697214c75b0358a1568e2f46aa3d2b449f7b5c..4ca4ed1a44fe585f534375701fc5fd8945ba7b79 100644 --- a/lib/linalg/ilazlr.f +++ b/lib/linalg/ilazlr.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ILAZLR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ILAZLR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION ILAZLR( M, N, A, LDA ) -* +* * .. Scalar Arguments .. * INTEGER M, N, LDA * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -66,22 +66,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILAZLR( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/iparam2stage.F b/lib/linalg/iparam2stage.F new file mode 100644 index 0000000000000000000000000000000000000000..60bd0b696b8398b2a7bb7aed329441e8432bb26d --- /dev/null +++ b/lib/linalg/iparam2stage.F @@ -0,0 +1,386 @@ +*> \brief \b IPARAM2STAGE +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download IPARAM2STAGE + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* INTEGER FUNCTION IPARAM2STAGE( ISPEC, NAME, OPTS, +* NI, NBI, IBI, NXI ) +* #if defined(_OPENMP) +* use omp_lib +* #endif +* IMPLICIT NONE +* +* .. Scalar Arguments .. +* CHARACTER*( * ) NAME, OPTS +* INTEGER ISPEC, NI, NBI, IBI, NXI +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> This program sets problem and machine dependent parameters +*> useful for xHETRD_2STAGE, xHETRD_H@2HB, xHETRD_HB2ST, +*> xGEBRD_2STAGE, xGEBRD_GE2GB, xGEBRD_GB2BD +*> and related subroutines for eigenvalue problems. +*> It is called whenever ILAENV is called with 17 <= ISPEC <= 21 +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] ISPEC +*> \verbatim +*> ISPEC is integer scalar +*> ISPEC specifies which tunable parameter IPARAM2STAGE should +*> return. +*> +*> ISPEC=17: the optimal blocksize nb for the reduction to +* BAND +*> +*> ISPEC=18: the optimal blocksize ib for the eigenvectors +*> singular vectors update routine +*> +*> ISPEC=19: The length of the array that store the Housholder +*> representation for the second stage +*> Band to Tridiagonal or Bidiagonal +*> +*> ISPEC=20: The workspace needed for the routine in input. +*> +*> ISPEC=21: For future release. +*> \endverbatim +*> +*> \param[in] NAME +*> \verbatim +*> NAME is character string +*> Name of the calling subroutine +*> \endverbatim +*> +*> \param[in] OPTS +*> \verbatim +*> OPTS is CHARACTER*(*) +*> The character options to the subroutine NAME, concatenated +*> into a single character string. For example, UPLO = 'U', +*> TRANS = 'T', and DIAG = 'N' for a triangular routine would +*> be specified as OPTS = 'UTN'. +*> \endverbatim +*> +*> \param[in] NI +*> \verbatim +*> NI is INTEGER which is the size of the matrix +*> \endverbatim +*> +*> \param[in] NBI +*> \verbatim +*> NBI is INTEGER which is the used in the reduciton, +* (e.g., the size of the band), needed to compute workspace +* and LHOUS2. +*> \endverbatim +*> +*> \param[in] IBI +*> \verbatim +*> IBI is INTEGER which represent the IB of the reduciton, +* needed to compute workspace and LHOUS2. +*> \endverbatim +*> +*> \param[in] NXI +*> \verbatim +*> NXI is INTEGER needed in the future release. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \date June 2016 +* +*> \ingroup auxOTHERauxiliary +* +*> \par Further Details: +* ===================== +*> +*> \verbatim +*> +*> Implemented by Azzam Haidar. +*> +*> All detail are available on technical report, SC11, SC13 papers. +*> +*> Azzam Haidar, Hatem Ltaief, and Jack Dongarra. +*> Parallel reduction to condensed forms for symmetric eigenvalue problems +*> using aggregated fine-grained and memory-aware kernels. In Proceedings +*> of 2011 International Conference for High Performance Computing, +*> Networking, Storage and Analysis (SC '11), New York, NY, USA, +*> Article 8 , 11 pages. +*> http://doi.acm.org/10.1145/2063384.2063394 +*> +*> A. Haidar, J. Kurzak, P. Luszczek, 2013. +*> An improved parallel singular value algorithm and its implementation +*> for multicore hardware, In Proceedings of 2013 International Conference +*> for High Performance Computing, Networking, Storage and Analysis (SC '13). +*> Denver, Colorado, USA, 2013. +*> Article 90, 12 pages. +*> http://doi.acm.org/10.1145/2503210.2503292 +*> +*> A. Haidar, R. Solca, S. Tomov, T. Schulthess and J. Dongarra. +*> A novel hybrid CPU-GPU generalized eigensolver for electronic structure +*> calculations based on fine-grained memory aware tasks. +*> International Journal of High Performance Computing Applications. +*> Volume 28 Issue 2, Pages 196-209, May 2014. +*> http://hpc.sagepub.com/content/28/2/196 +*> +*> \endverbatim +*> +* ===================================================================== + INTEGER FUNCTION IPARAM2STAGE( ISPEC, NAME, OPTS, + $ NI, NBI, IBI, NXI ) +#if defined(_OPENMP) + use omp_lib +#endif + IMPLICIT NONE +* +* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* June 2016 +* +* .. Scalar Arguments .. + CHARACTER*( * ) NAME, OPTS + INTEGER ISPEC, NI, NBI, IBI, NXI +* +* ================================================================ +* .. +* .. Local Scalars .. + INTEGER I, IC, IZ, KD, IB, LHOUS, LWORK, NTHREADS, + $ FACTOPTNB, QROPTNB, LQOPTNB + LOGICAL RPREC, CPREC + CHARACTER PREC*1, ALGO*3, STAG*5, SUBNAM*12, VECT*1 +* .. +* .. Intrinsic Functions .. + INTRINSIC CHAR, ICHAR, MAX +* .. +* .. External Functions .. + INTEGER ILAENV + EXTERNAL ILAENV +* .. +* .. Executable Statements .. +* +* Invalid value for ISPEC +* + IF( (ISPEC.LT.17).OR.(ISPEC.GT.21) ) THEN + IPARAM2STAGE = -1 + RETURN + ENDIF +* +* Get the number of threads +* + NTHREADS = 1 +#if defined(_OPENMP) +!$OMP PARALLEL + NTHREADS = OMP_GET_NUM_THREADS() +!$OMP END PARALLEL +#endif +* WRITE(*,*) 'IPARAM VOICI NTHREADS ISPEC ',NTHREADS, ISPEC +* + IF( ISPEC .NE. 19 ) THEN +* +* Convert NAME to upper case if the first character is lower case. +* + IPARAM2STAGE = -1 + SUBNAM = NAME + IC = ICHAR( SUBNAM( 1: 1 ) ) + IZ = ICHAR( 'Z' ) + IF( IZ.EQ.90 .OR. IZ.EQ.122 ) THEN +* +* ASCII character set +* + IF( IC.GE.97 .AND. IC.LE.122 ) THEN + SUBNAM( 1: 1 ) = CHAR( IC-32 ) + DO 100 I = 2, 12 + IC = ICHAR( SUBNAM( I: I ) ) + IF( IC.GE.97 .AND. IC.LE.122 ) + $ SUBNAM( I: I ) = CHAR( IC-32 ) + 100 CONTINUE + END IF +* + ELSE IF( IZ.EQ.233 .OR. IZ.EQ.169 ) THEN +* +* EBCDIC character set +* + IF( ( IC.GE.129 .AND. IC.LE.137 ) .OR. + $ ( IC.GE.145 .AND. IC.LE.153 ) .OR. + $ ( IC.GE.162 .AND. IC.LE.169 ) ) THEN + SUBNAM( 1: 1 ) = CHAR( IC+64 ) + DO 110 I = 2, 12 + IC = ICHAR( SUBNAM( I: I ) ) + IF( ( IC.GE.129 .AND. IC.LE.137 ) .OR. + $ ( IC.GE.145 .AND. IC.LE.153 ) .OR. + $ ( IC.GE.162 .AND. IC.LE.169 ) )SUBNAM( I: + $ I ) = CHAR( IC+64 ) + 110 CONTINUE + END IF +* + ELSE IF( IZ.EQ.218 .OR. IZ.EQ.250 ) THEN +* +* Prime machines: ASCII+128 +* + IF( IC.GE.225 .AND. IC.LE.250 ) THEN + SUBNAM( 1: 1 ) = CHAR( IC-32 ) + DO 120 I = 2, 12 + IC = ICHAR( SUBNAM( I: I ) ) + IF( IC.GE.225 .AND. IC.LE.250 ) + $ SUBNAM( I: I ) = CHAR( IC-32 ) + 120 CONTINUE + END IF + END IF +* + PREC = SUBNAM( 1: 1 ) + ALGO = SUBNAM( 4: 6 ) + STAG = SUBNAM( 8:12 ) + RPREC = PREC.EQ.'S' .OR. PREC.EQ.'D' + CPREC = PREC.EQ.'C' .OR. PREC.EQ.'Z' +* +* Invalid value for PRECISION +* + IF( .NOT.( RPREC .OR. CPREC ) ) THEN + IPARAM2STAGE = -1 + RETURN + ENDIF + ENDIF +* WRITE(*,*),'RPREC,CPREC ',RPREC,CPREC, +* $ ' ALGO ',ALGO,' STAGE ',STAG +* +* + IF (( ISPEC .EQ. 17 ) .OR. ( ISPEC .EQ. 18 )) THEN +* +* ISPEC = 17, 18: block size KD, IB +* Could be also dependent from N but for now it +* depend only on sequential or parallel +* + IF( NTHREADS.GT.4 ) THEN + IF( CPREC ) THEN + KD = 128 + IB = 32 + ELSE + KD = 160 + IB = 40 + ENDIF + ELSE IF( NTHREADS.GT.1 ) THEN + IF( CPREC ) THEN + KD = 64 + IB = 32 + ELSE + KD = 64 + IB = 32 + ENDIF + ELSE + IF( CPREC ) THEN + KD = 16 + IB = 16 + ELSE + KD = 32 + IB = 16 + ENDIF + ENDIF + IF( ISPEC.EQ.17 ) IPARAM2STAGE = KD + IF( ISPEC.EQ.18 ) IPARAM2STAGE = IB +* + ELSE IF ( ISPEC .EQ. 19 ) THEN +* +* ISPEC = 19: +* LHOUS length of the Houselholder representation +* matrix (V,T) of the second stage. should be >= 1. +* +* Will add the VECT OPTION HERE next release + VECT = OPTS(1:1) + IF( VECT.EQ.'N' ) THEN + LHOUS = MAX( 1, 4*NI ) + ELSE +* This is not correct, it need to call the ALGO and the stage2 + LHOUS = MAX( 1, 4*NI ) + IBI + ENDIF + IF( LHOUS.GE.0 ) THEN + IPARAM2STAGE = LHOUS + ELSE + IPARAM2STAGE = -1 + ENDIF +* + ELSE IF ( ISPEC .EQ. 20 ) THEN +* +* ISPEC = 20: (21 for future use) +* LWORK length of the workspace for +* either or both stages for TRD and BRD. should be >= 1. +* TRD: +* TRD_stage 1: = LT + LW + LS1 + LS2 +* = LDT*KD + N*KD + N*MAX(KD,FACTOPTNB) + LDS2*KD +* where LDT=LDS2=KD +* = N*KD + N*max(KD,FACTOPTNB) + 2*KD*KD +* TRD_stage 2: = (2NB+1)*N + KD*NTHREADS +* TRD_both : = max(stage1,stage2) + AB ( AB=(KD+1)*N ) +* = N*KD + N*max(KD+1,FACTOPTNB) +* + max(2*KD*KD, KD*NTHREADS) +* + (KD+1)*N + LWORK = -1 + SUBNAM(1:1) = PREC + SUBNAM(2:6) = 'GEQRF' + QROPTNB = ILAENV( 1, SUBNAM, ' ', NI, NBI, -1, -1 ) + SUBNAM(2:6) = 'GELQF' + LQOPTNB = ILAENV( 1, SUBNAM, ' ', NBI, NI, -1, -1 ) +* Could be QR or LQ for TRD and the max for BRD + FACTOPTNB = MAX(QROPTNB, LQOPTNB) + IF( ALGO.EQ.'TRD' ) THEN + IF( STAG.EQ.'2STAG' ) THEN + LWORK = NI*NBI + NI*MAX(NBI+1,FACTOPTNB) + $ + MAX(2*NBI*NBI, NBI*NTHREADS) + $ + (NBI+1)*NI + ELSE IF( (STAG.EQ.'HE2HB').OR.(STAG.EQ.'SY2SB') ) THEN + LWORK = NI*NBI + NI*MAX(NBI,FACTOPTNB) + 2*NBI*NBI + ELSE IF( (STAG.EQ.'HB2ST').OR.(STAG.EQ.'SB2ST') ) THEN + LWORK = (2*NBI+1)*NI + NBI*NTHREADS + ENDIF + ELSE IF( ALGO.EQ.'BRD' ) THEN + IF( STAG.EQ.'2STAG' ) THEN + LWORK = 2*NI*NBI + NI*MAX(NBI+1,FACTOPTNB) + $ + MAX(2*NBI*NBI, NBI*NTHREADS) + $ + (NBI+1)*NI + ELSE IF( STAG.EQ.'GE2GB' ) THEN + LWORK = NI*NBI + NI*MAX(NBI,FACTOPTNB) + 2*NBI*NBI + ELSE IF( STAG.EQ.'GB2BD' ) THEN + LWORK = (3*NBI+1)*NI + NBI*NTHREADS + ENDIF + ENDIF + LWORK = MAX ( 1, LWORK ) + + IF( LWORK.GT.0 ) THEN + IPARAM2STAGE = LWORK + ELSE + IPARAM2STAGE = -1 + ENDIF +* + ELSE IF ( ISPEC .EQ. 21 ) THEN +* +* ISPEC = 21 for future use + IPARAM2STAGE = NXI + ENDIF +* +* ==== End of IPARAM2STAGE ==== +* + END diff --git a/lib/linalg/iparmq.f b/lib/linalg/iparmq.f index bd5bd7a0db7202870f90950162b9bc84230ed7f5..e576e0db01ee375ec82dabda47eca89800e0aba7 100644 --- a/lib/linalg/iparmq.f +++ b/lib/linalg/iparmq.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download IPARMQ + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download IPARMQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK ) -* +* * .. Scalar Arguments .. * INTEGER IHI, ILO, ISPEC, LWORK, N * CHARACTER NAME*( * ), OPTS*( * ) -* +* * *> \par Purpose: * ============= @@ -31,8 +31,9 @@ *> \verbatim *> *> This program sets problem and machine dependent parameters -*> useful for xHSEQR and its subroutines. It is called whenever -*> ILAENV is called with 12 <= ISPEC <= 16 +*> useful for xHSEQR and related subroutines for eigenvalue +*> problems. It is called whenever +*> IPARMQ is called with 12 <= ISPEC <= 16 *> \endverbatim * * Arguments: @@ -40,7 +41,7 @@ * *> \param[in] ISPEC *> \verbatim -*> ISPEC is integer scalar +*> ISPEC is INTEGER *> ISPEC specifies which tunable parameter IPARMQ should *> return. *> @@ -75,19 +76,26 @@ *> *> ISPEC=16: (IACC22) IPARMQ is set to 0, 1 or 2 with the *> following meanings. -*> 0: During the multi-shift QR sweep, -*> xLAQR5 does not accumulate reflections and -*> does not use matrix-matrix multiply to -*> update the far-from-diagonal matrix -*> entries. -*> 1: During the multi-shift QR sweep, -*> xLAQR5 and/or xLAQRaccumulates reflections and uses -*> matrix-matrix multiply to update the +*> 0: During the multi-shift QR/QZ sweep, +*> blocked eigenvalue reordering, blocked +*> Hessenberg-triangular reduction, +*> reflections and/or rotations are not +*> accumulated when updating the *> far-from-diagonal matrix entries. -*> 2: During the multi-shift QR sweep. -*> xLAQR5 accumulates reflections and takes -*> advantage of 2-by-2 block structure during -*> matrix-matrix multiplies. +*> 1: During the multi-shift QR/QZ sweep, +*> blocked eigenvalue reordering, blocked +*> Hessenberg-triangular reduction, +*> reflections and/or rotations are +*> accumulated, and matrix-matrix +*> multiplication is used to update the +*> far-from-diagonal matrix entries. +*> 2: During the multi-shift QR/QZ sweep, +*> blocked eigenvalue reordering, blocked +*> Hessenberg-triangular reduction, +*> reflections and/or rotations are +*> accumulated, and 2-by-2 block structure +*> is exploited during matrix-matrix +*> multiplies. *> (If xTRMM is slower than xGEMM, then *> IPARMQ(ISPEC=16)=1 may be more efficient than *> IPARMQ(ISPEC=16)=2 despite the greater level of @@ -109,7 +117,7 @@ *> *> \param[in] N *> \verbatim -*> N is integer scalar +*> N is INTEGER *> N is the order of the Hessenberg matrix H. *> \endverbatim *> @@ -127,21 +135,21 @@ *> *> \param[in] LWORK *> \verbatim -*> LWORK is integer scalar +*> LWORK is INTEGER *> The amount of workspace available. *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date June 2017 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * *> \par Further Details: * ===================== @@ -214,10 +222,10 @@ * ===================================================================== INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK ) * -* -- LAPACK auxiliary routine (version 3.4.0) -- +* -- LAPACK auxiliary routine (version 3.7.1) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* June 2017 * * .. Scalar Arguments .. INTEGER IHI, ILO, ISPEC, LWORK, N @@ -236,6 +244,8 @@ * .. * .. Local Scalars .. INTEGER NH, NS + INTEGER I, IC, IZ + CHARACTER SUBNAM*6 * .. * .. Intrinsic Functions .. INTRINSIC LOG, MAX, MOD, NINT, REAL @@ -304,12 +314,75 @@ * . doing it. A small amount of work could be saved * . by making this choice dependent also upon the * . NH=IHI-ILO+1. +* +* +* Convert NAME to upper case if the first character is lower case. * IPARMQ = 0 - IF( NS.GE.KACMIN ) - $ IPARMQ = 1 - IF( NS.GE.K22MIN ) - $ IPARMQ = 2 + SUBNAM = NAME + IC = ICHAR( SUBNAM( 1: 1 ) ) + IZ = ICHAR( 'Z' ) + IF( IZ.EQ.90 .OR. IZ.EQ.122 ) THEN +* +* ASCII character set +* + IF( IC.GE.97 .AND. IC.LE.122 ) THEN + SUBNAM( 1: 1 ) = CHAR( IC-32 ) + DO I = 2, 6 + IC = ICHAR( SUBNAM( I: I ) ) + IF( IC.GE.97 .AND. IC.LE.122 ) + $ SUBNAM( I: I ) = CHAR( IC-32 ) + END DO + END IF +* + ELSE IF( IZ.EQ.233 .OR. IZ.EQ.169 ) THEN +* +* EBCDIC character set +* + IF( ( IC.GE.129 .AND. IC.LE.137 ) .OR. + $ ( IC.GE.145 .AND. IC.LE.153 ) .OR. + $ ( IC.GE.162 .AND. IC.LE.169 ) ) THEN + SUBNAM( 1: 1 ) = CHAR( IC+64 ) + DO I = 2, 6 + IC = ICHAR( SUBNAM( I: I ) ) + IF( ( IC.GE.129 .AND. IC.LE.137 ) .OR. + $ ( IC.GE.145 .AND. IC.LE.153 ) .OR. + $ ( IC.GE.162 .AND. IC.LE.169 ) )SUBNAM( I: + $ I ) = CHAR( IC+64 ) + END DO + END IF +* + ELSE IF( IZ.EQ.218 .OR. IZ.EQ.250 ) THEN +* +* Prime machines: ASCII+128 +* + IF( IC.GE.225 .AND. IC.LE.250 ) THEN + SUBNAM( 1: 1 ) = CHAR( IC-32 ) + DO I = 2, 6 + IC = ICHAR( SUBNAM( I: I ) ) + IF( IC.GE.225 .AND. IC.LE.250 ) + $ SUBNAM( I: I ) = CHAR( IC-32 ) + END DO + END IF + END IF +* + IF( SUBNAM( 2:6 ).EQ.'GGHRD' .OR. + $ SUBNAM( 2:6 ).EQ.'GGHD3' ) THEN + IPARMQ = 1 + IF( NH.GE.K22MIN ) + $ IPARMQ = 2 + ELSE IF ( SUBNAM( 4:6 ).EQ.'EXC' ) THEN + IF( NH.GE.KACMIN ) + $ IPARMQ = 1 + IF( NH.GE.K22MIN ) + $ IPARMQ = 2 + ELSE IF ( SUBNAM( 2:6 ).EQ.'HSEQR' .OR. + $ SUBNAM( 2:5 ).EQ.'LAQR' ) THEN + IF( NS.GE.KACMIN ) + $ IPARMQ = 1 + IF( NS.GE.K22MIN ) + $ IPARMQ = 2 + END IF * ELSE * ===== invalid value of ispec ===== diff --git a/lib/linalg/lsame.f b/lib/linalg/lsame.f index f19f9cda9e6859f0ac84cacdead1dabe5e144c0c..d8194786966a58489326d905c1e538cb9480bdf1 100644 --- a/lib/linalg/lsame.f +++ b/lib/linalg/lsame.f @@ -2,18 +2,18 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * LOGICAL FUNCTION LSAME(CA,CB) -* +* * .. Scalar Arguments .. * CHARACTER CA,CB * .. -* +* * *> \par Purpose: * ============= @@ -41,12 +41,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup aux_blas * @@ -56,7 +56,7 @@ * -- Reference BLAS level1 routine (version 3.1) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER CA,CB diff --git a/lib/linalg/xerbla.f b/lib/linalg/xerbla.f index 3e93bc4e0e467454b3e357dd1f815024e3e76d32..4a0350988c1fbdb20655d809c95082015cb9c30b 100644 --- a/lib/linalg/xerbla.f +++ b/lib/linalg/xerbla.f @@ -2,29 +2,29 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download XERBLA + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download XERBLA + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE XERBLA( SRNAME, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER*(*) SRNAME * INTEGER INFO * .. -* +* * *> \par Purpose: * ============= @@ -58,22 +58,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * -*> \ingroup auxOTHERauxiliary +*> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE XERBLA( SRNAME, INFO ) * -* -- LAPACK auxiliary routine (version 3.4.0) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER*(*) SRNAME diff --git a/lib/linalg/zaxpy.f b/lib/linalg/zaxpy.f index e6f5e1f6dbfe289ad666ffb6652387be9a808666..b7b9ee69e43838f1da325d311b4bbb98e890cc01 100644 --- a/lib/linalg/zaxpy.f +++ b/lib/linalg/zaxpy.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZAXPY(N,ZA,ZX,INCX,ZY,INCY) -* +* * .. Scalar Arguments .. * COMPLEX*16 ZA * INTEGER INCX,INCY,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 ZX(*),ZY(*) * .. -* +* * *> \par Purpose: * ============= @@ -27,15 +27,52 @@ *> ZAXPY constant times a vector plus a vector. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] ZA +*> \verbatim +*> ZA is COMPLEX*16 +*> On entry, ZA specifies the scalar alpha. +*> \endverbatim +*> +*> \param[in] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +*> +*> \param[in,out] ZY +*> \verbatim +*> ZY is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of ZY +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -51,10 +88,10 @@ * ===================================================================== SUBROUTINE ZAXPY(N,ZA,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ZA diff --git a/lib/linalg/zcopy.f b/lib/linalg/zcopy.f index baeafd5c3b211b62e3dd415508e861579461fcc9..3777079730d9f0d311016554849e3801f70607d3 100644 --- a/lib/linalg/zcopy.f +++ b/lib/linalg/zcopy.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZCOPY(N,ZX,INCX,ZY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * COMPLEX*16 ZX(*),ZY(*) * .. -* +* * *> \par Purpose: * ============= @@ -26,15 +26,46 @@ *> ZCOPY copies a vector, x, to a vector, y. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +*> +*> \param[out] ZY +*> \verbatim +*> ZY is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of ZY +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -50,10 +81,10 @@ * ===================================================================== SUBROUTINE ZCOPY(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N diff --git a/lib/linalg/zdotc.f b/lib/linalg/zdotc.f index 660648bbe1d61efca33f0d5c66d41577720bb18b..e6cd11b21db42a4cbbb97628089b70c76806273f 100644 --- a/lib/linalg/zdotc.f +++ b/lib/linalg/zdotc.f @@ -2,39 +2,72 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * COMPLEX*16 FUNCTION ZDOTC(N,ZX,INCX,ZY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * COMPLEX*16 ZX(*),ZY(*) * .. -* +* * *> \par Purpose: * ============= *> *> \verbatim *> -*> ZDOTC forms the dot product of a vector. +*> ZDOTC forms the dot product of two complex vectors +*> ZDOTC = X^H * Y +*> +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] ZX +*> \verbatim +*> ZX is REAL array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +*> +*> \param[in] ZY +*> \verbatim +*> ZY is REAL array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of ZY *> \endverbatim * * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -50,10 +83,10 @@ * ===================================================================== COMPLEX*16 FUNCTION ZDOTC(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N diff --git a/lib/linalg/zdscal.f b/lib/linalg/zdscal.f index 57a949023767cc8442b706b25e11f098bbc43bb0..71d4da55be40446f49faf11e4e65cfc09f963e8c 100644 --- a/lib/linalg/zdscal.f +++ b/lib/linalg/zdscal.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZDSCAL(N,DA,ZX,INCX) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION DA * INTEGER INCX,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 ZX(*) * .. -* +* * *> \par Purpose: * ============= @@ -27,15 +27,41 @@ *> ZDSCAL scales a vector by a constant. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] DA +*> \verbatim +*> DA is DOUBLE PRECISION +*> On entry, DA specifies the scalar alpha. +*> \endverbatim +*> +*> \param[in,out] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -52,10 +78,10 @@ * ===================================================================== SUBROUTINE ZDSCAL(N,DA,ZX,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA diff --git a/lib/linalg/zgemm.f b/lib/linalg/zgemm.f index f423315508a0de2fc5ce314db47bab240da9d7fa..c3ac7551d1c793c050c39c8c0f542e6459db8a13 100644 --- a/lib/linalg/zgemm.f +++ b/lib/linalg/zgemm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA,BETA * INTEGER K,LDA,LDB,LDC,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),B(LDB,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -97,7 +97,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, ka ), where ka is +*> A is COMPLEX*16 array, dimension ( LDA, ka ), where ka is *> k when TRANSA = 'N' or 'n', and is m otherwise. *> Before entry with TRANSA = 'N' or 'n', the leading m by k *> part of the array A must contain the matrix A, otherwise @@ -116,7 +116,7 @@ *> *> \param[in] B *> \verbatim -*> B is COMPLEX*16 array of DIMENSION ( LDB, kb ), where kb is +*> B is COMPLEX*16 array, dimension ( LDB, kb ), where kb is *> n when TRANSB = 'N' or 'n', and is k otherwise. *> Before entry with TRANSB = 'N' or 'n', the leading k by n *> part of the array B must contain the matrix B, otherwise @@ -142,7 +142,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is COMPLEX*16 array of DIMENSION ( LDC, n ). +*> C is COMPLEX*16 array, dimension ( LDC, N ) *> Before entry, the leading m by n part of the array C must *> contain the matrix C, except when beta is zero, in which *> case C need not be set on entry. @@ -161,12 +161,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level3 * @@ -187,10 +187,10 @@ * ===================================================================== SUBROUTINE ZGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA @@ -317,12 +317,10 @@ 60 CONTINUE END IF DO 80 L = 1,K - IF (B(L,J).NE.ZERO) THEN - TEMP = ALPHA*B(L,J) - DO 70 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 70 CONTINUE - END IF + TEMP = ALPHA*B(L,J) + DO 70 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 70 CONTINUE 80 CONTINUE 90 CONTINUE ELSE IF (CONJA) THEN @@ -376,17 +374,15 @@ 170 CONTINUE END IF DO 190 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*DCONJG(B(J,L)) - DO 180 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 180 CONTINUE - END IF + TEMP = ALPHA*DCONJG(B(J,L)) + DO 180 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 180 CONTINUE 190 CONTINUE 200 CONTINUE ELSE * -* Form C := alpha*A*B**T + beta*C +* Form C := alpha*A*B**T + beta*C * DO 250 J = 1,N IF (BETA.EQ.ZERO) THEN @@ -399,12 +395,10 @@ 220 CONTINUE END IF DO 240 L = 1,K - IF (B(J,L).NE.ZERO) THEN - TEMP = ALPHA*B(J,L) - DO 230 I = 1,M - C(I,J) = C(I,J) + TEMP*A(I,L) - 230 CONTINUE - END IF + TEMP = ALPHA*B(J,L) + DO 230 I = 1,M + C(I,J) = C(I,J) + TEMP*A(I,L) + 230 CONTINUE 240 CONTINUE 250 CONTINUE END IF diff --git a/lib/linalg/zgemv.f b/lib/linalg/zgemv.f index 4e174c956c9ee8cac85b1d5d765e92f838c4d777..7088d383f449fbb52ddf608fdea128d1f5fb3a9f 100644 --- a/lib/linalg/zgemv.f +++ b/lib/linalg/zgemv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA,BETA * INTEGER INCX,INCY,LDA,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -73,7 +73,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, n ). +*> A is COMPLEX*16 array, dimension ( LDA, N ) *> Before entry, the leading m by n part of the array A must *> contain the matrix of coefficients. *> \endverbatim @@ -88,7 +88,7 @@ *> *> \param[in] X *> \verbatim -*> X is COMPLEX*16 array of DIMENSION at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ) when TRANS = 'N' or 'n' *> and at least *> ( 1 + ( m - 1 )*abs( INCX ) ) otherwise. @@ -112,7 +112,7 @@ *> *> \param[in,out] Y *> \verbatim -*> Y is COMPLEX*16 array of DIMENSION at least +*> Y is COMPLEX*16 array, dimension at least *> ( 1 + ( m - 1 )*abs( INCY ) ) when TRANS = 'N' or 'n' *> and at least *> ( 1 + ( n - 1 )*abs( INCY ) ) otherwise. @@ -131,12 +131,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -158,10 +158,10 @@ * ===================================================================== SUBROUTINE ZGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA @@ -285,24 +285,20 @@ JX = KX IF (INCY.EQ.1) THEN DO 60 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - DO 50 I = 1,M - Y(I) = Y(I) + TEMP*A(I,J) - 50 CONTINUE - END IF + TEMP = ALPHA*X(JX) + DO 50 I = 1,M + Y(I) = Y(I) + TEMP*A(I,J) + 50 CONTINUE JX = JX + INCX 60 CONTINUE ELSE DO 80 J = 1,N - IF (X(JX).NE.ZERO) THEN - TEMP = ALPHA*X(JX) - IY = KY - DO 70 I = 1,M - Y(IY) = Y(IY) + TEMP*A(I,J) - IY = IY + INCY - 70 CONTINUE - END IF + TEMP = ALPHA*X(JX) + IY = KY + DO 70 I = 1,M + Y(IY) = Y(IY) + TEMP*A(I,J) + IY = IY + INCY + 70 CONTINUE JX = JX + INCX 80 CONTINUE END IF diff --git a/lib/linalg/zgerc.f b/lib/linalg/zgerc.f index accfeafc053ad42c844281de2739d62148d1a602..058dccfc1ccb941aabafb3de6a68d95cc933faae 100644 --- a/lib/linalg/zgerc.f +++ b/lib/linalg/zgerc.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZGERC(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA * INTEGER INCX,INCY,LDA,M,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -57,7 +57,7 @@ *> *> \param[in] X *> \verbatim -*> X is COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( m - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the m *> element vector x. @@ -72,7 +72,7 @@ *> *> \param[in] Y *> \verbatim -*> Y is COMPLEX*16 array of dimension at least +*> Y is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. @@ -87,7 +87,7 @@ *> *> \param[in,out] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, n ). +*> A is COMPLEX*16 array, dimension ( LDA, N ) *> Before entry, the leading m by n part of the array A must *> contain the matrix of coefficients. On exit, A is *> overwritten by the updated matrix. @@ -104,12 +104,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -130,10 +130,10 @@ * ===================================================================== SUBROUTINE ZGERC(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA diff --git a/lib/linalg/zheev.f b/lib/linalg/zheev.f index adba990f0a9d396198cf99711d38364e90f4e514..3e87778740750dab190b8180cfe12b92c245c964 100644 --- a/lib/linalg/zheev.f +++ b/lib/linalg/zheev.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZHEEV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZHEEV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZHEEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, RWORK, * INFO ) -* +* * .. Scalar Arguments .. * CHARACTER JOBZ, UPLO * INTEGER INFO, LDA, LWORK, N @@ -29,7 +29,7 @@ * DOUBLE PRECISION RWORK( * ), W( * ) * COMPLEX*16 A( LDA, * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -127,12 +127,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16HEeigen * @@ -140,10 +140,10 @@ SUBROUTINE ZHEEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, RWORK, $ INFO ) * -* -- LAPACK driver routine (version 3.4.0) -- +* -- LAPACK driver routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/zhemv.f b/lib/linalg/zhemv.f index 34216fbfff8a12b8d4c18cbdb2a7aa70a2d275e3..3ea0753f40b9d81ea154074b06131cd1491d18ab 100644 --- a/lib/linalg/zhemv.f +++ b/lib/linalg/zhemv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZHEMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA,BETA * INTEGER INCX,INCY,LDA,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -65,7 +65,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, n ). +*> A is COMPLEX*16 array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular part of the hermitian matrix and the strictly @@ -88,7 +88,7 @@ *> *> \param[in] X *> \verbatim -*> X is COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. @@ -110,7 +110,7 @@ *> *> \param[in,out] Y *> \verbatim -*> Y is COMPLEX*16 array of dimension at least +*> Y is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. On exit, Y is overwritten by the updated @@ -127,12 +127,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -154,10 +154,10 @@ * ===================================================================== SUBROUTINE ZHEMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA diff --git a/lib/linalg/zher2.f b/lib/linalg/zher2.f index e2a02c3c68fb3d705aa2c734d4e21fc722908def..e3a383189d92f46e2400d48b6247a22aadfd6d1e 100644 --- a/lib/linalg/zher2.f +++ b/lib/linalg/zher2.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZHER2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA * INTEGER INCX,INCY,LDA,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),X(*),Y(*) * .. -* +* * *> \par Purpose: * ============= @@ -65,7 +65,7 @@ *> *> \param[in] X *> \verbatim -*> X is COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. @@ -80,7 +80,7 @@ *> *> \param[in] Y *> \verbatim -*> Y is COMPLEX*16 array of dimension at least +*> Y is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCY ) ). *> Before entry, the incremented array Y must contain the n *> element vector y. @@ -95,7 +95,7 @@ *> *> \param[in,out] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, n ). +*> A is COMPLEX*16 array, dimension ( LDA, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular part of the hermitian matrix and the strictly @@ -124,12 +124,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -150,10 +150,10 @@ * ===================================================================== SUBROUTINE ZHER2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA diff --git a/lib/linalg/zher2k.f b/lib/linalg/zher2k.f index 0b91bd2cbbf09f79d782ac7b1b05313ca55c9f7e..474c65e5755eb6a910dba45896bbef33b3a5e219 100644 --- a/lib/linalg/zher2k.f +++ b/lib/linalg/zher2k.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZHER2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA * DOUBLE PRECISION BETA @@ -19,7 +19,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),B(LDB,*),C(LDC,*) * .. -* +* * *> \par Purpose: * ============= @@ -95,7 +95,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, ka ), where ka is +*> A is COMPLEX*16 array, dimension ( LDA, ka ), where ka is *> k when TRANS = 'N' or 'n', and is n otherwise. *> Before entry with TRANS = 'N' or 'n', the leading n by k *> part of the array A must contain the matrix A, otherwise @@ -114,7 +114,7 @@ *> *> \param[in] B *> \verbatim -*> B is COMPLEX*16 array of DIMENSION ( LDB, kb ), where kb is +*> B is COMPLEX*16 array, dimension ( LDB, kb ), where kb is *> k when TRANS = 'N' or 'n', and is n otherwise. *> Before entry with TRANS = 'N' or 'n', the leading n by k *> part of the array B must contain the matrix B, otherwise @@ -140,7 +140,7 @@ *> *> \param[in,out] C *> \verbatim -*> C is COMPLEX*16 array of DIMENSION ( LDC, n ). +*> C is COMPLEX*16 array, dimension ( LDC, N ) *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array C must contain the upper *> triangular part of the hermitian matrix and the strictly @@ -169,12 +169,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level3 * @@ -198,10 +198,10 @@ * ===================================================================== SUBROUTINE ZHER2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA diff --git a/lib/linalg/zhetd2.f b/lib/linalg/zhetd2.f index dd8f9cf0145642ee5db89462d087c668bb6a6bf7..6c5b8aae3dd4602faf5be92f8b325b8b81b1d8e3 100644 --- a/lib/linalg/zhetd2.f +++ b/lib/linalg/zhetd2.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZHETD2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZHETD2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZHETD2( UPLO, N, A, LDA, D, E, TAU, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION D( * ), E( * ) * COMPLEX*16 A( LDA, * ), TAU( * ) * .. -* +* * *> \par Purpose: * ============= @@ -117,12 +117,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16HEcomputational * @@ -175,10 +175,10 @@ * ===================================================================== SUBROUTINE ZHETD2( UPLO, N, A, LDA, D, E, TAU, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zhetrd.f b/lib/linalg/zhetrd.f index c6074846379f79f0ff837209d81e2d0fc28cecb2..51c9fc2ec9d0ffd42261631105dcac4744795fc2 100644 --- a/lib/linalg/zhetrd.f +++ b/lib/linalg/zhetrd.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZHETRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZHETRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZHETRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, LWORK, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION D( * ), E( * ) * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -134,12 +134,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16HEcomputational * @@ -192,10 +192,10 @@ * ===================================================================== SUBROUTINE ZHETRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zhpr.f b/lib/linalg/zhpr.f index 42e61196baad39aec6bd80f05a1e433e4947c07c..af82dfbd8c291c204ecae2d82d4234357be4d7de 100644 --- a/lib/linalg/zhpr.f +++ b/lib/linalg/zhpr.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZHPR(UPLO,N,ALPHA,X,INCX,AP) -* +* * .. Scalar Arguments .. * DOUBLE PRECISION ALPHA * INTEGER INCX,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 AP(*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -65,7 +65,7 @@ *> *> \param[in] X *> \verbatim -*> X is COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. @@ -80,7 +80,7 @@ *> *> \param[in,out] AP *> \verbatim -*> AP is COMPLEX*16 array of DIMENSION at least +*> AP is COMPLEX*16 array, dimension at least *> ( ( n*( n + 1 ) )/2 ). *> Before entry with UPLO = 'U' or 'u', the array AP must *> contain the upper triangular part of the hermitian matrix @@ -104,12 +104,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -130,10 +130,10 @@ * ===================================================================== SUBROUTINE ZHPR(UPLO,N,ALPHA,X,INCX,AP) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA diff --git a/lib/linalg/zlacgv.f b/lib/linalg/zlacgv.f index 315c4de5ce103048eeab7d103a20a8978de13005..1e3ca6e73ff918a5a1d358c4d8bc03b4dff832e9 100644 --- a/lib/linalg/zlacgv.f +++ b/lib/linalg/zlacgv.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLACGV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLACGV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLACGV( N, X, INCX ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * .. * .. Array Arguments .. * COMPLEX*16 X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -62,22 +62,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLACGV( N, X, INCX ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/zladiv.f b/lib/linalg/zladiv.f index 8f01fe3e63b2296c728d402a7d776f40b2c27539..0bf6ea87d5f08210a2dae8174a6fa758af91ad6c 100644 --- a/lib/linalg/zladiv.f +++ b/lib/linalg/zladiv.f @@ -2,28 +2,28 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLADIV + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLADIV + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * COMPLEX*16 FUNCTION ZLADIV( X, Y ) -* +* * .. Scalar Arguments .. * COMPLEX*16 X, Y * .. -* +* * *> \par Purpose: * ============= @@ -52,22 +52,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== COMPLEX*16 FUNCTION ZLADIV( X, Y ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 X, Y diff --git a/lib/linalg/zlanhe.f b/lib/linalg/zlanhe.f index 3093a151afe516731e2b2ccfb438407b0da3dbce..7c7f7f3be4c1751e08a510ee62cd001a422921d9 100644 --- a/lib/linalg/zlanhe.f +++ b/lib/linalg/zlanhe.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLANHE + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLANHE + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * DOUBLE PRECISION FUNCTION ZLANHE( NORM, UPLO, N, A, LDA, WORK ) -* +* * .. Scalar Arguments .. * CHARACTER NORM, UPLO * INTEGER LDA, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION WORK( * ) * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -112,22 +112,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16HEauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION ZLANHE( NORM, UPLO, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER NORM, UPLO diff --git a/lib/linalg/zlarf.f b/lib/linalg/zlarf.f index f51e1d73831544937bfb8f5f66c83bbb0edf6a8e..f1be80d37bdd56e329efa9304cf1907f8653ba62 100644 --- a/lib/linalg/zlarf.f +++ b/lib/linalg/zlarf.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLARF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLARF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) -* +* * .. Scalar Arguments .. * CHARACTER SIDE * INTEGER INCV, LDC, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * COMPLEX*16 C( LDC, * ), V( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,22 +116,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE diff --git a/lib/linalg/zlarfb.f b/lib/linalg/zlarfb.f index 99490f5827ffad2e19c79cf4da285dd6e4f8b681..b4a2b4d1a0474d4af19e412b82161eb3591343fe 100644 --- a/lib/linalg/zlarfb.f +++ b/lib/linalg/zlarfb.f @@ -2,25 +2,25 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLARFB + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLARFB + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, * T, LDT, C, LDC, WORK, LDWORK ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, SIDE, STOREV, TRANS * INTEGER K, LDC, LDT, LDV, LDWORK, M, N @@ -29,7 +29,7 @@ * COMPLEX*16 C( LDC, * ), T( LDT, * ), V( LDV, * ), * $ WORK( LDWORK, * ) * .. -* +* * *> \par Purpose: * ============= @@ -154,12 +154,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2013 * *> \ingroup complex16OTHERauxiliary * @@ -195,10 +195,10 @@ SUBROUTINE ZLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, $ T, LDT, C, LDC, WORK, LDWORK ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2013 * * .. Scalar Arguments .. CHARACTER DIRECT, SIDE, STOREV, TRANS @@ -217,12 +217,11 @@ * .. * .. Local Scalars .. CHARACTER TRANST - INTEGER I, J, LASTV, LASTC + INTEGER I, J * .. * .. External Functions .. LOGICAL LSAME - INTEGER ILAZLR, ILAZLC - EXTERNAL LSAME, ILAZLR, ILAZLC + EXTERNAL LSAME * .. * .. External Subroutines .. EXTERNAL ZCOPY, ZGEMM, ZLACGV, ZTRMM @@ -255,36 +254,33 @@ * * Form H * C or H**H * C where C = ( C1 ) * ( C2 ) -* - LASTV = MAX( K, ILAZLR( M, K, V, LDV ) ) - LASTC = ILAZLC( LASTV, N, C, LDC ) * * W := C**H * V = (C1**H * V1 + C2**H * V2) (stored in WORK) * * W := C1**H * DO 10 J = 1, K - CALL ZCOPY( LASTC, C( J, 1 ), LDC, WORK( 1, J ), 1 ) - CALL ZLACGV( LASTC, WORK( 1, J ), 1 ) + CALL ZCOPY( N, C( J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL ZLACGV( N, WORK( 1, J ), 1 ) 10 CONTINUE * * W := W * V1 * - CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', N, + $ K, ONE, V, LDV, WORK, LDWORK ) + IF( M.GT.K ) THEN * -* W := W + C2**H *V2 +* W := W + C2**H * V2 * - CALL ZGEMM( 'Conjugate transpose', 'No transpose', - $ LASTC, K, LASTV-K, ONE, C( K+1, 1 ), LDC, - $ V( K+1, 1 ), LDV, ONE, WORK, LDWORK ) + CALL ZGEMM( 'Conjugate transpose', 'No transpose', N, + $ K, M-K, ONE, C( K+1, 1 ), LDC, + $ V( K+1, 1 ), LDV, ONE, WORK, LDWORK ) END IF * * W := W * T**H or W * T * - CALL ZTRMM( 'Right', 'Upper', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V * W**H * @@ -293,20 +289,19 @@ * C2 := C2 - V2 * W**H * CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ LASTV-K, LASTC, K, - $ -ONE, V( K+1, 1 ), LDV, WORK, LDWORK, - $ ONE, C( K+1, 1 ), LDC ) + $ M-K, N, K, -ONE, V( K+1, 1 ), LDV, WORK, + $ LDWORK, ONE, C( K+1, 1 ), LDC ) END IF * * W := W * V1**H * CALL ZTRMM( 'Right', 'Lower', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V, LDV, WORK, LDWORK ) + $ 'Unit', N, K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W**H * DO 30 J = 1, K - DO 20 I = 1, LASTC + DO 20 I = 1, N C( J, I ) = C( J, I ) - DCONJG( WORK( I, J ) ) 20 CONTINUE 30 CONTINUE @@ -314,58 +309,53 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**H where C = ( C1 C2 ) -* - LASTV = MAX( K, ILAZLR( N, K, V, LDV ) ) - LASTC = ILAZLR( M, LASTV, C, LDC ) * * W := C * V = (C1*V1 + C2*V2) (stored in WORK) * * W := C1 * DO 40 J = 1, K - CALL ZCOPY( LASTC, C( 1, J ), 1, WORK( 1, J ), 1 ) + CALL ZCOPY( M, C( 1, J ), 1, WORK( 1, J ), 1 ) 40 CONTINUE * * W := W * V1 * - CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', M, + $ K, ONE, V, LDV, WORK, LDWORK ) + IF( N.GT.K ) THEN * * W := W + C2 * V2 * - CALL ZGEMM( 'No transpose', 'No transpose', - $ LASTC, K, LASTV-K, - $ ONE, C( 1, K+1 ), LDC, V( K+1, 1 ), LDV, - $ ONE, WORK, LDWORK ) + CALL ZGEMM( 'No transpose', 'No transpose', M, K, N-K, + $ ONE, C( 1, K+1 ), LDC, V( K+1, 1 ), LDV, + $ ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**H * - CALL ZTRMM( 'Right', 'Upper', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V**H * - IF( LASTV.GT.K ) THEN + IF( N.GT.K ) THEN * * C2 := C2 - W * V2**H * - CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ LASTC, LASTV-K, K, - $ -ONE, WORK, LDWORK, V( K+1, 1 ), LDV, - $ ONE, C( 1, K+1 ), LDC ) + CALL ZGEMM( 'No transpose', 'Conjugate transpose', M, + $ N-K, K, -ONE, WORK, LDWORK, V( K+1, 1 ), + $ LDV, ONE, C( 1, K+1 ), LDC ) END IF * * W := W * V1**H * CALL ZTRMM( 'Right', 'Lower', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V, LDV, WORK, LDWORK ) + $ 'Unit', M, K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 60 J = 1, K - DO 50 I = 1, LASTC + DO 50 I = 1, M C( I, J ) = C( I, J ) - WORK( I, J ) 50 CONTINUE 60 CONTINUE @@ -381,38 +371,33 @@ * * Form H * C or H**H * C where C = ( C1 ) * ( C2 ) -* - LASTC = ILAZLC( M, N, C, LDC ) * * W := C**H * V = (C1**H * V1 + C2**H * V2) (stored in WORK) * * W := C2**H * DO 70 J = 1, K - CALL ZCOPY( LASTC, C( M-K+J, 1 ), LDC, - $ WORK( 1, J ), 1 ) - CALL ZLACGV( LASTC, WORK( 1, J ), 1 ) + CALL ZCOPY( N, C( M-K+J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL ZLACGV( N, WORK( 1, J ), 1 ) 70 CONTINUE * * W := W * V2 * - CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( M-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', N, + $ K, ONE, V( M-K+1, 1 ), LDV, WORK, LDWORK ) IF( M.GT.K ) THEN * -* W := W + C1**H*V1 +* W := W + C1**H * V1 * - CALL ZGEMM( 'Conjugate transpose', 'No transpose', - $ LASTC, K, M-K, - $ ONE, C, LDC, V, LDV, - $ ONE, WORK, LDWORK ) + CALL ZGEMM( 'Conjugate transpose', 'No transpose', N, + $ K, M-K, ONE, C, LDC, V, LDV, ONE, WORK, + $ LDWORK ) END IF * * W := W * T**H or W * T * - CALL ZTRMM( 'Right', 'Lower', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V * W**H * @@ -421,21 +406,20 @@ * C1 := C1 - V1 * W**H * CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ M-K, LASTC, K, - $ -ONE, V, LDV, WORK, LDWORK, - $ ONE, C, LDC ) + $ M-K, N, K, -ONE, V, LDV, WORK, LDWORK, + $ ONE, C, LDC ) END IF * * W := W * V2**H * CALL ZTRMM( 'Right', 'Upper', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V( M-K+1, 1 ), LDV, - $ WORK, LDWORK ) + $ 'Unit', N, K, ONE, V( M-K+1, 1 ), LDV, WORK, + $ LDWORK ) * * C2 := C2 - W**H * DO 90 J = 1, K - DO 80 I = 1, LASTC + DO 80 I = 1, N C( M-K+J, I ) = C( M-K+J, I ) - $ DCONJG( WORK( I, J ) ) 80 CONTINUE @@ -444,36 +428,31 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**H where C = ( C1 C2 ) -* - LASTC = ILAZLR( M, N, C, LDC ) * * W := C * V = (C1*V1 + C2*V2) (stored in WORK) * * W := C2 * DO 100 J = 1, K - CALL ZCOPY( LASTC, C( 1, N-K+J ), 1, - $ WORK( 1, J ), 1 ) + CALL ZCOPY( M, C( 1, N-K+J ), 1, WORK( 1, J ), 1 ) 100 CONTINUE * * W := W * V2 * - CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( N-K+1, 1 ), LDV, - $ WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', M, + $ K, ONE, V( N-K+1, 1 ), LDV, WORK, LDWORK ) IF( N.GT.K ) THEN * * W := W + C1 * V1 * - CALL ZGEMM( 'No transpose', 'No transpose', - $ LASTC, K, N-K, - $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) + CALL ZGEMM( 'No transpose', 'No transpose', M, K, N-K, + $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**H * - CALL ZTRMM( 'Right', 'Lower', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V**H * @@ -481,23 +460,22 @@ * * C1 := C1 - W * V1**H * - CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ LASTC, N-K, K, -ONE, WORK, LDWORK, V, LDV, - $ ONE, C, LDC ) + CALL ZGEMM( 'No transpose', 'Conjugate transpose', M, + $ N-K, K, -ONE, WORK, LDWORK, V, LDV, ONE, + $ C, LDC ) END IF * * W := W * V2**H * CALL ZTRMM( 'Right', 'Upper', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V( N-K+1, 1 ), LDV, - $ WORK, LDWORK ) + $ 'Unit', M, K, ONE, V( N-K+1, 1 ), LDV, WORK, + $ LDWORK ) * * C2 := C2 - W * DO 120 J = 1, K - DO 110 I = 1, LASTC - C( I, N-K+J ) = C( I, N-K+J ) - $ - WORK( I, J ) + DO 110 I = 1, M + C( I, N-K+J ) = C( I, N-K+J ) - WORK( I, J ) 110 CONTINUE 120 CONTINUE END IF @@ -514,59 +492,56 @@ * * Form H * C or H**H * C where C = ( C1 ) * ( C2 ) -* - LASTV = MAX( K, ILAZLC( K, M, V, LDV ) ) - LASTC = ILAZLC( LASTV, N, C, LDC ) * * W := C**H * V**H = (C1**H * V1**H + C2**H * V2**H) (stored in WORK) * * W := C1**H * DO 130 J = 1, K - CALL ZCOPY( LASTC, C( J, 1 ), LDC, WORK( 1, J ), 1 ) - CALL ZLACGV( LASTC, WORK( 1, J ), 1 ) + CALL ZCOPY( N, C( J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL ZLACGV( N, WORK( 1, J ), 1 ) 130 CONTINUE * * W := W * V1**H * CALL ZTRMM( 'Right', 'Upper', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + $ 'Unit', N, K, ONE, V, LDV, WORK, LDWORK ) + IF( M.GT.K ) THEN * -* W := W + C2**H*V2**H +* W := W + C2**H * V2**H * CALL ZGEMM( 'Conjugate transpose', - $ 'Conjugate transpose', LASTC, K, LASTV-K, - $ ONE, C( K+1, 1 ), LDC, V( 1, K+1 ), LDV, - $ ONE, WORK, LDWORK ) + $ 'Conjugate transpose', N, K, M-K, ONE, + $ C( K+1, 1 ), LDC, V( 1, K+1 ), LDV, ONE, + $ WORK, LDWORK ) END IF * * W := W * T**H or W * T * - CALL ZTRMM( 'Right', 'Upper', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V**H * W**H * - IF( LASTV.GT.K ) THEN + IF( M.GT.K ) THEN * * C2 := C2 - V2**H * W**H * CALL ZGEMM( 'Conjugate transpose', - $ 'Conjugate transpose', LASTV-K, LASTC, K, - $ -ONE, V( 1, K+1 ), LDV, WORK, LDWORK, - $ ONE, C( K+1, 1 ), LDC ) + $ 'Conjugate transpose', M-K, N, K, -ONE, + $ V( 1, K+1 ), LDV, WORK, LDWORK, ONE, + $ C( K+1, 1 ), LDC ) END IF * * W := W * V1 * - CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', N, + $ K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W**H * DO 150 J = 1, K - DO 140 I = 1, LASTC + DO 140 I = 1, N C( J, I ) = C( J, I ) - DCONJG( WORK( I, J ) ) 140 CONTINUE 150 CONTINUE @@ -574,57 +549,53 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**H where C = ( C1 C2 ) -* - LASTV = MAX( K, ILAZLC( K, N, V, LDV ) ) - LASTC = ILAZLR( M, LASTV, C, LDC ) * * W := C * V**H = (C1*V1**H + C2*V2**H) (stored in WORK) * * W := C1 * DO 160 J = 1, K - CALL ZCOPY( LASTC, C( 1, J ), 1, WORK( 1, J ), 1 ) + CALL ZCOPY( M, C( 1, J ), 1, WORK( 1, J ), 1 ) 160 CONTINUE * * W := W * V1**H * CALL ZTRMM( 'Right', 'Upper', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V, LDV, WORK, LDWORK ) - IF( LASTV.GT.K ) THEN + $ 'Unit', M, K, ONE, V, LDV, WORK, LDWORK ) + IF( N.GT.K ) THEN * * W := W + C2 * V2**H * - CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ LASTC, K, LASTV-K, ONE, C( 1, K+1 ), LDC, - $ V( 1, K+1 ), LDV, ONE, WORK, LDWORK ) + CALL ZGEMM( 'No transpose', 'Conjugate transpose', M, + $ K, N-K, ONE, C( 1, K+1 ), LDC, + $ V( 1, K+1 ), LDV, ONE, WORK, LDWORK ) END IF * * W := W * T or W * T**H * - CALL ZTRMM( 'Right', 'Upper', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V * - IF( LASTV.GT.K ) THEN + IF( N.GT.K ) THEN * * C2 := C2 - W * V2 * - CALL ZGEMM( 'No transpose', 'No transpose', - $ LASTC, LASTV-K, K, - $ -ONE, WORK, LDWORK, V( 1, K+1 ), LDV, - $ ONE, C( 1, K+1 ), LDC ) + CALL ZGEMM( 'No transpose', 'No transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V( 1, K+1 ), LDV, ONE, + $ C( 1, K+1 ), LDC ) END IF * * W := W * V1 * - CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', - $ LASTC, K, ONE, V, LDV, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Upper', 'No transpose', 'Unit', M, + $ K, ONE, V, LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 180 J = 1, K - DO 170 I = 1, LASTC + DO 170 I = 1, M C( I, J ) = C( I, J ) - WORK( I, J ) 170 CONTINUE 180 CONTINUE @@ -640,37 +611,34 @@ * * Form H * C or H**H * C where C = ( C1 ) * ( C2 ) -* - LASTC = ILAZLC( M, N, C, LDC ) * * W := C**H * V**H = (C1**H * V1**H + C2**H * V2**H) (stored in WORK) * * W := C2**H * DO 190 J = 1, K - CALL ZCOPY( LASTC, C( M-K+J, 1 ), LDC, - $ WORK( 1, J ), 1 ) - CALL ZLACGV( LASTC, WORK( 1, J ), 1 ) + CALL ZCOPY( N, C( M-K+J, 1 ), LDC, WORK( 1, J ), 1 ) + CALL ZLACGV( N, WORK( 1, J ), 1 ) 190 CONTINUE * * W := W * V2**H * CALL ZTRMM( 'Right', 'Lower', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V( 1, M-K+1 ), LDV, - $ WORK, LDWORK ) + $ 'Unit', N, K, ONE, V( 1, M-K+1 ), LDV, WORK, + $ LDWORK ) IF( M.GT.K ) THEN * * W := W + C1**H * V1**H * CALL ZGEMM( 'Conjugate transpose', - $ 'Conjugate transpose', LASTC, K, M-K, - $ ONE, C, LDC, V, LDV, ONE, WORK, LDWORK ) + $ 'Conjugate transpose', N, K, M-K, ONE, C, + $ LDC, V, LDV, ONE, WORK, LDWORK ) END IF * * W := W * T**H or W * T * - CALL ZTRMM( 'Right', 'Lower', TRANST, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', TRANST, 'Non-unit', N, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - V**H * W**H * @@ -679,20 +647,19 @@ * C1 := C1 - V1**H * W**H * CALL ZGEMM( 'Conjugate transpose', - $ 'Conjugate transpose', M-K, LASTC, K, - $ -ONE, V, LDV, WORK, LDWORK, ONE, C, LDC ) + $ 'Conjugate transpose', M-K, N, K, -ONE, V, + $ LDV, WORK, LDWORK, ONE, C, LDC ) END IF * * W := W * V2 * - CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( 1, M-K+1 ), LDV, - $ WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', N, + $ K, ONE, V( 1, M-K+1 ), LDV, WORK, LDWORK ) * * C2 := C2 - W**H * DO 210 J = 1, K - DO 200 I = 1, LASTC + DO 200 I = 1, N C( M-K+J, I ) = C( M-K+J, I ) - $ DCONJG( WORK( I, J ) ) 200 CONTINUE @@ -701,36 +668,33 @@ ELSE IF( LSAME( SIDE, 'R' ) ) THEN * * Form C * H or C * H**H where C = ( C1 C2 ) -* - LASTC = ILAZLR( M, N, C, LDC ) * * W := C * V**H = (C1*V1**H + C2*V2**H) (stored in WORK) * * W := C2 * DO 220 J = 1, K - CALL ZCOPY( LASTC, C( 1, N-K+J ), 1, - $ WORK( 1, J ), 1 ) + CALL ZCOPY( M, C( 1, N-K+J ), 1, WORK( 1, J ), 1 ) 220 CONTINUE * * W := W * V2**H * CALL ZTRMM( 'Right', 'Lower', 'Conjugate transpose', - $ 'Unit', LASTC, K, ONE, V( 1, N-K+1 ), LDV, - $ WORK, LDWORK ) + $ 'Unit', M, K, ONE, V( 1, N-K+1 ), LDV, WORK, + $ LDWORK ) IF( N.GT.K ) THEN * * W := W + C1 * V1**H * - CALL ZGEMM( 'No transpose', 'Conjugate transpose', - $ LASTC, K, N-K, ONE, C, LDC, V, LDV, ONE, - $ WORK, LDWORK ) + CALL ZGEMM( 'No transpose', 'Conjugate transpose', M, + $ K, N-K, ONE, C, LDC, V, LDV, ONE, WORK, + $ LDWORK ) END IF * * W := W * T or W * T**H * - CALL ZTRMM( 'Right', 'Lower', TRANS, 'Non-unit', - $ LASTC, K, ONE, T, LDT, WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', TRANS, 'Non-unit', M, K, + $ ONE, T, LDT, WORK, LDWORK ) * * C := C - W * V * @@ -738,21 +702,19 @@ * * C1 := C1 - W * V1 * - CALL ZGEMM( 'No transpose', 'No transpose', - $ LASTC, N-K, K, -ONE, WORK, LDWORK, V, LDV, - $ ONE, C, LDC ) + CALL ZGEMM( 'No transpose', 'No transpose', M, N-K, K, + $ -ONE, WORK, LDWORK, V, LDV, ONE, C, LDC ) END IF * * W := W * V2 * - CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', - $ LASTC, K, ONE, V( 1, N-K+1 ), LDV, - $ WORK, LDWORK ) + CALL ZTRMM( 'Right', 'Lower', 'No transpose', 'Unit', M, + $ K, ONE, V( 1, N-K+1 ), LDV, WORK, LDWORK ) * * C1 := C1 - W * DO 240 J = 1, K - DO 230 I = 1, LASTC + DO 230 I = 1, M C( I, N-K+J ) = C( I, N-K+J ) - WORK( I, J ) 230 CONTINUE 240 CONTINUE diff --git a/lib/linalg/zlarfg.f b/lib/linalg/zlarfg.f index e37c683fc9acbf85612ff8fb338c2fa3a64944e3..f8a795d547cf925a2d12429e3f82798aed83a887 100644 --- a/lib/linalg/zlarfg.f +++ b/lib/linalg/zlarfg.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLARFG + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLARFG + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLARFG( N, ALPHA, X, INCX, TAU ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * COMPLEX*16 ALPHA, TAU @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -94,22 +94,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLARFG( N, ALPHA, X, INCX, TAU ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/zlarft.f b/lib/linalg/zlarft.f index 2278d11d2b3d89098c2f3296766a3e0ecd6ea485..78ad2f1481d54304eca6927939864560e1df7d84 100644 --- a/lib/linalg/zlarft.f +++ b/lib/linalg/zlarft.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLARFT + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLARFT + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, STOREV * INTEGER K, LDT, LDV, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 T( LDT, * ), TAU( * ), V( LDV, * ) * .. -* +* * *> \par Purpose: * ============= @@ -125,12 +125,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup complex16OTHERauxiliary * @@ -163,10 +163,10 @@ * ===================================================================== SUBROUTINE ZLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, STOREV @@ -187,7 +187,7 @@ INTEGER I, J, PREVLASTV, LASTV * .. * .. External Subroutines .. - EXTERNAL ZGEMV, ZLACGV, ZTRMV + EXTERNAL ZGEMV, ZTRMV, ZGEMM * .. * .. External Functions .. LOGICAL LSAME @@ -222,13 +222,13 @@ END DO DO J = 1, I-1 T( J, I ) = -TAU( I ) * CONJG( V( I , J ) ) - END DO + END DO J = MIN( LASTV, PREVLASTV ) * * T(1:i-1,i) := - tau(i) * V(i:j,1:i-1)**H * V(i:j,i) * CALL ZGEMV( 'Conjugate transpose', J-I, I-1, - $ -TAU( I ), V( I+1, 1 ), LDV, + $ -TAU( I ), V( I+1, 1 ), LDV, $ V( I+1, I ), 1, ONE, T( 1, I ), 1 ) ELSE * Skip any trailing zeros. @@ -237,14 +237,14 @@ END DO DO J = 1, I-1 T( J, I ) = -TAU( I ) * V( J , I ) - END DO + END DO J = MIN( LASTV, PREVLASTV ) * * T(1:i-1,i) := - tau(i) * V(1:i-1,i:j) * V(i,i:j)**H * CALL ZGEMM( 'N', 'C', I-1, 1, J-I, -TAU( I ), $ V( 1, I+1 ), LDV, V( I, I+1 ), LDV, - $ ONE, T( 1, I ), LDT ) + $ ONE, T( 1, I ), LDT ) END IF * * T(1:i-1,i) := T(1:i-1,1:i-1) * T(1:i-1,i) @@ -281,7 +281,7 @@ END DO DO J = I+1, K T( J, I ) = -TAU( I ) * CONJG( V( N-K+I , J ) ) - END DO + END DO J = MAX( LASTV, PREVLASTV ) * * T(i+1:k,i) = -tau(i) * V(j:n-k+i,i+1:k)**H * V(j:n-k+i,i) @@ -296,14 +296,14 @@ END DO DO J = I+1, K T( J, I ) = -TAU( I ) * V( J, N-K+I ) - END DO + END DO J = MAX( LASTV, PREVLASTV ) * * T(i+1:k,i) = -tau(i) * V(i+1:k,j:n-k+i) * V(i,j:n-k+i)**H * CALL ZGEMM( 'N', 'C', K-I, 1, N-K+I-J, -TAU( I ), $ V( I+1, J ), LDV, V( I, J ), LDV, - $ ONE, T( I+1, I ), LDT ) + $ ONE, T( I+1, I ), LDT ) END IF * * T(i+1:k,i) := T(i+1:k,i+1:k) * T(i+1:k,i) diff --git a/lib/linalg/zlascl.f b/lib/linalg/zlascl.f index 51a4f0f61494c3507dde135c77a2efa21c1d8053..c53c6f5ad7bc1c823d4b821ca7d05c682037c0d5 100644 --- a/lib/linalg/zlascl.f +++ b/lib/linalg/zlascl.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLASCL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLASCL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER TYPE * INTEGER INFO, KL, KU, LDA, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -114,7 +114,11 @@ *> \param[in] LDA *> \verbatim *> LDA is INTEGER -*> The leading dimension of the array A. LDA >= max(1,M). +*> The leading dimension of the array A. +*> If TYPE = 'G', 'L', 'U', 'H', LDA >= max(1,M); +*> TYPE = 'B', LDA >= KL+1; +*> TYPE = 'Q', LDA >= KU+1; +*> TYPE = 'Z', LDA >= 2*KL+KU+1. *> \endverbatim *> *> \param[out] INFO @@ -127,22 +131,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date June 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* June 2016 * * .. Scalar Arguments .. CHARACTER TYPE diff --git a/lib/linalg/zlaset.f b/lib/linalg/zlaset.f index 11f82361b741c14ee49356042759aadddc4f3b34..796678217b50613596a416e9c0730f6410d16903 100644 --- a/lib/linalg/zlaset.f +++ b/lib/linalg/zlaset.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLASET + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLASET + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER LDA, M, N @@ -28,7 +28,7 @@ * .. Array Arguments .. * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -77,7 +77,7 @@ *> All the diagonal array elements are set to BETA. *> \endverbatim *> -*> \param[in,out] A +*> \param[out] A *> \verbatim *> A is COMPLEX*16 array, dimension (LDA,N) *> On entry, the m by n matrix A. @@ -94,22 +94,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zlasr.f b/lib/linalg/zlasr.f index 5243d8304a953a7d9b47cfdaa41be83b2646907a..69891ba522aeef87189f6bd7257dd5cb4df37a52 100644 --- a/lib/linalg/zlasr.f +++ b/lib/linalg/zlasr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLASR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLASR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) -* +* * .. Scalar Arguments .. * CHARACTER DIRECT, PIVOT, SIDE * INTEGER LDA, M, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION C( * ), S( * ) * COMPLEX*16 A( LDA, * ) * .. -* +* * *> \par Purpose: * ============= @@ -49,23 +49,23 @@ *> where P is an orthogonal matrix consisting of a sequence of z plane *> rotations, with z = M when SIDE = 'L' and z = N when SIDE = 'R', *> and P**T is the transpose of P. -*> +*> *> When DIRECT = 'F' (Forward sequence), then -*> +*> *> P = P(z-1) * ... * P(2) * P(1) -*> +*> *> and when DIRECT = 'B' (Backward sequence), then -*> +*> *> P = P(1) * P(2) * ... * P(z-1) -*> +*> *> where P(k) is a plane rotation matrix defined by the 2-by-2 rotation -*> +*> *> R(k) = ( c(k) s(k) ) *> = ( -s(k) c(k) ). -*> +*> *> When PIVOT = 'V' (Variable pivot), the rotation is performed *> for the plane (k,k+1), i.e., P(k) has the form -*> +*> *> P(k) = ( 1 ) *> ( ... ) *> ( 1 ) @@ -74,13 +74,13 @@ *> ( 1 ) *> ( ... ) *> ( 1 ) -*> +*> *> where R(k) appears as a rank-2 modification to the identity matrix in *> rows and columns k and k+1. -*> +*> *> When PIVOT = 'T' (Top pivot), the rotation is performed for the *> plane (1,k+1), so P(k) has the form -*> +*> *> P(k) = ( c(k) s(k) ) *> ( 1 ) *> ( ... ) @@ -89,12 +89,12 @@ *> ( 1 ) *> ( ... ) *> ( 1 ) -*> +*> *> where R(k) appears in rows and columns 1 and k+1. -*> +*> *> Similarly, when PIVOT = 'B' (Bottom pivot), the rotation is *> performed for the plane (k,z), giving P(k) the form -*> +*> *> P(k) = ( 1 ) *> ( ... ) *> ( 1 ) @@ -103,7 +103,7 @@ *> ( ... ) *> ( 1 ) *> ( -s(k) c(k) ) -*> +*> *> where R(k) appears in rows and columns k and z. The rotations are *> performed without ever forming P(k) explicitly. *> \endverbatim @@ -188,22 +188,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, PIVOT, SIDE diff --git a/lib/linalg/zlassq.f b/lib/linalg/zlassq.f index 5b7e66c30bd421e41b836e4262903dc952022712..fd13811bd996cc8a548e7b9eb161f22ba9a0642f 100644 --- a/lib/linalg/zlassq.f +++ b/lib/linalg/zlassq.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLASSQ + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLASSQ + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLASSQ( N, X, INCX, SCALE, SUMSQ ) -* +* * .. Scalar Arguments .. * INTEGER INCX, N * DOUBLE PRECISION SCALE, SUMSQ @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 X( * ) * .. -* +* * *> \par Purpose: * ============= @@ -94,22 +94,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASSQ( N, X, INCX, SCALE, SUMSQ ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/zlatrd.f b/lib/linalg/zlatrd.f index 619d7280c482270f6117235e941bf529e347ebc0..ccc040993f81a1fc23d3ede5c58e3b64154f1943 100644 --- a/lib/linalg/zlatrd.f +++ b/lib/linalg/zlatrd.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZLATRD + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZLATRD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER LDA, LDW, N, NB @@ -28,7 +28,7 @@ * DOUBLE PRECISION E( * ) * COMPLEX*16 A( LDA, * ), TAU( * ), W( LDW, * ) * .. -* +* * *> \par Purpose: * ============= @@ -135,12 +135,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERauxiliary * @@ -199,10 +199,10 @@ * ===================================================================== SUBROUTINE ZLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) * -* -- LAPACK auxiliary routine (version 3.4.2) -- +* -- LAPACK auxiliary routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zpptrf.f b/lib/linalg/zpptrf.f index c34aff332a508c367cb881f5ae12e508f93506fc..6e50b4682859468ab43c4c10bdce954048f51f39 100644 --- a/lib/linalg/zpptrf.f +++ b/lib/linalg/zpptrf.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZPPTRF + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZPPTRF + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZPPTRF( UPLO, N, AP, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 AP( * ) * .. -* +* * *> \par Purpose: * ============= @@ -87,12 +87,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * @@ -119,10 +119,10 @@ * ===================================================================== SUBROUTINE ZPPTRF( UPLO, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zpptri.f b/lib/linalg/zpptri.f index 09467974502f8b57301352e23399988060b4e3ef..cde2f6dc72f6662baf82bac3753df36cee3af0a5 100644 --- a/lib/linalg/zpptri.f +++ b/lib/linalg/zpptri.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZPPTRI + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZPPTRI + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZPPTRI( UPLO, N, AP, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 AP( * ) * .. -* +* * *> \par Purpose: * ============= @@ -81,22 +81,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZPPTRI( UPLO, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zscal.f b/lib/linalg/zscal.f index ad28a10a9b8e35641cc08e70560a8d6fa112e67e..9f6d4b1d3911851bfcb15a431d2ed64797d2e4ec 100644 --- a/lib/linalg/zscal.f +++ b/lib/linalg/zscal.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZSCAL(N,ZA,ZX,INCX) -* +* * .. Scalar Arguments .. * COMPLEX*16 ZA * INTEGER INCX,N @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 ZX(*) * .. -* +* * *> \par Purpose: * ============= @@ -27,15 +27,41 @@ *> ZSCAL scales a vector by a constant. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in] ZA +*> \verbatim +*> ZA is COMPLEX*16 +*> On entry, ZA specifies the scalar alpha. +*> \endverbatim +*> +*> \param[in,out] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -52,10 +78,10 @@ * ===================================================================== SUBROUTINE ZSCAL(N,ZA,ZX,INCX) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ZA diff --git a/lib/linalg/zsteqr.f b/lib/linalg/zsteqr.f index 33af78e854425201ba713272e0532406d325ad8b..ac47890685db9e93e80bfff546ebfb1327c18500 100644 --- a/lib/linalg/zsteqr.f +++ b/lib/linalg/zsteqr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZSTEQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZSTEQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER COMPZ * INTEGER INFO, LDZ, N @@ -28,7 +28,7 @@ * DOUBLE PRECISION D( * ), E( * ), WORK( * ) * COMPLEX*16 Z( LDZ, * ) * .. -* +* * *> \par Purpose: * ============= @@ -120,22 +120,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER COMPZ diff --git a/lib/linalg/zswap.f b/lib/linalg/zswap.f index ca2f34721192c53ee11ec4e0dc05a722e5e4cfe8..6768d5e6e04e0c8e67065bbb79a7b53b299f6bff 100644 --- a/lib/linalg/zswap.f +++ b/lib/linalg/zswap.f @@ -2,21 +2,21 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZSWAP(N,ZX,INCX,ZY,INCY) -* +* * .. Scalar Arguments .. * INTEGER INCX,INCY,N * .. * .. Array Arguments .. * COMPLEX*16 ZX(*),ZY(*) * .. -* +* * *> \par Purpose: * ============= @@ -26,15 +26,46 @@ *> ZSWAP interchanges two vectors. *> \endverbatim * +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> number of elements in input vector(s) +*> \endverbatim +*> +*> \param[in,out] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> storage spacing between elements of ZX +*> \endverbatim +*> +*> \param[in,out] ZY +*> \verbatim +*> ZY is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> storage spacing between elements of ZY +*> \endverbatim +* * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level1 * @@ -50,10 +81,10 @@ * ===================================================================== SUBROUTINE ZSWAP(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.4.0) -- +* -- Reference BLAS level1 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N diff --git a/lib/linalg/ztpmv.f b/lib/linalg/ztpmv.f index e277ec1a6ed073a08a32c1da030760b6f0290776..65aa2a0abc131fe0ec4222f792ae4d8355c7d9ef 100644 --- a/lib/linalg/ztpmv.f +++ b/lib/linalg/ztpmv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZTPMV(UPLO,TRANS,DIAG,N,AP,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * CHARACTER DIAG,TRANS,UPLO @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 AP(*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -80,7 +80,7 @@ *> *> \param[in] AP *> \verbatim -*> AP is COMPLEX*16 array of DIMENSION at least +*> AP is COMPLEX*16 array, dimension at least *> ( ( n*( n + 1 ) )/2 ). *> Before entry with UPLO = 'U' or 'u', the array AP must *> contain the upper triangular matrix packed sequentially, @@ -96,13 +96,13 @@ *> A are not referenced, but are assumed to be unity. *> \endverbatim *> -*> \param[in] X +*> \param[in,out] X *> \verbatim -*> X is (input/output) COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. On exit, X is overwritten with the -*> tranformed vector x. +*> transformed vector x. *> \endverbatim *> *> \param[in] INCX @@ -115,12 +115,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -142,10 +142,10 @@ * ===================================================================== SUBROUTINE ZTPMV(UPLO,TRANS,DIAG,N,AP,X,INCX) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/ztpsv.f b/lib/linalg/ztpsv.f index 0e75f9facf5641676feca1c69c364372d845f4fc..538888424afe8f4a20b5cb373051d0978fb65668 100644 --- a/lib/linalg/ztpsv.f +++ b/lib/linalg/ztpsv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZTPSV(UPLO,TRANS,DIAG,N,AP,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,N * CHARACTER DIAG,TRANS,UPLO @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 AP(*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -83,7 +83,7 @@ *> *> \param[in] AP *> \verbatim -*> AP is COMPLEX*16 array of DIMENSION at least +*> AP is COMPLEX*16 array, dimension at least *> ( ( n*( n + 1 ) )/2 ). *> Before entry with UPLO = 'U' or 'u', the array AP must *> contain the upper triangular matrix packed sequentially, @@ -101,7 +101,7 @@ *> *> \param[in,out] X *> \verbatim -*> X is COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element right-hand side vector b. On exit, X is overwritten @@ -118,12 +118,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -144,10 +144,10 @@ * ===================================================================== SUBROUTINE ZTPSV(UPLO,TRANS,DIAG,N,AP,X,INCX) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N diff --git a/lib/linalg/ztptri.f b/lib/linalg/ztptri.f index 187c9ccac12875318e0ad719ef2912f6f64640aa..35388194c3aa03214a2fdd2c190bd95a338eb373 100644 --- a/lib/linalg/ztptri.f +++ b/lib/linalg/ztptri.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZTPTRI + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZTPTRI + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZTPTRI( UPLO, DIAG, N, AP, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER DIAG, UPLO * INTEGER INFO, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 AP( * ) * .. -* +* * *> \par Purpose: * ============= @@ -86,12 +86,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * @@ -117,10 +117,10 @@ * ===================================================================== SUBROUTINE ZTPTRI( UPLO, DIAG, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/ztrmm.f b/lib/linalg/ztrmm.f index ba7aead68b5df58348242a8497ded795e1215168..0f445f52a7803fa2c5842d897f9897dc946fc3d1 100644 --- a/lib/linalg/ztrmm.f +++ b/lib/linalg/ztrmm.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) -* +* * .. Scalar Arguments .. * COMPLEX*16 ALPHA * INTEGER LDA,LDB,M,N @@ -18,7 +18,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),B(LDB,*) * .. -* +* * *> \par Purpose: * ============= @@ -109,7 +109,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, k ), where k is m +*> A is COMPLEX*16 array, dimension ( LDA, k ), where k is m *> when SIDE = 'L' or 'l' and is n when SIDE = 'R' or 'r'. *> Before entry with UPLO = 'U' or 'u', the leading k by k *> upper triangular part of the array A must contain the upper @@ -132,9 +132,9 @@ *> then LDA must be at least max( 1, n ). *> \endverbatim *> -*> \param[in] B +*> \param[in,out] B *> \verbatim -*> B is (input/output) COMPLEX*16 array of DIMENSION ( LDB, n ). +*> B is COMPLEX*16 array, dimension ( LDB, N ). *> Before entry, the leading m by n part of the array B must *> contain the matrix B, and on exit is overwritten by the *> transformed matrix. @@ -151,12 +151,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level3 * @@ -177,10 +177,10 @@ * ===================================================================== SUBROUTINE ZTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.4.0) -- +* -- Reference BLAS level3 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA diff --git a/lib/linalg/ztrmv.f b/lib/linalg/ztrmv.f index 8d7974a059112c0604fd63890060bf17a1ff446c..52d1ae6799c5d6dec60b810ba66de046d216227e 100644 --- a/lib/linalg/ztrmv.f +++ b/lib/linalg/ztrmv.f @@ -2,14 +2,14 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * * Definition: * =========== * * SUBROUTINE ZTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) -* +* * .. Scalar Arguments .. * INTEGER INCX,LDA,N * CHARACTER DIAG,TRANS,UPLO @@ -17,7 +17,7 @@ * .. Array Arguments .. * COMPLEX*16 A(LDA,*),X(*) * .. -* +* * *> \par Purpose: * ============= @@ -80,7 +80,7 @@ *> *> \param[in] A *> \verbatim -*> A is COMPLEX*16 array of DIMENSION ( LDA, n ). +*> A is COMPLEX*16 array, dimension ( LDA, N ). *> Before entry with UPLO = 'U' or 'u', the leading n by n *> upper triangular part of the array A must contain the upper *> triangular matrix and the strictly lower triangular part of @@ -101,13 +101,13 @@ *> max( 1, n ). *> \endverbatim *> -*> \param[in] X +*> \param[in,out] X *> \verbatim -*> X is (input/output) COMPLEX*16 array of dimension at least +*> X is COMPLEX*16 array, dimension at least *> ( 1 + ( n - 1 )*abs( INCX ) ). *> Before entry, the incremented array X must contain the n *> element vector x. On exit, X is overwritten with the -*> tranformed vector x. +*> transformed vector x. *> \endverbatim *> *> \param[in] INCX @@ -120,12 +120,12 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16_blas_level2 * @@ -147,10 +147,10 @@ * ===================================================================== SUBROUTINE ZTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level2 routine (version 3.4.0) -- +* -- Reference BLAS level2 routine (version 3.7.0) -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N diff --git a/lib/linalg/zung2l.f b/lib/linalg/zung2l.f index f8fd3667d26cf7230a3402eafe3b4d6c2868ac7a..1a48c4d6bcc44c6aa4c79f91489334d0c31d0494 100644 --- a/lib/linalg/zung2l.f +++ b/lib/linalg/zung2l.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNG2L + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNG2L + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNG2L( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNG2L( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zung2r.f b/lib/linalg/zung2r.f index 63783ac01b65fabbe27433788720a21e1ec7bf9a..4a3fed0f0d8de3e2479a452464b49507b77ac795 100644 --- a/lib/linalg/zung2r.f +++ b/lib/linalg/zung2r.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNG2R + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNG2R + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNG2R( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -102,22 +102,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNG2R( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zungl2.f b/lib/linalg/zungl2.f index 44acba12a6e2885de1ae366063ec4174d1491301..0774cc440541d5db32a99212ec8aeb502e0d6948 100644 --- a/lib/linalg/zungl2.f +++ b/lib/linalg/zungl2.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNGL2 + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNGL2 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNGL2( M, N, K, A, LDA, TAU, WORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, M, N * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -101,22 +101,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date September 2012 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGL2( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.4.2) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* September 2012 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zungql.f b/lib/linalg/zungql.f index 5c77abbd4621d85ac27c9bb672f2f298f720c140..c63a47db56ad0a8973982f7d86266d74ef9992ab 100644 --- a/lib/linalg/zungql.f +++ b/lib/linalg/zungql.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNGQL + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNGQL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, LWORK, M, N * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,22 +116,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/zungqr.f b/lib/linalg/zungqr.f index 6b3e9220cd41560a85637d0cbceedf4a77a4f8f2..5f95b64e883f60a521dd694ac106eaed1b00ae9d 100644 --- a/lib/linalg/zungqr.f +++ b/lib/linalg/zungqr.f @@ -2,31 +2,31 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNGQR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNGQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * INTEGER INFO, K, LDA, LWORK, M, N * .. * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -116,22 +116,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/zungtr.f b/lib/linalg/zungtr.f index 422a55a921ffd166a06c76cd8f37d3da5420feb5..728854332f2aedeb2b84d0163268ffa4755fccc9 100644 --- a/lib/linalg/zungtr.f +++ b/lib/linalg/zungtr.f @@ -2,24 +2,24 @@ * * =========== DOCUMENTATION =========== * -* Online html documentation available at -* http://www.netlib.org/lapack/explore-html/ +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ * *> \htmlonly -*> Download ZUNGTR + dependencies -*> -*> [TGZ] -*> -*> [ZIP] -*> +*> Download ZUNGTR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> *> [TXT] -*> \endhtmlonly +*> \endhtmlonly * * Definition: * =========== * * SUBROUTINE ZUNGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) -* +* * .. Scalar Arguments .. * CHARACTER UPLO * INTEGER INFO, LDA, LWORK, N @@ -27,7 +27,7 @@ * .. Array Arguments .. * COMPLEX*16 A( LDA, * ), TAU( * ), WORK( * ) * .. -* +* * *> \par Purpose: * ============= @@ -111,22 +111,22 @@ * Authors: * ======== * -*> \author Univ. of Tennessee -*> \author Univ. of California Berkeley -*> \author Univ. of Colorado Denver -*> \author NAG Ltd. +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. * -*> \date November 2011 +*> \date December 2016 * *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.4.0) -- +* -- LAPACK computational routine (version 3.7.0) -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* November 2011 +* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F index 8c22f4ca89c4e85ae93a1a78e97155d750a7fc99..c94bce8b445602ca6a8d8d3b0b56028d425f67e4 100644 --- a/lib/meam/meam_setup_done.F +++ b/lib/meam/meam_setup_done.F @@ -232,7 +232,8 @@ c pairs, but need to include NN2 contributions to those pairs as c well. if (lattce_meam(a,b).eq.'b1'.or. $ lattce_meam(a,b).eq.'b2'.or. - $ lattce_meam(a,b).eq.'l12') then + $ lattce_meam(a,b).eq.'l12'.or. + $ lattce_meam(a,b).eq.'dia') then rarat = r*arat c phi_aa @@ -262,7 +263,8 @@ c phi_bb endif if (lattce_meam(a,b).eq.'b1'. - $ or.lattce_meam(a,b).eq.'b2') then + $ or.lattce_meam(a,b).eq.'b2'. + $ or.lattce_meam(a,b).eq.'dia') then c Add contributions to the B1 or B2 potential call get_Zij(Z1,lattce_meam(a,b)) call get_Zij2(Z2,arat,scrn,lattce_meam(a,b), @@ -720,9 +722,9 @@ c neighbor screening function for lattice type "latt" a = sqrt(2.d0) numscr = 4 else if (latt.eq.'dia') then - Zij2 = 0 + Zij2 = 12 a = sqrt(8.d0/3.d0) - numscr = 4 + numscr = 1 if (cmin.lt.0.500001) then c call error('can not do 2NN MEAM for dia') endif diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py index 76c986ef6d5f2409c448f7eeaec92d1e06d759b3..ec70f13f6e7fecc770c4d92ff04cf62b3f585a53 100644 --- a/lib/mscg/Install.py +++ b/lib/mscg/Install.py @@ -30,9 +30,10 @@ make lib-mscg args="-p /usr/local/mscg-release " # use existing MS-CG installati # settings -url = "http://github.com/uchicago-voth/MSCG-release/archive/master.tar.gz" -tarfile = "MS-CG-master.tar.gz" -tardir = "MSCG-release-master" +mscgver = "1.7.3.1" +url = "https://github.com/uchicago-voth/MSCG-release/archive/%s.tar.gz" % mscgver +tarfile = "MS-CG-%s.tar.gz" % mscgver +tardir = "MSCG-release-%s" % mscgver # print error message or help diff --git a/potentials/BNCH.ILP b/potentials/BNCH.ILP new file mode 100644 index 0000000000000000000000000000000000000000..3f38b5e35aea826c1732f61e68830cbedc874db0 --- /dev/null +++ b/potentials/BNCH.ILP @@ -0,0 +1,23 @@ +# Interlayer Potential (ILP) for graphene/graphene, graphene/hBN and hBN/hBN junctions +# +# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018). +# +# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************ +# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut +C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0 +B B 3.143737 9.825139 1.936405 2.7848400 14.495957 15.199263 0.7834022 3.682950 49.498013E3 1.0 2.0 +N N 3.443196 7.084490 1.747349 2.9139991 46.508553 15.020370 0.8008370 3.551843 14.810151E3 1.0 2.0 +H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2 +C B 3.303662 10.54415 2.926741 16.719972 0.3571734 15.305254 0.7001581 3.097327 30.162869E3 1.0 2.0 +C N 3.253564 8.825921 1.059550 18.344740 21.913573 15.000000 0.7234983 3.013117 19.063095E3 1.0 2.0 +B N 3.295257 7.224311 2.872667 1.3715032 0.4347152 14.594578 0.8044028 3.765728 24.669996E3 1.0 2.0 +C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5 +B H 2.718657 9.214551 3.273063 14.015714 14.760509 15.084752 0.7768383 3.640866 7.9642467E3 1.0 1.5 +N H 2.753464 8.226713 3.106390 0.8073613 0.3944229 15.033188 0.7451414 2.733583 3.8461530E3 1.0 1.5 +# Symmetric part +B C 3.303662 10.54415 2.926741 16.719972 0.3571734 15.305254 0.7001581 3.097327 30.162869E3 1.0 2.0 +N C 3.253564 8.825921 1.059550 18.344740 21.913573 15.000000 0.7234983 3.013117 19.063095E3 1.0 2.0 +N B 3.295257 7.224311 2.872667 1.3715032 0.4347152 14.594578 0.8044028 3.765728 24.669996E3 1.0 2.0 +H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 2.2 +H B 2.718657 9.214551 3.273063 14.015714 14.760509 15.084752 0.7768383 3.640866 7.9642467E3 1.0 2.2 +H N 2.753464 8.226713 3.106390 0.8073614 0.3944229 15.033188 0.7451414 2.733583 3.8461530E3 1.0 2.2 diff --git a/potentials/CH.KC b/potentials/CH.KC new file mode 100644 index 0000000000000000000000000000000000000000..d2fe543cf8f11cd21581767edcb0ad0a1e93121f --- /dev/null +++ b/potentials/CH.KC @@ -0,0 +1,9 @@ +# Refined parameters for Kolmogorov-Crespi Potential +# +# Cite as Wengen Ouyang,Davide Mandelli, Michael Urbakh, Oded Hod, arXiv:1806.09555 (2018). +# +# z0 C0 C2 C4 C delta lambda A S rcut +C C 3.328819 21.847167 12.060173 4.711099 6.678908e-4 0.7718101 3.143921 12.660270 1.0 2.0 +C H 3.156492 37.400478 8.3910462e-3 55.06177 5.176215e-5 0.4437309 2.508847 11.479055 1.0 1.5 +H H 2.218816 4.5283006e-5 4.8685736e-5 2.027741 1.193945 0.8968523 0.238105 9.2194017e-5 1.0 1.2 +H C 3.156492 37.400478 8.3910462e-3 55.06177 5.176215e-5 0.4437309 2.508847 11.479055 1.0 2.2 diff --git a/potentials/ffield.reax.lg b/potentials/ffield.reax.lg index e8650d7a9a9a6a88dc7b0889e0d193208570c218..15f303ac12b593c55f2d560d2b9b123def2e3f57 100644 --- a/potentials/ffield.reax.lg +++ b/potentials/ffield.reax.lg @@ -39,7 +39,7 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 5.0000 !Molecular energy (not used) 0.0000 !Molecular energy (not used) 6.9784 !Valency angle conjugation parameter - 7 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# + 5 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;# alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u. cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u. ov/un;val1;n.u.;val3,vval4 @@ -68,17 +68,7 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 1.4703 9.4922 70.0338 8.5146 28.0801 8.5010 0.9745 0.0000 -10.0773 2.7466 1.0338 6.2998 2.8793 1.8000 0.0000 14.0000 180.0000 2.0783 - Si 2.0276 4.0000 28.0600 2.2042 0.1322 0.8218 1.5758 4.0000 - 11.9413 2.0618 4.0000 11.8211 136.4845 1.8038 7.3852 0.0000 - -1.0000 0.0000 126.5331 6.4918 8.5961 0.2368 0.8563 0.0000 - -3.8112 3.1873 1.0338 4.0000 2.5791 0.0000 0.0000 0.0000 - 180.0000 2.2042 - X -0.1000 2.0000 1.0080 2.0000 0.0000 1.0000 -0.1000 6.0000 - 10.0000 2.5000 4.0000 0.0000 0.0000 8.5000 1.5000 0.0000 - -0.1000 0.0000 -2.3700 8.7410 13.3640 0.6690 0.9745 0.0000 - -11.0000 2.7466 1.0338 4.0000 2.8793 0.0000 0.0000 0.0000 - 180.0000 2.0000 - 18 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 + 10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6 pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr 1 1 141.9346 113.4487 67.6027 0.1554 -0.3045 1.0000 30.4515 0.4283 0.0801 -0.2113 8.5395 1.0000 -0.0933 6.6967 1.0000 0.0000 @@ -100,34 +90,14 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 5.1146 1.0000 0.0000 1.0000 -0.0532 5.1189 0.0000 0.0000 2 4 208.0443 0.0000 0.0000 -0.3923 0.0000 1.0000 6.0000 0.3221 10.5505 1.0000 0.0000 1.0000 -0.0690 6.2949 0.0000 0.0000 - 1 5 128.7959 56.4134 39.0716 0.0688 -0.4463 1.0000 31.1766 0.4530 - 0.1955 -0.3587 6.2148 1.0000 -0.0770 6.6386 1.0000 0.0000 - 2 5 128.6090 0.0000 0.0000 -0.5555 0.0000 1.0000 6.0000 0.4721 - 10.8735 1.0000 0.0000 1.0000 -0.0242 9.1937 1.0000 0.0000 - 3 5 0.0000 0.0000 0.0000 0.5563 -0.4038 1.0000 49.5611 0.6000 - 0.4259 -0.4577 12.7569 1.0000 -0.1100 7.1145 1.0000 0.0000 - 4 5 0.0000 0.0000 0.0000 0.4438 -0.2034 1.0000 40.3399 0.6000 - 0.3296 -0.3153 9.1227 1.0000 -0.1805 5.6864 1.0000 0.0000 - 5 5 96.1871 93.7006 68.6860 0.0955 -0.4781 1.0000 17.8574 0.6000 - 0.2723 -0.2373 9.7875 1.0000 -0.0950 6.4757 1.0000 0.0000 - 6 6 109.1904 70.8314 30.0000 0.2765 -0.3000 1.0000 16.0000 0.1583 - 0.2804 -0.1994 8.1117 1.0000 -0.0675 8.2993 0.0000 0.0000 - 2 6 137.1002 0.0000 0.0000 -0.1902 0.0000 1.0000 6.0000 0.4256 - 17.7186 1.0000 0.0000 1.0000 -0.0377 6.4281 0.0000 0.0000 - 3 6 191.1743 52.0733 43.3991 -0.2584 -0.3000 1.0000 36.0000 0.8764 - 1.0248 -0.3658 4.2151 1.0000 -0.5004 4.2605 1.0000 0.0000 - 10 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 + 6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2 1 2 0.0464 1.8296 9.9214 1.0029 -1.0000 -1.0000 0.0000 2 3 0.0403 1.6913 10.4801 0.8774 -1.0000 -1.0000 0.0000 2 4 0.0524 1.7325 10.1306 0.9982 -1.0000 -1.0000 294.9500 1 3 0.1028 1.9277 9.1521 1.3399 1.1104 1.1609 631.8500 1 4 0.2070 1.7366 9.5916 1.2960 1.2008 1.1262 650.0000 3 4 0.0491 1.7025 10.6101 1.3036 1.1276 1.0173 880.0000 - 2 6 0.0470 1.6738 11.6877 1.1931 -1.0000 -1.0000 0.0000 - 3 6 0.1263 1.8163 10.6833 1.6266 1.2052 -1.0000 0.0000 - 1 5 0.1408 1.8161 9.9393 1.7986 1.3021 1.4031 0.0000 - 2 5 0.0895 1.6239 10.0104 1.4640 -1.0000 -1.0000 0.0000 - 62 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 + 41 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2 1 1 1 74.0317 32.2712 0.9501 0.0000 0.1780 10.5736 1.0400 1 1 2 70.6558 14.3658 5.3224 0.0000 0.0058 0.0000 1.0400 2 1 2 76.7339 14.4217 3.3631 0.0000 0.0127 0.0000 1.0400 @@ -164,33 +134,12 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 2 4 2 55.8679 14.2331 2.9225 0.0000 0.2000 0.0000 2.9932 1 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 1 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 - 1 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 3 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 3 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 4 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 2 2 3 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 - 1 1 5 74.4180 33.4273 1.7018 0.1463 0.5000 0.0000 1.6178 - 1 5 1 79.7037 28.2036 1.7073 0.1463 0.5000 0.0000 1.6453 - 2 1 5 63.3289 29.4225 2.1326 0.0000 0.5000 0.0000 3.0000 - 1 5 2 85.9449 38.3109 1.2492 0.0000 0.5000 0.0000 1.1000 - 1 5 5 85.6645 40.0000 2.9274 0.1463 0.5000 0.0000 1.3830 - 2 5 2 83.8555 5.1317 0.4377 0.0000 0.5000 0.0000 3.0000 - 2 5 5 97.0064 32.1121 2.0242 0.0000 0.5000 0.0000 2.8568 - 6 6 6 69.3456 21.7361 1.4283 0.0000 -0.2101 0.0000 1.3241 - 2 6 6 75.6168 21.5317 1.0435 0.0000 2.5179 0.0000 1.0400 - 2 6 2 78.3939 20.9772 0.8630 0.0000 2.8421 0.0000 1.0400 - 3 6 6 70.3016 15.4081 1.3267 0.0000 2.1459 0.0000 1.0400 - 2 6 3 73.8232 16.6592 3.7425 0.0000 0.8613 0.0000 1.0400 - 3 6 3 90.0344 7.7656 1.7264 0.0000 0.7689 0.0000 1.0400 - 6 3 6 22.1715 3.6615 0.3160 0.0000 4.1125 0.0000 1.0400 - 2 3 6 83.7634 5.6693 2.7780 0.0000 1.6982 0.0000 1.0400 - 3 3 6 73.4663 25.0761 0.9143 0.0000 2.2466 0.0000 1.0400 - 2 2 6 0.0000 47.1300 6.0000 0.0000 1.6371 0.0000 1.0400 - 6 2 6 0.0000 31.5209 6.0000 0.0000 1.6371 0.0000 1.0400 - 3 2 6 0.0000 31.0427 4.5625 0.0000 1.6371 0.0000 1.0400 - 2 2 5 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400 - 31 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n + 25 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n 1 1 1 1 0.0000 48.4194 0.3163 -8.6506 -1.7255 0.0000 0.0000 1 1 1 2 0.0000 63.3484 0.2210 -8.8401 -1.8081 0.0000 0.0000 2 1 1 2 0.0000 45.2741 0.4171 -6.9800 -1.2359 0.0000 0.0000 @@ -205,12 +154,6 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 0 4 4 0 2.0000 75.3685 -0.7852 -9.0000 -2.0000 0.0000 0.0000 0 1 1 0 0.0930 18.6070 -1.3191 -9.0000 -1.0000 0.0000 0.0000 4 1 4 4 -2.0000 20.6655 -1.5000 -9.0000 -2.0000 0.0000 0.0000 - 0 1 5 0 4.0885 78.7058 0.1174 -2.1639 0.0000 0.0000 0.0000 - 0 5 5 0 -0.0170 -56.0786 0.6132 -2.2092 0.0000 0.0000 0.0000 - 0 2 5 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 0 6 6 0 0.0000 0.0000 0.1200 -2.4426 0.0000 0.0000 0.0000 - 0 2 6 0 0.0000 0.0000 0.1200 -2.4847 0.0000 0.0000 0.0000 - 0 3 6 0 0.0000 0.0000 0.1200 -2.4703 0.0000 0.0000 0.0000 1 1 3 3 1.2707 21.6200 1.5000 -9.0000 -2.0000 0.0000 0.0000 1 3 3 1 -1.8804 79.9255 -1.5000 -4.1940 -2.0000 0.0000 0.0000 3 1 3 3 -2.0000 22.5092 1.5000 -8.9500 -2.0000 0.0000 0.0000 @@ -222,13 +165,8 @@ DATE: 2012-01-06 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Liu, 1 1 4 3 -2.0000 47.8326 -1.5000 -9.0000 -2.0000 0.0000 0.0000 2 3 4 3 -0.2997 152.9040 -1.5000 -4.4564 -2.0000 0.0000 0.0000 2 4 4 3 0.1040 70.1152 0.5284 -3.5026 -2.0000 0.0000 0.0000 - 9 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 + 4 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1 3 2 3 2.1845 -2.3549 3.0582 19.1627 3 2 4 1.6658 -3.8907 3.0582 19.1627 4 2 3 1.8738 -3.5421 3.0582 19.1627 4 2 4 1.8075 -4.1846 3.0582 19.1627 - 3 2 5 2.6644 -3.0000 3.0000 3.0000 - 4 2 5 4.0476 -3.0000 3.0000 3.0000 - 5 2 3 2.1126 -4.5790 3.0000 3.0000 - 5 2 4 2.2066 -5.7038 3.0000 3.0000 - 5 2 5 1.9461 -4.0000 3.0000 3.0000 diff --git a/python/lammps.py b/python/lammps.py index 417427eb4b715bb64cdabeceb65b93ae036f492c..2f4ffb642ef084fbbd1b7567bfc363220288dafc 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -209,6 +209,7 @@ class lammps(object): self.c_bigint = get_ctypes_int(self.extract_setting("bigint")) self.c_tagint = get_ctypes_int(self.extract_setting("tagint")) self.c_imageint = get_ctypes_int(self.extract_setting("imageint")) + self._installed_packages = None # shut-down LAMMPS instance @@ -235,7 +236,7 @@ class lammps(object): if cmd: cmd = cmd.encode() self.lib.lammps_command(self.lmp,cmd) - if self.uses_exceptions and self.lib.lammps_has_error(self.lmp): + if self.has_exceptions and self.lib.lammps_has_error(self.lmp): sb = create_string_buffer(100) error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100) error_msg = sb.value.decode().strip() @@ -562,13 +563,36 @@ class lammps(object): shrinkexceed) @property - def uses_exceptions(self): + def has_exceptions(self): """ Return whether the LAMMPS shared library was compiled with C++ exceptions handling enabled """ - try: - if self.lib.lammps_has_error: - return True - except(AttributeError): - return False + return self.lib.lammps_config_has_exceptions() != 0 + + @property + def has_gzip_support(self): + return self.lib.lammps_config_has_gzip_support() != 0 + + @property + def has_png_support(self): + return self.lib.lammps_config_has_png_support() != 0 + + @property + def has_jpeg_support(self): + return self.lib.lammps_config_has_jpeg_support() != 0 + + @property + def has_ffmpeg_support(self): + return self.lib.lammps_config_has_ffmpeg_support() != 0 + + @property + def installed_packages(self): + if self._installed_packages is None: + self._installed_packages = [] + npackages = self.lib.lammps_config_package_count() + sb = create_string_buffer(100) + for idx in range(npackages): + self.lib.lammps_config_package_name(idx, sb, 100) + self._installed_packages.append(sb.value.decode()) + return self._installed_packages # ------------------------------------------------------------------------- # ------------------------------------------------------------------------- @@ -684,6 +708,12 @@ class Atom(object): self.lmp.eval("vy[%d]" % self.index), self.lmp.eval("vz[%d]" % self.index)) + @velocity.setter + def velocity(self, value): + self.lmp.set("atom", self.index, "vx", value[0]) + self.lmp.set("atom", self.index, "vy", value[1]) + self.lmp.set("atom", self.index, "vz", value[2]) + @property def force(self): return (self.lmp.eval("fx[%d]" % self.index), @@ -714,6 +744,11 @@ class Atom2D(Atom): return (self.lmp.eval("vx[%d]" % self.index), self.lmp.eval("vy[%d]" % self.index)) + @velocity.setter + def velocity(self, value): + self.lmp.set("atom", self.index, "vx", value[0]) + self.lmp.set("atom", self.index, "vy", value[1]) + @property def force(self): return (self.lmp.eval("fx[%d]" % self.index), diff --git a/src/.gitignore b/src/.gitignore index 3ae05079d211d2c043615cf93be2013449090506..058833ffb38dfca1ea188bebfe5522f943a1c6df 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -5,6 +5,7 @@ /lmp_* /style_*.h +/lmpinstalledpkgs.h /*_gpu.h /*_gpu.cpp @@ -130,6 +131,27 @@ /pair_lj_charmmfsw_coul_long.cpp /pair_lj_charmmfsw_coul_long.h +/atom_vec_spin.cpp +/atom_vec_spin.h +/compute_spin.cpp +/compute_spin.h +/fix_langevin_spin.cpp +/fix_langevin_spin.h +/fix_nve_spin.cpp +/fix_nve_spin.h +/fix_precession_spin.cpp +/fix_precession_spin.h +/pair_spin.cpp +/pair_spin.h +/pair_spin_dmi.cpp +/pair_spin_dmi.h +/pair_spin_exchange.cpp +/pair_spin_exchange.h +/pair_spin_magelec.cpp +/pair_spin_magelec.h +/pair_spin_neel.cpp +/pair_spin_neel.h + /angle_cg_cmm.cpp /angle_cg_cmm.h /angle_charmm.cpp diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp new file mode 100644 index 0000000000000000000000000000000000000000..1e232f0f3f59fbbdab6bf470920bcf2a70ff2036 --- /dev/null +++ b/src/BODY/body_rounded_polygon.cpp @@ -0,0 +1,452 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include "body_rounded_polygon.h" +#include "atom_vec_body.h" +#include "atom.h" +#include "force.h" +#include "domain.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-7 +enum{SPHERE,LINE}; // also in DumpImage + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) : + Body(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command"); + + if (domain->dimension != 2) + error->all(FLERR,"Atom_style body rounded/polygon " + "can only be used in 2d simulations"); + + // nmin and nmax are minimum and maximum number of vertices + + int nmin = force->inumeric(FLERR,arg[1]); + int nmax = force->inumeric(FLERR,arg[2]); + if (nmin <= 0 || nmin > nmax) + error->all(FLERR,"Invalid body rounded/polygon command"); + + size_forward = 0; + + // 1 integer for number of vertices, + // 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends + // 1 double for the enclosing radius + // 1 double for the rounded radius + + size_border = 1 + 3*nmax + 2*nmax + 1 + 1; + + // NOTE: need to set appropriate nnbin param for dcp + + icp = new MyPoolChunk(1,1); + dcp = new MyPoolChunk(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1); + + memory->create(imflag,nmax,"body/rounded/polygon:imflag"); + memory->create(imdata,nmax,7,"body/nparticle:imdata"); +} + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolygon::~BodyRoundedPolygon() +{ + delete icp; + delete dcp; + memory->destroy(imflag); + memory->destroy(imdata); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::nsub(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolygon::coords(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::nedges(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1) return 0; + else if (nvertices == 2) return 1; + return nvertices; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolygon::edges(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue+3*nsub(bonus); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolygon::enclosing_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolygon::rounded_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2+1); + return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::pack_border_body(AtomVecBody::Bonus *bonus, double *buf) +{ + int nsub = bonus->ivalue[0]; + buf[0] = nsub; + memcpy(&buf[1],bonus->dvalue,(3*nsub+2*nsub+1+1)*sizeof(double)); + return 1+(3*nsub+2*nsub+1+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus, + double *buf) +{ + int nsub = static_cast (buf[0]); + bonus->ivalue[0] = nsub; + memcpy(bonus->dvalue,&buf[1],(3*nsub+2*nsub+1+1)*sizeof(double)); + return 1+(3*nsub+2*nsub+1+1); +} + +/* ---------------------------------------------------------------------- + populate bonus data structure with data file values +------------------------------------------------------------------------- */ + +void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, + int *ifile, double *dfile) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles + + if (ninteger != 1) + error->one(FLERR,"Incorrect # of integer values in " + "Bodies section of data file"); + int nsub = ifile[0]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + + // nentries = number of double entries to be read from Body section: + // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius + + int nentries = 6 + 3*nsub + 1; + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + bonus->ninteger = 1; + bonus->ivalue = icp->get(bonus->iindex); + bonus->ivalue[0] = nsub; + bonus->ndouble = 3*nsub + 2*nsub + 1 + 1; + bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex); + + // diagonalize inertia tensor + + double tensor[3][3]; + tensor[0][0] = dfile[0]; + tensor[1][1] = dfile[1]; + tensor[2][2] = dfile[2]; + tensor[0][1] = tensor[1][0] = dfile[3]; + tensor[0][2] = tensor[2][0] = dfile[4]; + tensor[1][2] = tensor[2][1] = dfile[5]; + + double *inertia = bonus->inertia; + double evectors[3][3]; + int ierror = MathExtra::jacobi(tensor,inertia,evectors); + if (ierror) error->one(FLERR, + "Insufficient Jacobi rotations for body nparticle"); + + // if any principal moment < scaled EPSILON, set to 0.0 + + double max; + max = MAX(inertia[0],inertia[1]); + max = MAX(max,inertia[2]); + + if (inertia[0] < EPSILON*max) inertia[0] = 0.0; + if (inertia[1] < EPSILON*max) inertia[1] = 0.0; + if (inertia[2] < EPSILON*max) inertia[2] = 0.0; + + // exyz_space = principal axes in space frame + + double ex_space[3],ey_space[3],ez_space[3]; + + ex_space[0] = evectors[0][0]; + ex_space[1] = evectors[1][0]; + ex_space[2] = evectors[2][0]; + ey_space[0] = evectors[0][1]; + ey_space[1] = evectors[1][1]; + ey_space[2] = evectors[2][1]; + ez_space[0] = evectors[0][2]; + ez_space[1] = evectors[1][2]; + ez_space[2] = evectors[2][2]; + + // enforce 3 evectors as a right-handed coordinate system + // flip 3rd vector if needed + + double cross[3]; + MathExtra::cross3(ex_space,ey_space,cross); + if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space); + + // create initial quaternion + + MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat); + + // bonus->dvalue = the first 3*nsub elements are sub-particle displacements + // find the enclosing radius of the body from the maximum displacement + + int i,m; + double delta[3], rsq, erad, rrad; + double erad2 = 0; + int j = 6; + int k = 0; + for (i = 0; i < nsub; i++) { + delta[0] = dfile[j]; + delta[1] = dfile[j+1]; + delta[2] = dfile[j+2]; + MathExtra::transpose_matvec(ex_space,ey_space,ez_space, + delta,&bonus->dvalue[k]); + rsq = delta[0] * delta[0] + delta[1] * delta[1] + + delta[2] * delta[2]; + if (rsq > erad2) erad2 = rsq; + j += 3; + k += 3; + } + + // .. the next 2*nsub elements are edge ends + + int nedges; + if (nsub == 1) { // spheres + nedges = 0; + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 0; + k += 2; + + // the last element of bonus->dvalue is the rounded & enclosing radius + + rrad = 0.5 * dfile[j]; + bonus->dvalue[k] = rrad; + erad = rrad; + + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad; + + } else if (nsub == 2) { // rods + nedges = 1; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 1; + k += 2; + } + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + + } else { // polygons + nedges = nsub; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = i; + m = i+1; + if (m == nedges) m = 0; + *(&bonus->dvalue[k]+1) = m; + k += 2; + } + + // the next to last element is the enclosing radius + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + } +} + +/* ---------------------------------------------------------------------- + return radius of body particle defined by ifile/dfile params + params are ordered as in data file + called by Molecule class which needs single body size +------------------------------------------------------------------------- */ + +double BodyRoundedPolygon::radius_body(int ninteger, int ndouble, + int *ifile, double *dfile) +{ + int nsub = ifile[0]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + if (ndouble != 6 + 3*nsub + 1) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + // sub-particle coords are relative to body center at (0,0,0) + // offset = 6 for sub-particle coords + + double onerad; + double maxrad = 0.0; + double delta[3]; + + int offset = 6; + for (int i = 0; i < nsub; i++) { + delta[0] = dfile[offset]; + delta[1] = dfile[offset+1]; + delta[2] = dfile[offset+2]; + offset += 3; + onerad = MathExtra::len3(delta); + maxrad = MAX(maxrad,onerad); + } + + // add in radius of rounded corners + + return maxrad + 0.5*dfile[offset]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::noutcol() +{ + // the number of columns for the vertex coordinates + + return 3; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::noutrow(int ibonus) +{ + // only return the first nsub rows for the vertex coordinates + + return avec->bonus[ibonus].ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +void BodyRoundedPolygon::output(int ibonus, int m, double *values) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*m],values); + + double *x = atom->x[bonus->ilocal]; + values[0] += x[0]; + values[1] += x[1]; + values[2] += x[2]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolygon::image(int ibonus, double flag1, double flag2, + int *&ivec, double **&darray) +{ + int j; + double p[3][3]; + double *x, rrad; + + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int n = bonus->ivalue[0]; + + if (n == 1) { + for (int i = 0; i < n; i++) { + imflag[i] = SPHERE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = enclosing_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][3] = 2*rrad; + else imdata[i][3] = flag1; + } + + } else { + + // first end pt of each line + + for (int i = 0; i < n; i++) { + imflag[i] = LINE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = rounded_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][6] = 2*rrad; + else imdata[i][6] = flag1; + } + + // second end pt of each line + + for (int i = 0; i < n; i++) { + j = i+1; + if (j == n) j = 0; + imdata[i][3] = imdata[j][0]; + imdata[i][4] = imdata[j][1]; + imdata[i][5] = imdata[j][2]; + } + } + + ivec = imflag; + darray = imdata; + return n; +} diff --git a/src/BODY/body_rounded_polygon.h b/src/BODY/body_rounded_polygon.h new file mode 100644 index 0000000000000000000000000000000000000000..b6f45c5cf551cc35fc1ff2d817684f5250cf23f4 --- /dev/null +++ b/src/BODY/body_rounded_polygon.h @@ -0,0 +1,86 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BODY_CLASS + +BodyStyle(rounded/polygon,BodyRoundedPolygon) + +#else + +#ifndef LMP_BODY_ROUNDED_POLYGON_H +#define LMP_BODY_ROUNDED_POLYGON_H + +#include "body.h" +#include "atom_vec_body.h" + +namespace LAMMPS_NS { + +class BodyRoundedPolygon : public Body { + public: + BodyRoundedPolygon(class LAMMPS *, int, char **); + ~BodyRoundedPolygon(); + int nsub(struct AtomVecBody::Bonus *); + double *coords(struct AtomVecBody::Bonus *); + int nedges(struct AtomVecBody::Bonus *); + double *edges(struct AtomVecBody::Bonus *); + double enclosing_radius(struct AtomVecBody::Bonus *); + double rounded_radius(struct AtomVecBody::Bonus *); + + int pack_border_body(struct AtomVecBody::Bonus *, double *); + int unpack_border_body(struct AtomVecBody::Bonus *, double *); + void data_body(int, int, int, int *, double *); + double radius_body(int, int, int *, double *); + + int noutrow(int); + int noutcol(); + void output(int, int, double *); + int image(int, double, double, int *&, double **&); + + private: + int *imflag; + double **imdata; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Invalid body rounded/polygon command + +Arguments in atom-style command are not correct. + +E: Invalid format in Bodies section of data file + +The specified number of integer or floating point values does not +appear. + +E: Incorrect # of integer values in Bodies section of data file + +See doc page for body style. + +E: Incorrect integer value in Bodies section of data file + +See doc page for body style. + +E: Incorrect # of floating-point values in Bodies section of data file + +See doc page for body style. + +E: Insufficient Jacobi rotations for body nparticle + +Eigensolve for rigid body was not sufficiently accurate. + +*/ diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6a9b97ae2348ec344b75656afbb3d5261282e5b5 --- /dev/null +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -0,0 +1,526 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include "body_rounded_polyhedron.h" +#include "atom_vec_body.h" +#include "atom.h" +#include "force.h" +#include "domain.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define EPSILON 1.0e-7 +#define MAX_FACE_SIZE 4 // maximum number of vertices per face (for now) + +enum{SPHERE,LINE}; // also in DumpImage + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg) : + Body(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command"); + + // nmin and nmax are minimum and maximum number of vertices + + int nmin = force->inumeric(FLERR,arg[1]); + int nmax = force->inumeric(FLERR,arg[2]); + if (nmin <= 0 || nmin > nmax) + error->all(FLERR,"Invalid body rounded/polyhedron command"); + + size_forward = 0; + + // 3 integers: 1 for no. of vertices, 1 for no. of edges, 1 for no. of faces + // 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends + + // (MAX_FACE_SIZE+1)*nmax for faces + // 1 double for the enclosing radius + // 1 double for the rounded radius + + size_border = 3 + 3*nmax + 2*nmax + MAX_FACE_SIZE*nmax + 1 + 1; + + // NOTE: need to set appropriate nnbin param for dcp + + icp = new MyPoolChunk(1,3); + dcp = new MyPoolChunk(3*nmin+2+1+1, + 3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1); + + memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag"); + memory->create(imdata,2*nmax,7,"body/polyhedron:imdata"); +} + +/* ---------------------------------------------------------------------- */ + +BodyRoundedPolyhedron::~BodyRoundedPolyhedron() +{ + delete icp; + delete dcp; + memory->destroy(imflag); + memory->destroy(imdata); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nsub(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::coords(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + int nedges = bonus->ivalue[1]; + int nfaces = bonus->ivalue[2]; + if (nvertices == 1) return 0; + else if (nvertices == 2) return 1; + return nedges; //(nvertices+nfaces-2); // Euler's polyon formula: V-E+F=2 +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus) +{ + return bonus->dvalue+3*nsub(bonus); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus) +{ + return bonus->ivalue[2]; +} + +/* ---------------------------------------------------------------------- */ + +double *BodyRoundedPolyhedron::faces(AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) return NULL; + return bonus->dvalue+3*nsub(bonus)+2*nedges(bonus); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2); + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + MAX_FACE_SIZE*nfaces(bonus)); +} + +/* ---------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::rounded_radius(struct AtomVecBody::Bonus *bonus) +{ + int nvertices = bonus->ivalue[0]; + if (nvertices == 1 || nvertices == 2) + return *(bonus->dvalue+3*nsub(bonus)+2+1); + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + MAX_FACE_SIZE*nfaces(bonus)+1); +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::pack_border_body(AtomVecBody::Bonus *bonus, double *buf) +{ + int nsub = bonus->ivalue[0]; + int ned = bonus->ivalue[1]; + int nfac = bonus->ivalue[2]; + buf[0] = nsub; + buf[1] = ned; + buf[2] = nfac; + int ndouble; + if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1; + else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1; + memcpy(&buf[3],bonus->dvalue,ndouble*sizeof(double)); + return 3+ndouble; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::unpack_border_body(AtomVecBody::Bonus *bonus, + double *buf) +{ + int nsub = static_cast (buf[0]); + int ned = static_cast (buf[1]); + int nfac = static_cast (buf[2]); + bonus->ivalue[0] = nsub; + bonus->ivalue[1] = ned; + bonus->ivalue[2] = nfac; + int ndouble; + if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1; + else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1; + memcpy(bonus->dvalue,&buf[3],ndouble*sizeof(double)); + return 3+ndouble; +} + +/* ---------------------------------------------------------------------- + populate bonus data structure with data file values +------------------------------------------------------------------------- */ + +void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, + int *ifile, double *dfile) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + // set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles + + if (ninteger != 3) + error->one(FLERR,"Incorrect # of integer values in " + "Bodies section of data file"); + int nsub = ifile[0]; + int ned = ifile[1]; + int nfac = ifile[2]; + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + + // nentries = number of double entries to be read from Body section: + // nsub == 1 || nsub == 2 || nsub == 3: + // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius + // nsub > 3: + // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges + + // 3*nfaces + 1 for rounded radius + + int nedges,nentries; + if (nsub == 1 || nsub == 2) { + nentries = 6 + 3*nsub + 1; + } else { + nedges = ned; //nsub + nfac - 2; + nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1; + } + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + bonus->ninteger = 3; + bonus->ivalue = icp->get(bonus->iindex); + bonus->ivalue[0] = nsub; + bonus->ivalue[1] = ned; + bonus->ivalue[2] = nfac; + if (nsub == 1 || nsub == 2) bonus->ndouble = 3*nsub + 2*nsub + 1 + 1; + else bonus->ndouble = 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1 + 1; + bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex); + + // diagonalize inertia tensor + + double tensor[3][3]; + tensor[0][0] = dfile[0]; + tensor[1][1] = dfile[1]; + tensor[2][2] = dfile[2]; + tensor[0][1] = tensor[1][0] = dfile[3]; + tensor[0][2] = tensor[2][0] = dfile[4]; + tensor[1][2] = tensor[2][1] = dfile[5]; + + double *inertia = bonus->inertia; + double evectors[3][3]; + int ierror = MathExtra::jacobi(tensor,inertia,evectors); + if (ierror) error->one(FLERR, + "Insufficient Jacobi rotations for body nparticle"); + + // if any principal moment < scaled EPSILON, set to 0.0 + + double max; + max = MAX(inertia[0],inertia[1]); + max = MAX(max,inertia[2]); + + if (inertia[0] < EPSILON*max) inertia[0] = 0.0; + if (inertia[1] < EPSILON*max) inertia[1] = 0.0; + if (inertia[2] < EPSILON*max) inertia[2] = 0.0; + + // exyz_space = principal axes in space frame + + double ex_space[3],ey_space[3],ez_space[3]; + + ex_space[0] = evectors[0][0]; + ex_space[1] = evectors[1][0]; + ex_space[2] = evectors[2][0]; + ey_space[0] = evectors[0][1]; + ey_space[1] = evectors[1][1]; + ey_space[2] = evectors[2][1]; + ez_space[0] = evectors[0][2]; + ez_space[1] = evectors[1][2]; + ez_space[2] = evectors[2][2]; + + // enforce 3 evectors as a right-handed coordinate system + // flip 3rd vector if needed + + double cross[3]; + MathExtra::cross3(ex_space,ey_space,cross); + if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space); + + // create initial quaternion + + MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat); + + // bonus->dvalue = the first 3*nsub elements are sub-particle displacements + // find the enclosing radius of the body from the maximum displacement + + int i,m; + double delta[3], rsq, erad, rrad; + double erad2 = 0; + int j = 6; + int k = 0; + for (i = 0; i < nsub; i++) { + delta[0] = dfile[j]; + delta[1] = dfile[j+1]; + delta[2] = dfile[j+2]; + MathExtra::transpose_matvec(ex_space,ey_space,ez_space, + delta,&bonus->dvalue[k]); + rsq = delta[0] * delta[0] + delta[1] * delta[1] + + delta[2] * delta[2]; + if (rsq > erad2) erad2 = rsq; + j += 3; + k += 3; + } + + // .. the next 2*nsub elements are edge ends + + if (nsub == 1) { // spheres + nedges = 0; + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 0; + k += 2; + + rrad = 0.5 * dfile[j]; + bonus->dvalue[k] = rrad; + erad = rrad; // enclosing radius = rounded_radius + + // the last element of bonus->dvalue is the rounded radius + + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad; + + } else if (nsub == 2) { // rods + nedges = 1; + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = 0; + *(&bonus->dvalue[k]+1) = 1; + k += 2; + } + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element of bonus->dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + + } else { // polyhedra + + // edges + + for (i = 0; i < nedges; i++) { + bonus->dvalue[k] = dfile[j]; + *(&bonus->dvalue[k]+1) = dfile[j+1]; + k += 2; + j += 2; + } + + // faces + + for (i = 0; i < nfac; i++) { + for (m = 0; m < MAX_FACE_SIZE; m++) + *(&bonus->dvalue[k]+m) = dfile[j+m]; + k += MAX_FACE_SIZE; + j += MAX_FACE_SIZE; + } + + // the next to last element is the enclosing radius + + erad = sqrt(erad2); + bonus->dvalue[k] = erad; + + // the last element bonus-> dvalue is the rounded radius + + rrad = 0.5 * dfile[j]; + k++; + bonus->dvalue[k] = rrad; + + atom->radius[bonus->ilocal] = erad + rrad; + } +} + +/* ---------------------------------------------------------------------- + return radius of body particle defined by ifile/dfile params + params are ordered as in data file + called by Molecule class which needs single body size +------------------------------------------------------------------------- */ + +double BodyRoundedPolyhedron::radius_body(int ninteger, int ndouble, + int *ifile, double *dfile) +{ + int nsub = ifile[0]; + int ned = ifile[1]; + int nfac = ifile[2]; + int nedges = ned; //nsub + nfac - 2; + + int nentries; + if (nsub == 1 || nsub == 2) nentries = 6 + 3*nsub + 1; + else nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1; + + if (nsub < 1) + error->one(FLERR,"Incorrect integer value in " + "Bodies section of data file"); + if (ndouble != nentries) + error->one(FLERR,"Incorrect # of floating-point values in " + "Bodies section of data file"); + + // sub-particle coords are relative to body center at (0,0,0) + // offset = 6 for sub-particle coords + + double onerad; + double maxrad = 0.0; + double delta[3]; + + int offset = 6; + for (int i = 0; i < nsub; i++) { + delta[0] = dfile[offset]; + delta[1] = dfile[offset+1]; + delta[2] = dfile[offset+2]; + offset += 3; + onerad = MathExtra::len3(delta); + maxrad = MAX(maxrad,onerad); + } + + if (nsub > 2) offset += (2*nedges+MAX_FACE_SIZE*nfac); + + // add in radius of rounded corners + + return maxrad + 0.5*dfile[offset]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::noutcol() +{ + // the number of columns for the vertex coordinates + + return 3; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::noutrow(int ibonus) +{ + // only return the first nsub rows for the vertex coordinates + + return avec->bonus[ibonus].ivalue[0]; +} + +/* ---------------------------------------------------------------------- */ + +void BodyRoundedPolyhedron::output(int ibonus, int m, double *values) +{ + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*m],values); + + double *x = atom->x[bonus->ilocal]; + values[0] += x[0]; + values[1] += x[1]; + values[2] += x[2]; +} + +/* ---------------------------------------------------------------------- */ + +int BodyRoundedPolyhedron::image(int ibonus, double flag1, double flag2, + int *&ivec, double **&darray) +{ + int j, nelements; + double p[3][3]; + double *x, rrad; + + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nvertices = bonus->ivalue[0]; + + if (nvertices == 1) { // spheres + + for (int i = 0; i < nvertices; i++) { + imflag[i] = SPHERE; + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]); + + rrad = enclosing_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + if (flag1 <= 0) imdata[i][3] = 2*rrad; + else imdata[i][3] = flag1; + } + + nelements = nvertices; + } else { + int nfaces = bonus->ivalue[2]; + int nedges = bonus->ivalue[1]; //nvertices + nfaces - 2; + if (nvertices == 2) nedges = 1; // special case: rods + double* edge_ends = &bonus->dvalue[3*nvertices]; + int pt1, pt2; + + for (int i = 0; i < nedges; i++) { + imflag[i] = LINE; + + pt1 = static_cast(edge_ends[2*i]); + pt2 = static_cast(edge_ends[2*i+1]); + + MathExtra::quat_to_mat(bonus->quat,p); + MathExtra::matvec(p,&bonus->dvalue[3*pt1],imdata[i]); + MathExtra::matvec(p,&bonus->dvalue[3*pt2],&imdata[i][3]); + + rrad = rounded_radius(bonus); + x = atom->x[bonus->ilocal]; + imdata[i][0] += x[0]; + imdata[i][1] += x[1]; + imdata[i][2] += x[2]; + imdata[i][3] += x[0]; + imdata[i][4] += x[1]; + imdata[i][5] += x[2]; + + if (flag1 <= 0) imdata[i][6] = 2*rrad; + else imdata[i][6] = flag1; + } + + nelements = nedges; + } + + ivec = imflag; + darray = imdata; + return nelements; +} diff --git a/src/BODY/body_rounded_polyhedron.h b/src/BODY/body_rounded_polyhedron.h new file mode 100644 index 0000000000000000000000000000000000000000..e5b15fd8f93f6c0a65d896262a52dd85d7569c41 --- /dev/null +++ b/src/BODY/body_rounded_polyhedron.h @@ -0,0 +1,88 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BODY_CLASS + +BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron) + +#else + +#ifndef LMP_BODY_ROUNDED_POLYHEDRON_H +#define LMP_BODY_ROUNDED_POLYHEDRON_H + +#include "body.h" +#include "atom_vec_body.h" + +namespace LAMMPS_NS { + +class BodyRoundedPolyhedron : public Body { + public: + BodyRoundedPolyhedron(class LAMMPS *, int, char **); + ~BodyRoundedPolyhedron(); + int nsub(struct AtomVecBody::Bonus *); + double *coords(struct AtomVecBody::Bonus *); + int nedges(struct AtomVecBody::Bonus *); + double *edges(struct AtomVecBody::Bonus *); + int nfaces(struct AtomVecBody::Bonus *); + double *faces(struct AtomVecBody::Bonus *); + double enclosing_radius(struct AtomVecBody::Bonus *); + double rounded_radius(struct AtomVecBody::Bonus *); + + int pack_border_body(struct AtomVecBody::Bonus *, double *); + int unpack_border_body(struct AtomVecBody::Bonus *, double *); + void data_body(int, int, int, int *, double *); + double radius_body(int, int, int *, double *); + + int noutrow(int); + int noutcol(); + void output(int, int, double *); + int image(int, double, double, int *&, double **&); + + private: + int *imflag; + double **imdata; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Invalid body rounded/polyhedron command + +Arguments in atom-style command are not correct. + +E: Invalid format in Bodies section of data file + +The specified number of integer or floating point values does not +appear. + +E: Incorrect # of integer values in Bodies section of data file + +See doc page for body style. + +E: Incorrect integer value in Bodies section of data file + +See doc page for body style. + +E: Incorrect # of floating-point values in Bodies section of data file + +See doc page for body style. + +E: Insufficient Jacobi rotations for body rounded/polyhedron + +Eigensolve for rigid body was not sufficiently accurate. + +*/ diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0e7aaea1e1a2a6c9ac0060c092eb703eaf90f2b6 --- /dev/null +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -0,0 +1,829 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_wall_body_polygon.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polygon.h" +#include "domain.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "respa.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{XPLANE=0,YPLANE=1,ZCYLINDER}; // XYZ PLANE need to be 0,1,2 +enum{HOOKE,HOOKE_HISTORY}; + +enum {INVALID=0,NONE=1,VERTEX=2}; +enum {FAR=0,XLO,XHI,YLO,YHI}; + +//#define _POLYGON_DEBUG +#define DELTA 10000 +#define EPSILON 1e-2 +#define BIG 1.0e20 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polygon command"); + + if (!atom->body_flag) + error->all(FLERR,"Fix wall/body/polygon requires " + "atom style body/rounded/polygon"); + + restart_peratom = 1; + create_attribute = 1; + + // wall/particle coefficients + + kn = force->numeric(FLERR,arg[3]); + + c_n = force->numeric(FLERR,arg[4]); + if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n; + else c_t = force->numeric(FLERR,arg[5]); + + if (kn < 0.0 || c_n < 0.0 || c_t < 0.0) + error->all(FLERR,"Illegal fix wall/body/polygon command"); + + // wallstyle args + + int iarg = 6; + if (strcmp(arg[iarg],"xplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = XPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"yplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = YPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"zcylinder") == 0) { + if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/body/polygon command"); + wallstyle = ZCYLINDER; + lo = hi = 0.0; + cylradius = force->numeric(FLERR,arg[iarg+1]); + iarg += 2; + } + + // check for trailing keyword/values + + wiggle = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"wiggle") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polygon command"); + if (strcmp(arg[iarg+1],"x") == 0) axis = 0; + else if (strcmp(arg[iarg+1],"y") == 0) axis = 1; + else if (strcmp(arg[iarg+1],"z") == 0) axis = 2; + else error->all(FLERR,"Illegal fix wall/body/polygon command"); + amplitude = force->numeric(FLERR,arg[iarg+2]); + period = force->numeric(FLERR,arg[iarg+3]); + wiggle = 1; + iarg += 4; + } else error->all(FLERR,"Illegal fix wall/body/polygon command"); + } + + if (wallstyle == XPLANE && domain->xperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == YPLANE && domain->yperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic)) + error->all(FLERR,"Cannot use wall in periodic dimension"); + + if (wiggle && wallstyle == ZCYLINDER && axis != 2) + error->all(FLERR,"Invalid wiggle direction for fix wall/body/polygon"); + + // setup oscillations + + if (wiggle) omega = 2.0*MY_PI / period; + + time_origin = update->ntimestep; + + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolygon::~FixWallBodyPolygon() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); +} + +/* ---------------------------------------------------------------------- */ + +int FixWallBodyPolygon::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::init() +{ + dt = update->dt; + + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polygon") != 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "body style rounded/polygon"); + bptr = (BodyRoundedPolygon *) avec->bptr; + + // set pairstyle from body/polygonular pair style + + if (force->pair_match("body/rounded/polygon",1)) + pairstyle = HOOKE; + else error->all(FLERR,"Fix wall/body/polygon is incompatible with Pair style"); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::post_force(int vflag) +{ + double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos; + int i,ni,npi,ifirst,nei,iefirst,side; + double facc[3]; + + // set position of wall to initial settings and velocity to 0.0 + // if wiggle, set wall position and velocity accordingly + + double wlo = lo; + double whi = hi; + vwall[0] = vwall[1] = vwall[2] = 0.0; + if (wiggle) { + double arg = omega * (update->ntimestep - time_origin) * dt; + if (wallstyle == axis) { + wlo = lo + amplitude - amplitude*cos(arg); + whi = hi + amplitude - amplitude*cos(arg); + } + vwall[axis] = amplitude*omega*sin(arg); + } + + // loop over all my atoms + // rsq = distance from wall + // dx,dy,dz = signed distance from wall + // for rotating cylinder, reset vwall based on particle position + // skip atom if not close enough to wall + // if wall was set to NULL, it's skipped since lo/hi are infinity + // compute force and torque on atom if close enough to wall + // via wall potential matched to pair potential + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *body = atom->body; + double *radius = atom->radius; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"fix:dnum"); + memory->create(dfirst,nmax,"fix:dfirst"); + memory->create(ednum,nmax,"fix:ednum"); + memory->create(edfirst,nmax,"fix:edfirst"); + memory->create(enclosing_radius,nmax,"fix:enclosing_radius"); + memory->create(rounded_radius,nmax,"fix:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = 0; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + if (body[i] < 0) continue; + + dx = dy = dz = 0.0; + side = FAR; + if (wallstyle == XPLANE) { + del1 = x[i][0] - wlo; + del2 = whi - x[i][0]; + if (del1 < del2) { + dx = del1; + wall_pos = wlo; + side = XLO; + } else { + dx = -del2; + wall_pos = whi; + side = XHI; + } + } else if (wallstyle == YPLANE) { + del1 = x[i][1] - wlo; + del2 = whi - x[i][1]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = YLO; + } else { + dy = -del2; + wall_pos = whi; + side = YHI; + } + } else if (wallstyle == ZCYLINDER) { + delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]); + delr = cylradius - delxy; + if (delr > eradi) dz = cylradius; + else { + dx = -delr/delxy * x[i][0]; + dy = -delr/delxy * x[i][1]; + } + } + + rsq = dx*dx + dy*dy + dz*dz; + if (rsq > radius[i]*radius[i]) continue; + + double r = sqrt(rsq); + double rsqinv = 1.0 / rsq; + + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + } + + int interact, num_contacts, done; + double delta_a, delta_ua, j_a; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + facc[0] = facc[1] = facc[2] = 0; + interact = vertex_against_wall(i, wall_pos, x, f, torque, side, + contact_list, num_contacts, facc); + + if (num_contacts >= 2) { + + // find the first two distinct contacts + + done = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + delta_a = contact_separation(contact_list[m], contact_list[n]); + if (delta_a > 0) { + delta_ua = 1.0; + j_a = delta_a / (EFF_CONTACTS * delta_ua); + if (j_a < 1.0) j_a = 1.0; + + // scale the force at both contacts + + contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, + vwall, facc); + contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, + vwall, facc); + done = 1; + break; + } + } + if (done == 1) break; + } + + } else if (num_contacts == 1) { + + // if there's only one contact, it should be handled here + // since forces/torques have not been accumulated from vertex2wall() + + contact_forces(contact_list[0], 1.0, x, v, angmom, f, torque, + vwall, facc); + } + } // group bit + } +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::reset_dt() +{ + dt = update->dt; +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* vertices = bptr->edges(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,6,"fix:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, + // the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,5,"fix:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(vertices[2*m+0]); + edge[nedge][1] = static_cast(vertices[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + nedge++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + Return: + contact_list = list of contacts between i and the wall + num_contacts = number of contacts between i's vertices and the wall + interact = 0 no interaction with the wall + 1 there's at least one vertex of i interacts + with the wall +---------------------------------------------------------------------- */ + +int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos, + double** x, double** f, double** torque, int side, + Contact* contact_list, int &num_contacts, double* facc) +{ + int ni, npi, ifirst, interact; + double xpi[3], xpj[3], dist, eradi, rradi; + double fx, fy, fz, rx, ry, rz; + int nlocal = atom->nlocal; + + npi = dnum[i]; + ifirst = dfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + interact = 0; + + // loop through body i's vertices + + for (ni = 0; ni < npi; ni++) { + + // convert body-fixed coordinates to space-fixed, xi + + xpi[0] = x[i][0] + discrete[ifirst+ni][0]; + xpi[1] = x[i][1] + discrete[ifirst+ni][1]; + xpi[2] = x[i][2] + discrete[ifirst+ni][2]; + + int mode, contact, p2vertex; + double d, R, hi[3], t, delx, dely, delz, fpair, shift; + double xj[3], rij; + + // compute the distance from the vertex xpi to the wall + + mode = compute_distance_to_wall(xpi, rradi, wall_pos, side, + d, hi, contact); + + if (mode == INVALID || mode == NONE) continue; + + if (mode == VERTEX) { + + interact = 1; + + // vertex i interacts with the wall + + delx = xpi[0] - hi[0]; + dely = xpi[1] - hi[1]; + delz = xpi[2] - hi[2]; + + // R = surface separation = d shifted by the rounded radius + // R = d - p1.rounded_radius; + // note: the force is defined for R, not for d + // R > 0: no interaction + // R <= 0: deformation between vertex i and the wall + + rij = sqrt(delx*delx + dely*dely + delz*delz); + R = rij - rradi; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -kn * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and wall:", ni); + printf(" mode = %d; contact = %d; d = %f; rij = %f\n", + mode, contact, d, rij); + printf(" R = %f\n", R); + printf(" fpair = %f\n", fpair); + #endif + + if (contact == 1) { + + // vertex ni of body i contacts with edge nj of body j + + contact_list[num_contacts].ibody = i; + contact_list[num_contacts].jbody = -1; + contact_list[num_contacts].vertex = ni; + contact_list[num_contacts].edge = -1; + contact_list[num_contacts].xv[0] = xpi[0]; + contact_list[num_contacts].xv[1] = xpi[1]; + contact_list[num_contacts].xv[2] = xpi[2]; + contact_list[num_contacts].xe[0] = hi[0]; + contact_list[num_contacts].xe[1] = hi[1]; + contact_list[num_contacts].xe[2] = hi[2]; + contact_list[num_contacts].separation = R; + num_contacts++; + + // store forces to vertex ni to be rescaled later, + // if there are 2 contacts + + discrete[ifirst+ni][3] = fx; + discrete[ifirst+ni][4] = fy; + discrete[ifirst+ni][5] = fz; + + #ifdef _POLYGON_DEBUG + printf(" Stored forces at vertex and edge for accumulating later.\n"); + #endif + + } else { // no contact + + // accumulate force and torque to the body directly + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + } // end if contact + + } // end if mode + + } // end for looping through the vertices of body i + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between a vertex to the wall + another body + Input: + x0 = coordinate of the tested vertex + rradi = rounded radius of the vertex + wall_pos = position of the wall + Output: + d = Distance from a point x0 to an wall + hi = coordinates of the projection of x0 on the wall + contact = 0 no contact between the queried vertex and the wall + 1 contact detected + return NONE if there is no interaction + EDGE if the tested vertex interacts with the wall +------------------------------------------------------------------------- */ + +int FixWallBodyPolygon::compute_distance_to_wall(double* x0, double rradi, + double wall_pos, int side, double &d, double hi[3], int &contact) +{ + int mode; + double delxy; + + // h0 = position of the projection of x0 on the wall + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = x0[1]; + hi[2] = x0[2]; + } else if (wallstyle == YPLANE) { + hi[0] = x0[0]; + hi[1] = wall_pos; + hi[2] = x0[2]; + } else if (wallstyle == ZCYLINDER) { + delxy = sqrt(x0[0]*x0[0] + x0[1]*x0[1]); + hi[0] = x0[0]*cylradius/delxy; + hi[1] = x0[1]*cylradius/delxy; + hi[2] = x0[2]; + } + + // distance from x0 to the wall = distance from x0 to hi + + distance(hi, x0, d); + + // determine the interaction mode + + if (d < rradi) { + mode = VERTEX; + contact = 1; + } else { + mode = NONE; + if (side == XLO) { + if (x0[0] < wall_pos) mode = VERTEX; + } else if (side == XHI) { + if (x0[0] > wall_pos) mode = VERTEX; + } else if (side == YLO) { + if (x0[1] < wall_pos) mode = VERTEX; + } else if (side == YHI) { + if (x0[1] > wall_pos) mode = VERTEX; + } + } + + if (mode == NONE) contact = 0; + else contact = 1; + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute the contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * vrt) +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double* vwall, double* facc) +{ + int ibody,ibonus,ifirst, jefirst, ni; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the vertex to the point on the wall + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts +------------------------------------------------------------------------- */ + +double FixWallBodyPolygon::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void FixWallBodyPolygon::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolygon::distance(const double* x2, const double* x1, + double& r) { + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} diff --git a/src/BODY/fix_wall_body_polygon.h b/src/BODY/fix_wall_body_polygon.h new file mode 100644 index 0000000000000000000000000000000000000000..b71dcb06832ba312fb6a3853d185d1c37d23d314 --- /dev/null +++ b/src/BODY/fix_wall_body_polygon.h @@ -0,0 +1,131 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(wall/body/polygon,FixWallBodyPolygon) + +#else + +#ifndef LMP_FIX_WALL_BODY_POLYGON_H +#define LMP_FIX_WALL_BODY_POLYGON_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixWallBodyPolygon : public Fix { + public: + FixWallBodyPolygon(class LAMMPS *, int, char **); + virtual ~FixWallBodyPolygon(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + void reset_dt(); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + int wallstyle,pairstyle,wiggle,axis; + double kn; // normal repulsion strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double lo,hi,cylradius; + double amplitude,period,omega; + double dt; + int time_origin; + + class AtomVecBody *avec; + class BodyRoundedPolygon *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + + void body2space(int); + + int vertex_against_wall(int ibody, double wall_pos, double** x, + double** f, double** torque, int side, + Contact* contact_list, int &num_contacts, + double* facc); + + int compute_distance_to_wall(double* x0, double rradi, double wall_pos, + int side, double &d, double hi[3], int &contact); + double contact_separation(const Contact& c1, const Contact& c2); + void contact_forces(Contact& contact, double j_a, double** x, + double** v, double** angmom, double** f, double** torque, + double* vwall, double* facc); + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void distance(const double* x2, const double* x1, double& r); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix wall/body/polygon requires atom style body rounded/polygon + +Self-explanatory. + +E: Cannot use wall in periodic dimension + +Self-explanatory. + +E: Cannot wiggle and shear fix wall/body/polygon + +Cannot specify both options at the same time. + +E: Invalid wiggle direction for fix wall/body/polygon + +Self-explanatory. + +E: Fix wall/body/polygon is incompatible with Pair style + +Must use a body pair style to define the parameters needed for +this fix. + +*/ diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp new file mode 100644 index 0000000000000000000000000000000000000000..17e9f0b8b5e05441dff0c93f333dde24793fd3e8 --- /dev/null +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -0,0 +1,945 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "fix_wall_body_polyhedron.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polyhedron.h" +#include "domain.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "modify.h" +#include "respa.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{XPLANE=0,YPLANE=1,ZPLANE}; // XYZ PLANE need to be 0,1,2 +enum{HOOKE,HOOKE_HISTORY}; + +enum {INVALID=0,NONE=1,VERTEX=2}; +enum {FAR=0,XLO,XHI,YLO,YHI,ZLO,ZHI}; + +//#define _POLYHEDRON_DEBUG +#define DELTA 10000 +#define EPSILON 1e-2 +#define BIG 1.0e20 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + + if (!atom->body_flag) + error->all(FLERR,"Fix wall/body/polyhedron requires " + "atom style body/rounded/polyhedron"); + + restart_peratom = 1; + create_attribute = 1; + + // wall/particle coefficients + + kn = force->numeric(FLERR,arg[3]); + + c_n = force->numeric(FLERR,arg[4]); + if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n; + else c_t = force->numeric(FLERR,arg[5]); + + if (kn < 0.0 || c_n < 0.0 || c_t < 0.0) + error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + + // wallstyle args + + int iarg = 6; + if (strcmp(arg[iarg],"xplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = XPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"yplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = YPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"zplane") == 0) { + if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + wallstyle = ZPLANE; + if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG; + else lo = force->numeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; + else hi = force->numeric(FLERR,arg[iarg+2]); + iarg += 3; + } + + // check for trailing keyword/values + + wiggle = 0; + + while (iarg < narg) { + if (strcmp(arg[iarg],"wiggle") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + if (strcmp(arg[iarg+1],"x") == 0) axis = 0; + else if (strcmp(arg[iarg+1],"y") == 0) axis = 1; + else if (strcmp(arg[iarg+1],"z") == 0) axis = 2; + else error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + amplitude = force->numeric(FLERR,arg[iarg+2]); + period = force->numeric(FLERR,arg[iarg+3]); + wiggle = 1; + iarg += 4; + } else error->all(FLERR,"Illegal fix wall/body/polyhedron command"); + } + + if (wallstyle == XPLANE && domain->xperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == YPLANE && domain->yperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + if (wallstyle == ZPLANE && domain->zperiodic) + error->all(FLERR,"Cannot use wall in periodic dimension"); + + // setup oscillations + + if (wiggle) omega = 2.0*MY_PI / period; + + time_origin = update->ntimestep; + + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + facmax = facnummax = 0; + face = NULL; + facnum = facfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; +} + +/* ---------------------------------------------------------------------- */ + +FixWallBodyPolyhedron::~FixWallBodyPolyhedron() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(face); + memory->destroy(facnum); + memory->destroy(facfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); +} + +/* ---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::init() +{ + dt = update->dt; + + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "body style rounded/polyhedron"); + bptr = (BodyRoundedPolyhedron *) avec->bptr; + + // set pairstyle from body/polyhedronular pair style + + if (force->pair_match("body/rounded/polyhedron",1)) + pairstyle = HOOKE; + else error->all(FLERR,"Fix wall/body/polyhedron is incompatible with Pair style"); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::post_force(int vflag) +{ + double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos; + int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side; + double facc[3]; + + // set position of wall to initial settings and velocity to 0.0 + // if wiggle, set wall position and velocity accordingly + + double wlo = lo; + double whi = hi; + vwall[0] = vwall[1] = vwall[2] = 0.0; + if (wiggle) { + double arg = omega * (update->ntimestep - time_origin) * dt; + if (wallstyle == axis) { + wlo = lo + amplitude - amplitude*cos(arg); + whi = hi + amplitude - amplitude*cos(arg); + } + vwall[axis] = amplitude*omega*sin(arg); + } + + // loop over all my atoms + // rsq = distance from wall + // dx,dy,dz = signed distance from wall + // for rotating cylinder, reset vwall based on particle position + // skip atom if not close enough to wall + // if wall was set to NULL, it's skipped since lo/hi are infinity + // compute force and torque on atom if close enough to wall + // via wall potential matched to pair potential + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + int *body = atom->body; + double *radius = atom->radius; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"fix:dnum"); + memory->create(dfirst,nmax,"fix:dfirst"); + memory->create(ednum,nmax,"fix:ednum"); + memory->create(edfirst,nmax,"fix:edfirst"); + memory->create(facnum,nmax,"fix:facnum"); + memory->create(facfirst,nmax,"fix:facfirst"); + memory->create(enclosing_radius,nmax,"fix:enclosing_radius"); + memory->create(rounded_radius,nmax,"fix:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + + if (body[i] < 0) continue; + + dx = dy = dz = 0.0; + side = FAR; + if (wallstyle == XPLANE) { + del1 = x[i][0] - wlo; + del2 = whi - x[i][0]; + if (del1 < del2) { + dx = del1; + wall_pos = wlo; + side = XLO; + } else { + dx = -del2; + wall_pos = whi; + side = XHI; + } + } else if (wallstyle == YPLANE) { + del1 = x[i][1] - wlo; + del2 = whi - x[i][1]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = YLO; + } else { + dy = -del2; + wall_pos = whi; + side = YHI; + } + } else if (wallstyle == ZPLANE) { + del1 = x[i][2] - wlo; + del2 = whi - x[i][2]; + if (del1 < del2) { + dy = del1; + wall_pos = wlo; + side = ZLO; + } else { + dy = -del2; + wall_pos = whi; + side = ZHI; + } + } + + rsq = dx*dx + dy*dy + dz*dz; + if (rsq > radius[i]*radius[i]) continue; + + double r = sqrt(rsq); + double rsqinv = 1.0 / rsq; + + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + nfi = facnum[i]; + iffirst = facfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + if (npi == 1) { + sphere_against_wall(i, wall_pos, side, vwall, x, v, f, angmom, torque); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + discrete[ifirst+ni][6] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + edge[iefirst+ni][5] = 0; + } + + int interact, num_contacts, done; + double delta_a, delta_ua, j_a; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + facc[0] = facc[1] = facc[2] = 0; + interact = edge_against_wall(i, wall_pos, side, vwall, x, f, torque, + contact_list, num_contacts, facc); + + } // group bit + } +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::reset_dt() +{ + dt = update->dt; +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + int body_num_faces = bptr->nfaces(bonus); + double* face_pts = bptr->faces(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,7,"fix:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + discrete[ndiscrete][6] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, + // the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,6,"fix:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + edge[nedge][5] = 0; + nedge++; + } + + // get the number of faces and the index of the first face + + facnum[i] = body_num_faces; + facfirst[i] = nface; + + // grow the face list if necessary + // the first 3 columns are for vertex indices within body, the last 3 for forces + + if (nface + body_num_faces > facmax) { + facmax += DELTA; + memory->grow(face,facmax,6,"pair:face"); + } + + for (int m = 0; m < body_num_faces; m++) { + face[nface][0] = static_cast(face_pts[3*m+0]); + face[nface][1] = static_cast(face_pts[3*m+1]); + face[nface][2] = static_cast(face_pts[3*m+2]); + face[nface][3] = 0; + face[nface][4] = 0; + face[nface][5] = 0; + nface++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between a sphere against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques +---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos, + int side, double* vwall, double** x, double** v, double** f, + double** angmom, double** torque) +{ + int mode; + double rradi,hi[3],d,delx,dely,delz,R,fpair,fx,fy,fz; + + rradi = rounded_radius[i]; + mode = NONE; + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = x[i][1]; + hi[2] = x[i][2]; + } else if (wallstyle == YPLANE) { + hi[0] = x[i][0]; + hi[1] = wall_pos; + hi[2] = x[i][2]; + } else if (wallstyle == ZPLANE) { + hi[0] = x[i][0]; + hi[1] = x[i][1]; + hi[2] = wall_pos; + } + + distance(hi, x[i], d); + + if (d <= rradi) { + delx = x[i][0] - hi[0]; + dely = x[i][1] - hi[1]; + delz = x[i][2] - hi[2]; + R = d - rradi; + + fpair = -kn * R; + + fx = delx*fpair/d; + fy = dely*fpair/d; + fz = delz*fpair/d; + + contact_forces(i, 1.0, x[i], hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + mode = VERTEX; + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against the wall + + i = atom i (body i) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + Output: + contact_list = list of contacts between i and the wall + num_contacts = number of contacts between i's vertices and the wall + Return: + number of contacts of the edge to the wall (0, 1 or 2) +---------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos, + int side, double* vwall, double** x, double** f, double** torque, + Contact* contact_list, int &num_contacts, double* facc) +{ + int ni, nei, mode, contact; + double rradi; + int nlocal = atom->nlocal; + + nei = ednum[i]; + rradi = rounded_radius[i]; + + contact = 0; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) + mode = compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall, + contact); + + return contact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between a vertex to the wall + another body + Input: + x0 = coordinate of the tested vertex + rradi = rounded radius of the vertex + wall_pos = position of the wall + Output: + d = Distance from a point x0 to an wall + hi = coordinates of the projection of x0 on the wall + contact = 0 no contact between the queried vertex and the wall + 1 contact detected + return NONE if there is no interaction + VERTEX if the tested vertex interacts with the wall +------------------------------------------------------------------------- */ + +int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index, + double *xmi, double rounded_radius_i, double wall_pos, + int side, double* vwall, int &contact) +{ + int mode,ifirst,iefirst,npi1,npi2; + double d1,d2,xpi1[3],xpi2[3],hi[3]; + double fx,fy,fz,fpair,delx,dely,delz,R; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + // two ends of the edge from body i + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index][0]); + npi2 = static_cast(edge[iefirst+edge_index][1]); + + xpi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xpi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xpi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xpi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xpi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xpi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // determine the intersection of the edge to the wall + + mode = NONE; + double j_a = 1.0; + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = xpi1[1]; + hi[2] = xpi1[2]; + } else if (wallstyle == YPLANE) { + hi[0] = xpi1[0]; + hi[1] = wall_pos; + hi[2] = xpi1[2]; + } else if (wallstyle == ZPLANE) { + hi[0] = xpi1[0]; + hi[1] = xpi1[1]; + hi[2] = wall_pos; + } + + distance(hi, xpi1, d1); + + if (d1 <= rounded_radius_i && static_cast(discrete[ifirst+npi1][6]) == 0) { + delx = xpi1[0] - hi[0]; + dely = xpi1[1] - hi[1]; + delz = xpi1[2] - hi[2]; + R = d1 - rounded_radius_i; + + fpair = -kn * R; + + fx = delx*fpair/d1; + fy = dely*fpair/d1; + fz = delz*fpair/d1; + + contact_forces(ibody, j_a, xpi1, hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + discrete[ifirst+npi1][6] = 1; + contact++; + mode = VERTEX; + } + + if (wallstyle == XPLANE) { + hi[0] = wall_pos; + hi[1] = xpi2[1]; + hi[2] = xpi2[2]; + } else if (wallstyle == YPLANE) { + hi[0] = xpi2[0]; + hi[1] = wall_pos; + hi[2] = xpi2[2]; + } else if (wallstyle == ZPLANE) { + hi[0] = xpi2[0]; + hi[1] = xpi2[1]; + hi[2] = wall_pos; + } + + distance(hi, xpi2, d2); + + if (d2 <= rounded_radius_i && static_cast(discrete[ifirst+npi2][6]) == 0) { + delx = xpi2[0] - hi[0]; + dely = xpi2[1] - hi[1]; + delz = xpi2[2] - hi[2]; + R = d2 - rounded_radius_i; + + fpair = -kn * R; + + fx = delx*fpair/d2; + fy = dely*fpair/d2; + fz = delz*fpair/d2; + + contact_forces(ibody, j_a, xpi2, hi, delx, dely, delz, + fx, fy, fz, x, v, angmom, f, torque, vwall); + discrete[ifirst+npi2][6] = 1; + contact++; + mode = VERTEX; + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::contact_forces(int ibody, + double j_a, double *xi, double *xj, double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, double** angmom, + double** f, double** torque, double* vwall) +{ + int ibonus,jbonus; + double fxt,fyt,fzt,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3],vj[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xi, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the contact point on ibody to the wall + + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fxt = fx; fyt = fy; fzt = fz; + fx = fxt * j_a + fn[0] + ft[0]; + fy = fyt * j_a + fn[1] + ft[1]; + fz = fzt * j_a + fn[2] + ft[2]; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]); + + #ifdef _POLYHEDRON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", + fxt, fyt, fzt, + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2], + atom->tag[jbody],torque[jbody][0],torque[jbody][1],torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Compute the contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * vrt) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double* vwall, double* facc) +{ + int ibody,ibonus,ifirst, jefirst, ni; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // vector pointing from the vertex to the point on the wall + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vwall[0]; + vr2 = vi[1] - vwall[1]; + vr3 = vi[2] - vwall[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYHEDRON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts +------------------------------------------------------------------------- */ + +double FixWallBodyPolyhedron::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void FixWallBodyPolyhedron::distance(const double* x2, const double* x1, + double& r) { + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h new file mode 100644 index 0000000000000000000000000000000000000000..ff7b7ca7cfd0806de2d5f4fcd16c79b48c980954 --- /dev/null +++ b/src/BODY/fix_wall_body_polyhedron.h @@ -0,0 +1,143 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(wall/body/polyhedron,FixWallBodyPolyhedron) + +#else + +#ifndef LMP_FIX_WALL_BODY_POLYHERON_H +#define LMP_FIX_WALL_BODY_POLYHERON_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixWallBodyPolyhedron : public Fix { + public: + FixWallBodyPolyhedron(class LAMMPS *, int, char **); + virtual ~FixWallBodyPolyhedron(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + void reset_dt(); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + int wallstyle,pairstyle,wiggle,axis; + double kn,c_n,c_t; + double lo,hi,cylradius; + double amplitude,period,omega; + double dt; + int time_origin; + + class AtomVecBody *avec; + class BodyRoundedPolyhedron *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double **face; // list of all edge for all bodies + int nface; // number of faces in list + int facmax; // allocated size of face list + int *facnum; // number of faces per line, 0 if uninit + int *facfirst; // index of first face per each line + int facnummax; // allocated size of facnum,facfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + + void body2space(int); + + int edge_against_wall(int ibody, double wall_pos, int side, double* vwall, + double** x, double** f, double** torque, Contact* contact_list, + int &num_contacts, double* facc); + int sphere_against_wall(int i, double wall_pos, int side, double* vwall, + double** x, double** v, double** f, double** angmom, double** torque); + + int compute_distance_to_wall(int ibody, int edge_index, double *xmi, + double rounded_radius_i, double wall_pos, int side, + double* vwall, int &contact); + double contact_separation(const Contact& c1, const Contact& c2); + void contact_forces(int ibody, double j_a, double *xi, double *xj, + double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, + double** angmom, double** f, double** torque, double* vwall); + + void contact_forces(Contact& contact, double j_a, double** x, + double** v, double** angmom, double** f, double** torque, + double* vwall, double* facc); + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void distance(const double* x2, const double* x1, double& r); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix wall/body/polyhedron requires atom style body rounded/polyhedron + +Self-explanatory. + +E: Cannot use wall in periodic dimension + +Self-explanatory. + +E: Cannot wiggle and shear fix wall/body/polygon + +Cannot specify both options at the same time. + +E: Invalid wiggle direction for fix wall/body/polygon + +Self-explanatory. + +E: Fix wall/body/polygon is incompatible with Pair style + +Must use a body pair style to define the parameters needed for +this fix. + +*/ diff --git a/src/BODY/pair_body.cpp b/src/BODY/pair_body_nparticle.cpp similarity index 95% rename from src/BODY/pair_body.cpp rename to src/BODY/pair_body_nparticle.cpp index 8c12c0cf36aa0384c50e3745b45c969c8aa29cc2..80b45beb4e9ecf174503ea7f46c19c0e8a7f46a1 100644 --- a/src/BODY/pair_body.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -15,7 +15,7 @@ #include #include #include -#include "pair_body.h" +#include "pair_body_nparticle.h" #include "math_extra.h" #include "atom.h" #include "atom_vec_body.h" @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairBody::PairBody(LAMMPS *lmp) : Pair(lmp) +PairBodyNparticle::PairBodyNparticle(LAMMPS *lmp) : Pair(lmp) { dmax = nmax = 0; discrete = NULL; @@ -44,7 +44,7 @@ PairBody::PairBody(LAMMPS *lmp) : Pair(lmp) /* ---------------------------------------------------------------------- */ -PairBody::~PairBody() +PairBodyNparticle::~PairBodyNparticle() { memory->destroy(discrete); memory->destroy(dnum); @@ -66,7 +66,7 @@ PairBody::~PairBody() /* ---------------------------------------------------------------------- */ -void PairBody::compute(int eflag, int vflag) +void PairBodyNparticle::compute(int eflag, int vflag) { int i,j,ii,jj,inum,jnum,itype,jtype; int ni,nj,npi,npj,ifirst,jfirst; @@ -336,7 +336,7 @@ void PairBody::compute(int eflag, int vflag) allocate all arrays ------------------------------------------------------------------------- */ -void PairBody::allocate() +void PairBodyNparticle::allocate() { allocated = 1; int n = atom->ntypes; @@ -361,7 +361,7 @@ void PairBody::allocate() global settings ------------------------------------------------------------------------- */ -void PairBody::settings(int narg, char **arg) +void PairBodyNparticle::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); @@ -381,7 +381,7 @@ void PairBody::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairBody::coeff(int narg, char **arg) +void PairBodyNparticle::coeff(int narg, char **arg) { if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); @@ -415,12 +415,12 @@ void PairBody::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairBody::init_style() +void PairBodyNparticle::init_style() { avec = (AtomVecBody *) atom->style_match("body"); - if (!avec) error->all(FLERR,"Pair body requires atom style body"); + if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body"); if (strcmp(avec->bptr->style,"nparticle") != 0) - error->all(FLERR,"Pair body requires body style nparticle"); + error->all(FLERR,"Pair body/nparticle requires body style nparticle"); bptr = (BodyNparticle *) avec->bptr; neighbor->request(this,instance_me); @@ -430,7 +430,7 @@ void PairBody::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairBody::init_one(int i, int j) +double PairBodyNparticle::init_one(int i, int j) { if (setflag[i][j] == 0) { epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], @@ -459,7 +459,7 @@ double PairBody::init_one(int i, int j) store sub-particle space-frame displacements from COM in discrete list ------------------------------------------------------------------------- */ -void PairBody::body2space(int i) +void PairBodyNparticle::body2space(int i) { int ibonus = atom->body[i]; AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; diff --git a/src/BODY/pair_body.h b/src/BODY/pair_body_nparticle.h similarity index 90% rename from src/BODY/pair_body.h rename to src/BODY/pair_body_nparticle.h index 94fbdf34dffd12000165d4f0e936bc64dcc5ae00..9c7d832b64bcacf7fa61baaa0b3ca917f9cbd4ce 100644 --- a/src/BODY/pair_body.h +++ b/src/BODY/pair_body_nparticle.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS -PairStyle(body,PairBody) +PairStyle(body/nparticle,PairBodyNparticle) #else -#ifndef LMP_PAIR_BODY_H -#define LMP_PAIR_BODY_H +#ifndef LMP_PAIR_BODY_NPARTICLE_H +#define LMP_PAIR_BODY_NPARTICLE_H #include "pair.h" namespace LAMMPS_NS { -class PairBody : public Pair { +class PairBodyNparticle : public Pair { public: - PairBody(class LAMMPS *); - ~PairBody(); + PairBodyNparticle(class LAMMPS *); + ~PairBodyNparticle(); void compute(int, int); void settings(int, char **); void coeff(int, char **); diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp new file mode 100644 index 0000000000000000000000000000000000000000..14ef70f476061f1240dad92b7e694e6aa1f5957c --- /dev/null +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -0,0 +1,1380 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) + Ref: Fraige, Langston, Matchett and Dodds, Particuology 2008, 6:455-466 + Note: The current implementation has not taken into account + the contact history for friction forces. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_body_rounded_polygon.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polygon.h" +#include "comm.h" +#include "force.h" +#include "fix.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define DELTA 10000 +#define EPSILON 1e-3 +#define MAX_CONTACTS 4 // maximum number of contacts for 2D models +#define EFF_CONTACTS 2 // effective contacts for 2D models + +//#define _CONVEX_POLYGON +//#define _POLYGON_DEBUG + +enum {INVALID=0,NONE=1,VERTEXI=2,VERTEXJ=3,EDGE=4}; + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolygon::PairBodyRoundedPolygon(LAMMPS *lmp) : Pair(lmp) +{ + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; + maxerad = NULL; + + single_enable = 0; + restartinfo = 0; + + c_n = 0.1; + c_t = 0.2; + mu = 0.0; + delta_ua = 1.0; +} + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolygon::~PairBodyRoundedPolygon() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(k_n); + memory->destroy(k_na); + memory->destroy(maxerad); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + int ni,nj,npi,npj,ifirst,jfirst; + int nei,nej,iefirst,jefirst; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fx,fy,fz; + double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij; + double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3],facc[3]; + double *dxi,*dxj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **torque = atom->torque; + double **angmom = atom->angmom; + double *radius = atom->radius; + tagint* tag = atom->tag; + int *body = atom->body; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nall; i++) + dnum[i] = ednum[i] = 0; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + radi = radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + radj = radius[j]; + + // body/body interactions + + evdwl = 0.0; + facc[0] = facc[1] = facc[2] = 0; + + if (body[i] < 0 || body[j] < 0) continue; + + if (dnum[j] == 0) body2space(j); + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + k_nij = k_n[itype][jtype]; + k_naij = k_na[itype][jtype]; + + // no interaction + + r = sqrt(rsq); + if (r > radi + radj + cut_inner) continue; + rsqinv = 1.0 / rsq; + + if (npi == 1 && npj == 1) { + sphere_against_sphere(i, j, delx, dely, delz, rsq, + k_nij, k_naij, x, v, f, evflag); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + } + + for (nj = 0; nj < npj; nj++) { + discrete[jfirst+nj][3] = 0; + discrete[jfirst+nj][4] = 0; + discrete[jfirst+nj][5] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + } + + for (nj = 0; nj < nej; nj++) { + edge[jefirst+nj][2] = 0; + edge[jefirst+nj][3] = 0; + edge[jefirst+nj][4] = 0; + } + + int interact, num_contacts, done; + double delta_a, j_a; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + + // check interaction between i's vertices and j' edges + + interact = vertex_against_edge(i, j, k_nij, k_naij, + x, f, torque, tag, contact_list, + num_contacts, evdwl, facc); + + // check interaction between j's vertices and i' edges + + interact = vertex_against_edge(j, i, k_nij, k_naij, + x, f, torque, tag, contact_list, + num_contacts, evdwl, facc); + + if (num_contacts >= 2) { + + // find the first two distinct contacts + + done = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + delta_a = contact_separation(contact_list[m], contact_list[n]); + if (delta_a > 0) { + j_a = delta_a / (EFF_CONTACTS * delta_ua); + if (j_a < 1.0) j_a = 1.0; + + // scale the force at both contacts + + contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, + evdwl, facc); + contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, + evdwl, facc); + done = 1; + + #ifdef _POLYGON_DEBUG + printf(" Two separate contacts %d and %d: delta_a = %f; j_a = %f\n", + m, n, delta_a, j_a); + printf(" %d: vertex %d of body %d and edge %d of body %d; " + "xv = %f %f %f; xe = %f %f %f\n", + m, contact_list[m].vertex, contact_list[m].ibody, + contact_list[m].edge, contact_list[m].jbody, + contact_list[m].xv[0], contact_list[m].xv[1], + contact_list[m].xv[2], contact_list[m].xe[0], + contact_list[m].xe[1], contact_list[m].xe[2]); + printf(" %d: vertex %d of body %d and edge %d of body %d; " + "xv = %f %f %f; xe = %f %f %f\n", + n, contact_list[n].vertex, contact_list[n].ibody, + contact_list[n].edge, contact_list[n].jbody, + contact_list[n].xv[0], contact_list[n].xv[1], + contact_list[n].xv[2], contact_list[n].xe[0], + contact_list[n].xe[1], contact_list[n].xe[2]); + #endif + + break; + } + } + if (done == 1) break; + } + + + } else if (num_contacts == 1) { + + // if there's only one contact, it should be handled here + // since forces/torques have not been accumulated from vertex2edge() + + contact_forces(contact_list[0], 1.0, x, v, angmom, f, torque, evdwl, facc); + + #ifdef _POLYGON_DEBUG + printf("One contact between vertex %d of body %d and edge %d of body %d:\n", + contact_list[0].vertex, tag[contact_list[0].ibody], + contact_list[0].edge, tag[contact_list[0].jbody]); + printf("xv = %f %f %f; xe = %f %f %f\n", + contact_list[0].xv[0], contact_list[0].xv[1], contact_list[0].xv[2], + contact_list[0].xe[0], contact_list[0].xe[1], contact_list[0].xe[2]); + #endif + } + + #ifdef _POLYGON_DEBUG + int num_overlapping_contacts = 0; + for (int m = 0; m < num_contacts-1; m++) { + for (int n = m+1; n < num_contacts; n++) { + double l = contact_separation(contact_list[m], contact_list[n]); + if (l < EPSILON) num_overlapping_contacts++; + } + } + printf("There are %d contacts detected, %d of which overlap.\n", + num_contacts, num_overlapping_contacts); + #endif + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0, + facc[0],facc[1],facc[2],delx,dely,delz); + + } // end for jj + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(k_n,n+1,n+1,"pair:k_n"); + memory->create(k_na,n+1,n+1,"pair:k_na"); + memory->create(maxerad,n+1,"pair:maxerad"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::settings(int narg, char **arg) +{ + if (narg < 5) error->all(FLERR,"Illegal pair_style command"); + + c_n = force->numeric(FLERR,arg[0]); + c_t = force->numeric(FLERR,arg[1]); + mu = force->numeric(FLERR,arg[2]); + delta_ua = force->numeric(FLERR,arg[3]); + cut_inner = force->numeric(FLERR,arg[4]); + + if (delta_ua < 0) delta_ua = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double k_n_one = force->numeric(FLERR,arg[2]); + double k_na_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + k_n[i][j] = k_n_one; + k_na[i][j] = k_na_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::init_style() +{ + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) + error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); + if (strcmp(avec->bptr->style,"rounded/polygon") != 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "body style rounded/polygon"); + bptr = (BodyRoundedPolygon *) avec->bptr; + + if (force->newton_pair == 0) + error->all(FLERR,"Pair style body/rounded/polygon requires " + "newton pair on"); + + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair body/rounded/polygon requires " + "ghost atoms store velocity"); + + neighbor->request(this); + + // find the maximum enclosing radius for each atom type + + int i, itype; + double eradi; + int* body = atom->body; + int* type = atom->type; + int ntypes = atom->ntypes; + int nlocal = atom->nlocal; + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = 0; + + double *merad = NULL; + memory->create(merad,ntypes+1,"pair:merad"); + for (i = 1; i <= ntypes; i++) + maxerad[i] = merad[i] = 0; + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + for (i = 1; i <= ntypes; i++) { + merad[i] = 0.0; + if (ipour >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[ipour]->extract("radius",itype)); + } + if (idep >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[idep]->extract("radius",itype)); + } + } + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + eradi = enclosing_radius[i]; + if (eradi > merad[itype]) merad[itype] = eradi; + } else + merad[itype] = 0; + } + + MPI_Allreduce(&merad[1],&maxerad[1],ntypes,MPI_DOUBLE,MPI_MAX,world); + + memory->destroy(merad); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolygon::init_one(int i, int j) +{ + k_n[j][i] = k_n[i][j]; + k_na[j][i] = k_na[i][j]; + + return (maxerad[i]+maxerad[j]); +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,6,"pair:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,5,"pair:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + nedge++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Interaction between two spheres with different radii + according to the 2D model from Fraige et al. +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j, + double delx, double dely, double delz, double rsq, + double k_n, double k_na, double** x, double** v, + double** f, int evflag) +{ + double eradi,eradj,rradi,rradj; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + rsqinv = 1.0/rsq; + rij = sqrt(rsq); + R = rij - (rradi + rradj); + shift = k_na * cut_inner; + + energy = 0; + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy = (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy = (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= EPSILON) { // in contact + + // relative translational velocity + + vr1 = v[i][0] - v[j][0]; + vr2 = v[i][1] - v[j][1]; + vr3 = v[i][2] - v[j][2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + } + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + + if (newton_pair || j < nlocal) { + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's vertices against j's edges + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's vertices and j's edges + Return: + interact = 0 no interaction at all + 1 there's at least one case where i's vertices interacts + with j's edges +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::vertex_against_edge(int i, int j, + double k_n, double k_na, + double** x, double** f, + double** torque, tagint* tag, + Contact* contact_list, + int &num_contacts, + double &evdwl, double* facc) +{ + int ni, npi, ifirst, nei, iefirst; + int nj, npj, jfirst, nej, jefirst; + double xpi[3], xpj[3], dist, eradi, eradj, rradi, rradj; + double fx, fy, fz, rx, ry, rz, energy; + int interact; + int nlocal = atom->nlocal; + + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + rradi = rounded_radius[i]; + + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + rradj = rounded_radius[j]; + + energy = 0; + interact = 0; + + // loop through body i's vertices + + for (ni = 0; ni < npi; ni++) { + + // convert body-fixed coordinates to space-fixed, xi + + xpi[0] = x[i][0] + discrete[ifirst+ni][0]; + xpi[1] = x[i][1] + discrete[ifirst+ni][1]; + xpi[2] = x[i][2] + discrete[ifirst+ni][2]; + + // compute the distance from the vertex to the COM of body j + + distance(xpi, x[j], dist); + + #ifdef _POLYGON_DEBUG + printf("Distance between vertex %d of body %d (%0.1f %0.1f %0.1f) " + "to body %d's COM: %f (cut = %0.1f)\n", + ni, xpi[0], xpi[1], xpi[2], atom->tag[i], atom->tag[j], dist, + eradj + rradi + rradj + cut_inner); + #endif + + // the vertex is within the enclosing circle (sphere) of body j, + // possibly interacting + + if (dist > eradj + rradj + rradi + cut_inner) continue; + + int mode, contact, p2vertex; + double d, R, hi[3], t, delx, dely, delz, fpair, shift; + double xj[3], rij; + + // loop through body j's edges + + for (nj = 0; nj < nej; nj++) { + + // compute the distance between the edge nj to the vertex xpi + + mode = compute_distance_to_vertex(j, nj, x[j], rradj, + xpi, rradi, cut_inner, + d, hi, t, contact); + + if (mode == INVALID || mode == NONE) continue; + + if (mode == VERTEXI || mode == VERTEXJ) { + + interact = 1; + + // vertex i interacts with a vertex of the edge, but does not contact + + if (mode == VERTEXI) p2vertex = edge[jefirst+nj][0]; + else if (mode == VERTEXJ) p2vertex = edge[jefirst+nj][1]; + + // p2.body2space(p2vertex, xj); + xpj[0] = x[j][0] + discrete[jfirst+p2vertex][0]; + xpj[1] = x[j][1] + discrete[jfirst+p2vertex][1]; + xpj[2] = x[j][2] + discrete[jfirst+p2vertex][2]; + + delx = xpi[0] - xpj[0]; + dely = xpi[1] - xpj[1]; + delz = xpi[2] - xpj[2]; + + // R = surface separation = rij shifted by the rounded radii + // R = rij - (p1.rounded_radius + p2.rounded_radius); + // note: the force is defined for R, not for rij + // R > rc: no interaction between vertex ni and p2vertex + // 0 < R < rc: cohesion between vertex ni and p2vertex + // R < 0: deformation between vertex ni and p2vertex + + rij = sqrt(delx*delx + dely*dely + delz*delz); + R = rij - (rradi + rradj); + shift = k_na * cut_inner; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy += (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy += (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and vertex %d of %d:", + ni, tag[i], p2vertex, tag[j]); + printf(" mode = %d; contact = %d; d = %f; rij = %f, t = %f\n", + mode, contact, d, rij, t); + printf(" R = %f; cut_inner = %f\n", R, cut_inner); + printf(" fpair = %f\n", fpair); + #endif + + // add forces to body i and body j directly + // avoid double counts this pair of vertices + // i and j can be either local or ghost atoms (bodies) + // probably need more work here when the vertices' interaction + // are not symmetric, e.g. j interacts with the edge + // consisting of i but in mode = EDGE instead of VERTEX*. + // OR, for the time being assume that the edge length is + // sufficiently greater than the rounded radius to distinguish + // vertex-vertex from vertex-edge contact modes. + // Special case: when i is a sphere, also accumulate + + if (tag[i] < tag[j] || npi == 1) { + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + sum_torque(x[j], xpj, -fx, -fy, -fz, torque[j]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf(" from vertex-vertex: " + "force on vertex %d of body %d: fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", ni, tag[i], fx, fy, fz, + tag[i],torque[i][0],torque[i][1],torque[i][2], + tag[j],torque[j][0],torque[j][1],torque[j][2]); + #endif + } + + #ifdef _CONVEX_POLYGON + // done with the edges from body j, + // given that vertex ni interacts with only one vertex + // from one edge of body j + break; + #endif + + } else if (mode == EDGE) { + + interact = 1; + + // vertex i interacts with the edge + + delx = xpi[0] - hi[0]; + dely = xpi[1] - hi[1]; + delz = xpi[2] - hi[2]; + + // R = surface separation = d shifted by the rounded radii + // R = d - (p1.rounded_radius + p2.rounded_radius); + // Note: the force is defined for R, not for d + // R > rc: no interaction between vertex i and edge j + // 0 < R < rc: cohesion between vertex i and edge j + // R < 0: deformation between vertex i and edge j + // rij = sqrt(delx*delx + dely*dely + delz*delz); + + R = d - (rradi + rradj); + shift = k_na * cut_inner; + + // the normal frictional term -c_n * vn will be added later + + if (R <= 0) { // deformation occurs + fpair = -k_n * R - shift; + energy += (0.5 * k_n * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = k_na * R - shift; + energy += (-0.5 * k_na * R + shift) * R; + } else fpair = 0.0; + + fx = delx*fpair/d; + fy = dely*fpair/d; + fz = delz*fpair/d; + + #ifdef _POLYGON_DEBUG + printf(" Interaction between vertex %d of %d and edge %d of %d:", + ni, tag[i], nj, tag[j]); + printf(" mode = %d; contact = %d; d = %f; t = %f\n", + mode, contact, d, t); + printf(" R = %f; cut_inner = %f\n", R, cut_inner); + printf(" fpair = %f\n", fpair); + #endif + + if (contact == 1) { + + // vertex ni of body i contacts with edge nj of body j + + contact_list[num_contacts].ibody = i; + contact_list[num_contacts].jbody = j; + contact_list[num_contacts].vertex = ni; + contact_list[num_contacts].edge = nj; + contact_list[num_contacts].xv[0] = xpi[0]; + contact_list[num_contacts].xv[1] = xpi[1]; + contact_list[num_contacts].xv[2] = xpi[2]; + contact_list[num_contacts].xe[0] = hi[0]; + contact_list[num_contacts].xe[1] = hi[1]; + contact_list[num_contacts].xe[2] = hi[2]; + contact_list[num_contacts].separation = R; + num_contacts++; + + // store forces to vertex ni and the edge nj + // to be rescaled later + + discrete[ifirst+ni][3] = fx; + discrete[ifirst+ni][4] = fy; + discrete[ifirst+ni][5] = fz; + + edge[jefirst+nj][2] = -fx; + edge[jefirst+nj][3] = -fy; + edge[jefirst+nj][4] = -fz; + + #ifdef _POLYGON_DEBUG + printf(" Stored forces at vertex and edge for accumulating later.\n"); + #endif + + } else { // no contact + + // accumulate force and torque to both bodies directly + + f[i][0] += fx; + f[i][1] += fy; + f[i][2] += fz; + sum_torque(x[i], xpi, fx, fy, fz, torque[i]); + + f[j][0] -= fx; + f[j][1] -= fy; + f[j][2] -= fz; + sum_torque(x[j], hi, -fx, -fy, -fz, torque[j]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYGON_DEBUG + printf(" from vertex-edge, no contact: " + "force on vertex %d of body %d: fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", ni, tag[i], fx, fy, fz, + tag[i],torque[i][0],torque[i][1],torque[i][2], + tag[j],torque[j][0],torque[j][1],torque[j][2]); + #endif + } // end if contact + + #ifdef _CONVEX_POLYGON + // done with the edges from body j, + // given that vertex ni interacts with only one edge from body j + break; + #endif + } // end if mode + + } // end for looping through the edges of body j + + } // end for looping through the vertices of body i + + evdwl += energy; + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between an edge of body i and a vertex from + another body + Input: + ibody = body i (i.e. atom i) + edge_index = edge index of body i + xmi = atom i's coordinates (body i's center of mass) + x0 = coordinate of the tested vertex from another body + x0_rounded_radius = rounded radius of the tested vertex + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + t = ratio to determine the relative position of hi + wrt xi and xj on the segment + contact = 0 no contact between the queried vertex and the edge + 1 contact detected + return + INVALID if the edge index is invalid + NONE if there is no interaction + VERTEXI if the tested vertex interacts with the first vertex of the edge + VERTEXJ if the tested vertex interacts with the second vertex of the edge + EDGE if the tested vertex interacts with the edge +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody, + int edge_index, + double *xmi, + double rounded_radius, + double* x0, + double x0_rounded_radius, + double cut_inner, + double &d, + double hi[3], + double &t, + int &contact) +{ + if (edge_index >= ednum[ibody]) return INVALID; + + int mode,ifirst,iefirst,npi1,npi2; + double xi1[3],xi2[3],u[3],v[3],uij[3]; + double udotv, magv, magucostheta; + double delx,dely,delz; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index][0]); + npi2 = static_cast(edge[iefirst+edge_index][1]); + + // compute the space-fixed coordinates for the vertices of the edge + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // u = x0 - xi1 + + u[0] = x0[0] - xi1[0]; + u[1] = x0[1] - xi1[1]; + u[2] = x0[2] - xi1[2]; + + // v = xi2 - xi1 + + v[0] = xi2[0] - xi1[0]; + v[1] = xi2[1] - xi1[1]; + v[2] = xi2[2] - xi1[2]; + + // dot product between u and v = magu * magv * costheta + + udotv = u[0] * v[0] + u[1] * v[1] + u[2] * v[2]; + magv = sqrt(v[0] * v[0] + v[1] * v[1] + v[2] * v[2]); + magucostheta = udotv / magv; + + // uij is the unit vector pointing from xi to xj + + uij[0] = v[0] / magv; + uij[1] = v[1] / magv; + uij[2] = v[2] / magv; + + // position of the projection of x0 on the line (xi, xj) + + hi[0] = xi1[0] + magucostheta * uij[0]; + hi[1] = xi1[1] + magucostheta * uij[1]; + hi[2] = xi1[2] + magucostheta * uij[2]; + + // distance from x0 to the line (xi, xj) = distance from x0 to hi + + distance(hi, x0, d); + + // determine the interaction mode + // for 2D: a vertex can interact with one edge at most + // for 3D: a vertex can interact with one face at most + + mode = NONE; + contact = 0; + + if (d > rounded_radius + x0_rounded_radius + cut_inner) { + + // if the vertex is far away from the edge + + mode = NONE; + + } else { + + // check if x0 (the queried vertex) and xmi (the body's center of mass) + // are on the different sides of the edge + + #ifdef _CONVEX_POLYGON + int m = opposite_sides(xi1, xi2, x0, xmi); + #else + int m = 1; + #endif + + if (m == 0) { + + // x0 and xmi are on not the opposite sides of the edge + // leave xpi for another edge to detect + + mode = NONE; + + } else { + + // x0 and xmi are on the different sides + // t is the ratio to detect if x0 is closer to the vertices xi or xj + + if (fabs(xi2[0] - xi1[0]) > EPSILON) + t = (hi[0] - xi1[0]) / (xi2[0] - xi1[0]); + else if (fabs(xi2[1] - xi1[1]) > EPSILON) + t = (hi[1] - xi1[1]) / (xi2[1] - xi1[1]); + else if (fabs(xi2[2] - xi1[2]) > EPSILON) + t = (hi[2] - xi1[2]) / (xi2[2] - xi1[2]); + + double contact_dist = rounded_radius + x0_rounded_radius; + if (t >= 0 && t <= 1) { + mode = EDGE; + if (d < contact_dist + EPSILON) + contact = 1; + + } else { // t < 0 || t > 1: closer to either vertices of the edge + + if (t < 0) { + // measure the distance from x0 to xi1 + delx = x0[0] - xi1[0]; + dely = x0[1] - xi1[1]; + delz = x0[2] - xi1[2]; + double dx0xi1 = sqrt(delx*delx + dely*dely + delz*delz); + if (dx0xi1 > contact_dist + cut_inner) + mode = NONE; + else + mode = VERTEXI; + } else { + // measure the distance from x0 to xi2 + delx = x0[0] - xi2[0]; + dely = x0[1] - xi2[1]; + delz = x0[2] - xi2[2]; + double dx0xi2 = sqrt(delx*delx + dely*dely + delz*delz); + if (dx0xi2 > contact_dist + cut_inner) + mode = NONE; + else + mode = VERTEXJ; + } + } // end if t >= 0 && t <= 1 + } // end if x0 and xmi are on the same side of the edge + } + + return mode; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double &evdwl, double* facc) +{ + int ibody,jbody,ibonus,jbonus,ifirst,jefirst,ni,nj; + double fx,fy,fz,delx,dely,delz,rsq,rsqinv; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3],vj[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + ibody = contact.ibody; + jbody = contact.jbody; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // compute the velocity of the point on the edge in the space-fixed frame + + jbonus = atom->body[jbody]; + bonus = &avec->bonus[jbonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(contact.xe, x[jbody], v[jbody], angmom[jbody], + inertia, quat, vj); + + // vector pointing from the vertex to the point on the edge + + delx = contact.xv[0] - contact.xe[0]; + dely = contact.xv[1] - contact.xe[1]; + delz = contact.xv[2] - contact.xe[2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vj[0]; + vr2 = vi[1] - vj[1]; + vr3 = vi[2] - vj[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // only the cohesive force is scaled by j_a + // mu * fne = tangential friction deformation during gross sliding + // see Eq. 4, Fraige et al. + + ifirst = dfirst[ibody]; + ni = contact.vertex; + + fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0] + + mu * discrete[ifirst+ni][3]; + fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1] + + mu * discrete[ifirst+ni][4]; + fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2] + + mu * discrete[ifirst+ni][5]; + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]); + + // accumulate forces to the vertex only + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + // only the cohesive force is scaled by j_a + // mu * fne = tangential friction deformation during gross sliding + // Eq. 4, Fraige et al. + + jefirst = edfirst[jbody]; + nj = contact.edge; + + fx = edge[jefirst+nj][2] * j_a - fn[0] - ft[0] + + mu * edge[jefirst+nj][2]; + fy = edge[jefirst+nj][3] * j_a - fn[1] - ft[1] + + mu * edge[jefirst+nj][3]; + fz = edge[jefirst+nj][4] * j_a - fn[2] - ft[2] + + mu * edge[jefirst+nj][4]; + f[jbody][0] += fx; + f[jbody][1] += fy; + f[jbody][2] += fz; + sum_torque(x[jbody], contact.xe, fx, fy, fz, torque[jbody]); + + #ifdef _POLYGON_DEBUG + printf("From contact forces: vertex fx %f fy %f fz %f\n" + " torque body %d: %f %f %f\n" + " torque body %d: %f %f %f\n", + discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5], + atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2], + atom->tag[jbody],torque[jbody][0],torque[jbody][1],torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts, should be extended for 3D models. +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolygon::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = c1.xv[0]; + double y1 = c1.xv[1]; + double x2 = c1.xe[0]; + double y2 = c1.xe[1]; + double x3 = c2.xv[0]; + double y3 = c2.xv[1]; + + double delta_a = 0.0; + if (fabs(x2 - x1) > EPSILON) { + double A = (y2 - y1) / (x2 - x1); + delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A); + } else { + delta_a = fabs(x1 - x3); + } + + return delta_a; +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Test if two points a and b are in opposite sides of the line that + connects two points x1 and x2 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolygon::opposite_sides(double* x1, double* x2, + double* a, double* b) +{ + double m_a = (x1[1] - x2[1])*(a[0] - x1[0]) + (x2[0] - x1[0])*(a[1] - x1[1]); + double m_b = (x1[1] - x2[1])*(b[0] - x1[0]) + (x2[0] - x1[0])*(b[1] - x1[1]); + // equal to zero when either a or b is inline with the line x1-x2 + if (m_a * m_b <= 0) + return 1; + else + return 0; +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, + double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolygon::distance(const double* x2, const double* x1, + double& r) +{ + r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0]) + + (x2[1] - x1[1]) * (x2[1] - x1[1]) + + (x2[2] - x1[2]) * (x2[2] - x1[2])); +} + diff --git a/src/BODY/pair_body_rounded_polygon.h b/src/BODY/pair_body_rounded_polygon.h new file mode 100644 index 0000000000000000000000000000000000000000..aabe86270cd621a56836370130532cf42c93be59 --- /dev/null +++ b/src/BODY/pair_body_rounded_polygon.h @@ -0,0 +1,137 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(body/rounded/polygon,PairBodyRoundedPolygon) + +#else + +#ifndef LMP_PAIR_BODY_ROUNDED_POLYGON_H +#define LMP_PAIR_BODY_ROUNDED_POLYGON_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBodyRoundedPolygon : public Pair { + public: + PairBodyRoundedPolygon(class LAMMPS *); + ~PairBodyRoundedPolygon(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int vertex; // vertex of the first polygon + int edge; // edge of the second polygon + double xv[3]; // coordinates of the vertex + double xe[3]; // coordinates of the projection of the vertex on the edge + double separation;// separation at contact + }; + + protected: + double **k_n; // normal repulsion strength + double **k_na; // normal attraction strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double mu; // normal friction coefficient during gross sliding + double delta_ua; // contact line (area for 3D models) modification factor + double cut_inner; // cutoff for interaction between vertex-edge surfaces + + class AtomVecBody *avec; + class BodyRoundedPolygon *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + double *maxerad; // per-type maximum enclosing radius + + void allocate(); + void body2space(int); + + // sphere-sphere interaction + void sphere_against_sphere(int i, int j, double delx, double dely, double delz, + double rsq, double k_n, double k_na, + double** x, double** v, double** f, int evflag); + // vertex-edge interaction + int vertex_against_edge(int i, int j, double k_n, double k_na, + double** x, double** f, double** torque, + tagint* tag, Contact* contact_list, + int &num_contacts, double &evdwl, double* facc); + // compute distance between a point and an edge from another body + int compute_distance_to_vertex(int ibody, int edge_index, double* xmi, + double rounded_radius, double* x0, + double x0_rounded_radius, double cut_inner, + double &d, double hi[3], double &t, + int &contact); + // compute contact forces if contact points are detected + void contact_forces(Contact& contact, double j_a, + double** x, double** v, double** angmom, double** f, + double** torque, double &evdwl, double* facc); + + // compute the separation between two contacts + double contact_separation(const Contact& c1, const Contact& c2); + + // accumulate torque to a body given a force at a given point + void sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque); + // helper functions + int opposite_sides(double* x1, double* x2, double* a, double* b); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + inline void distance(const double* x2, const double* x1, double& r); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair body/rounded/polygon requires atom style body rounded/polygon + +Self-explanatory. + +E: Pair body requires body style rounded/polygon + +This pair style is specific to the rounded/polygon body style. + +*/ diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp new file mode 100644 index 0000000000000000000000000000000000000000..051be762e5a432193326596e6acbc3ad7bb9e616 --- /dev/null +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -0,0 +1,2389 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (ndactrung@gmail.com) + Ref: Wang, Yu, Langston, Fraige, Particle shape effects in discrete + element modelling of cohesive angular particles, Granular Matter 2011, + 13:1-12. + Note: The current implementation has not taken into account + the contact history for friction forces. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_body_rounded_polyhedron.h" +#include "math_extra.h" +#include "atom.h" +#include "atom_vec_body.h" +#include "body_rounded_polyhedron.h" +#include "comm.h" +#include "force.h" +#include "fix.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" +#include "math_extra.h" +#include "math_const.h" + +using namespace LAMMPS_NS; +using namespace MathExtra; +using namespace MathConst; + +#define DELTA 10000 +#define EPSILON 1e-3 +#define MAX_FACE_SIZE 4 // maximum number of vertices per face (same as BodyRoundedPolyhedron) +#define MAX_CONTACTS 32 // for 3D models (including duplicated counts) + +//#define _POLYHEDRON_DEBUG + +enum {EE_INVALID=0,EE_NONE,EE_INTERACT}; +enum {EF_INVALID=0,EF_NONE,EF_PARALLEL,EF_SAME_SIDE_OF_FACE, + EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE}; + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolyhedron::PairBodyRoundedPolyhedron(LAMMPS *lmp) : Pair(lmp) +{ + dmax = nmax = 0; + discrete = NULL; + dnum = dfirst = NULL; + + edmax = ednummax = 0; + edge = NULL; + ednum = edfirst = NULL; + + facmax = facnummax = 0; + face = NULL; + facnum = facfirst = NULL; + + enclosing_radius = NULL; + rounded_radius = NULL; + maxerad = NULL; + + single_enable = 0; + restartinfo = 0; + + c_n = 0.1; + c_t = 0.2; + mu = 0.0; + A_ua = 1.0; + + k_n = NULL; + k_na = NULL; +} + +/* ---------------------------------------------------------------------- */ + +PairBodyRoundedPolyhedron::~PairBodyRoundedPolyhedron() +{ + memory->destroy(discrete); + memory->destroy(dnum); + memory->destroy(dfirst); + + memory->destroy(edge); + memory->destroy(ednum); + memory->destroy(edfirst); + + memory->destroy(face); + memory->destroy(facnum); + memory->destroy(facfirst); + + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + memory->destroy(maxerad); + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(k_n); + memory->destroy(k_na); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + int ni,nj,npi,npj,ifirst,jfirst,nei,nej,iefirst,jefirst; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,facc[3]; + double rsq,eradi,eradj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double **torque = atom->torque; + double **angmom = atom->angmom; + int *body = atom->body; + int *type = atom->type; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // grow the per-atom lists if necessary and initialize + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(facnum,nmax,"pair:facnum"); + memory->create(facfirst,nmax,"pair:facfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nall; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + npi = dnum[i]; + ifirst = dfirst[i]; + nei = ednum[i]; + iefirst = edfirst[i]; + eradi = enclosing_radius[i]; + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + // body/body interactions + + evdwl = 0.0; + facc[0] = facc[1] = facc[2] = 0; + + if (body[i] < 0 || body[j] < 0) continue; + + if (dnum[j] == 0) body2space(j); + npj = dnum[j]; + jfirst = dfirst[j]; + nej = ednum[j]; + jefirst = edfirst[j]; + eradj = enclosing_radius[j]; + + // no interaction + + double r = sqrt(rsq); + if (r > eradi + eradj + cut_inner) continue; + + // sphere-sphere interaction + + if (npi == 1 && npj == 1) { + sphere_against_sphere(i, j, itype, jtype, delx, dely, delz, + rsq, v, f, evflag); + continue; + } + + // reset vertex and edge forces + + for (ni = 0; ni < npi; ni++) { + discrete[ifirst+ni][3] = 0; + discrete[ifirst+ni][4] = 0; + discrete[ifirst+ni][5] = 0; + discrete[ifirst+ni][6] = 0; + } + + for (nj = 0; nj < npj; nj++) { + discrete[jfirst+nj][3] = 0; + discrete[jfirst+nj][4] = 0; + discrete[jfirst+nj][5] = 0; + discrete[jfirst+nj][6] = 0; + } + + for (ni = 0; ni < nei; ni++) { + edge[iefirst+ni][2] = 0; + edge[iefirst+ni][3] = 0; + edge[iefirst+ni][4] = 0; + edge[iefirst+ni][5] = 0; + } + + for (nj = 0; nj < nej; nj++) { + edge[jefirst+nj][2] = 0; + edge[jefirst+nj][3] = 0; + edge[jefirst+nj][4] = 0; + edge[jefirst+nj][5] = 0; + } + + // one of the two bodies is a sphere + + if (npj == 1) { + sphere_against_face(i, j, itype, jtype, x, v, f, torque, + angmom, evflag); + sphere_against_edge(i, j, itype, jtype, x, v, f, torque, + angmom, evflag); + continue; + } else if (npi == 1) { + sphere_against_face(j, i, jtype, itype, x, v, f, torque, + angmom, evflag); + sphere_against_edge(j, i, jtype, itype, x, v, f, torque, + angmom, evflag); + continue; + } + + int interact, num_contacts; + Contact contact_list[MAX_CONTACTS]; + + num_contacts = 0; + + // check interaction between i's edges and j' faces + #ifdef _POLYHEDRON_DEBUG + printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j); + #endif + interact = edge_against_face(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); + + // check interaction between j's edges and i' faces + #ifdef _POLYHEDRON_DEBUG + printf("\nINTERACTION between edges of %d vs. faces of %d:\n", j, i); + #endif + interact = edge_against_face(j, i, jtype, itype, x, contact_list, + num_contacts, evdwl, facc); + + // check interaction between i's edges and j' edges + #ifdef _POLYHEDRON_DEBUG + printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j); + #endif + interact = edge_against_edge(i, j, itype, jtype, x, contact_list, + num_contacts, evdwl, facc); + + // estimate the contact area + // also consider point contacts and line contacts + + if (num_contacts > 0) { + rescale_cohesive_forces(x, f, torque, contact_list, num_contacts, + itype, jtype, facc); + } + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0, + facc[0],facc[1],facc[2],delx,dely,delz); + + } // end for jj + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(k_n,n+1,n+1,"pair:k_n"); + memory->create(k_na,n+1,n+1,"pair:k_na"); + memory->create(maxerad,n+1,"pair:maxerad"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::settings(int narg, char **arg) +{ + if (narg < 5) error->all(FLERR,"Illegal pair_style command"); + + c_n = force->numeric(FLERR,arg[0]); + c_t = force->numeric(FLERR,arg[1]); + mu = force->numeric(FLERR,arg[2]); + A_ua = force->numeric(FLERR,arg[3]); + cut_inner = force->numeric(FLERR,arg[4]); + + if (A_ua < 0) A_ua = 1; +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::coeff(int narg, char **arg) +{ + if (narg < 4 || narg > 5) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double k_n_one = force->numeric(FLERR,arg[2]); + double k_na_one = force->numeric(FLERR,arg[3]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + k_n[i][j] = k_n_one; + k_na[i][j] = k_na_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::init_style() +{ + avec = (AtomVecBody *) atom->style_match("body"); + if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires " + "atom style body"); + if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "body style rounded/polyhedron"); + bptr = (BodyRoundedPolyhedron *) avec->bptr; + + if (force->newton_pair == 0) + error->all(FLERR,"Pair style body/rounded/polyhedron requires " + "newton pair on"); + + if (comm->ghost_velocity == 0) + error->all(FLERR,"Pair body/rounded/polyhedron requires " + "ghost atoms store velocity"); + + neighbor->request(this); + + // find the maximum enclosing radius for each atom type + + int i, itype; + double eradi; + int* body = atom->body; + int* type = atom->type; + int ntypes = atom->ntypes; + int nlocal = atom->nlocal; + + if (atom->nmax > nmax) { + memory->destroy(dnum); + memory->destroy(dfirst); + memory->destroy(ednum); + memory->destroy(edfirst); + memory->destroy(facnum); + memory->destroy(facfirst); + memory->destroy(enclosing_radius); + memory->destroy(rounded_radius); + nmax = atom->nmax; + memory->create(dnum,nmax,"pair:dnum"); + memory->create(dfirst,nmax,"pair:dfirst"); + memory->create(ednum,nmax,"pair:ednum"); + memory->create(edfirst,nmax,"pair:edfirst"); + memory->create(facnum,nmax,"pair:facnum"); + memory->create(facfirst,nmax,"pair:facfirst"); + memory->create(enclosing_radius,nmax,"pair:enclosing_radius"); + memory->create(rounded_radius,nmax,"pair:rounded_radius"); + } + + ndiscrete = nedge = nface = 0; + for (i = 0; i < nlocal; i++) + dnum[i] = ednum[i] = facnum[i] = 0; + + double *merad = NULL; + memory->create(merad,ntypes+1,"pair:merad"); + for (i = 1; i <= ntypes; i++) + maxerad[i] = merad[i] = 0; + + int ipour; + for (ipour = 0; ipour < modify->nfix; ipour++) + if (strcmp(modify->fix[ipour]->style,"pour") == 0) break; + if (ipour == modify->nfix) ipour = -1; + + int idep; + for (idep = 0; idep < modify->nfix; idep++) + if (strcmp(modify->fix[idep]->style,"deposit") == 0) break; + if (idep == modify->nfix) idep = -1; + + for (i = 1; i <= ntypes; i++) { + merad[i] = 0.0; + if (ipour >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[ipour]->extract("radius",itype)); + } + if (idep >= 0) { + itype = i; + merad[i] = + *((double *) modify->fix[idep]->extract("radius",itype)); + } + } + + for (i = 0; i < nlocal; i++) { + itype = type[i]; + if (body[i] >= 0) { + if (dnum[i] == 0) body2space(i); + eradi = enclosing_radius[i]; + if (eradi > merad[itype]) merad[itype] = eradi; + } else + merad[itype] = 0; + } + + MPI_Allreduce(&merad[1],&maxerad[1],ntypes,MPI_DOUBLE,MPI_MAX,world); + + memory->destroy(merad); + + sanity_check(); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolyhedron::init_one(int i, int j) +{ + k_n[j][i] = k_n[i][j]; + k_na[j][i] = k_na[i][j]; + + return (maxerad[i]+maxerad[j]); +} + +/* ---------------------------------------------------------------------- + convert N sub-particles in body I to space frame using current quaternion + store sub-particle space-frame displacements from COM in discrete list +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::body2space(int i) +{ + int ibonus = atom->body[i]; + AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; + int nsub = bptr->nsub(bonus); + double *coords = bptr->coords(bonus); + int body_num_edges = bptr->nedges(bonus); + double* edge_ends = bptr->edges(bonus); + int body_num_faces = bptr->nfaces(bonus); + double* face_pts = bptr->faces(bonus); + double eradius = bptr->enclosing_radius(bonus); + double rradius = bptr->rounded_radius(bonus); + + // get the number of sub-particles (vertices) + // and the index of the first vertex of my body in the list + + dnum[i] = nsub; + dfirst[i] = ndiscrete; + + // grow the vertex list if necessary + // the first 3 columns are for coords, the last 3 for forces + + if (ndiscrete + nsub > dmax) { + dmax += DELTA; + memory->grow(discrete,dmax,7,"pair:discrete"); + } + + double p[3][3]; + MathExtra::quat_to_mat(bonus->quat,p); + + for (int m = 0; m < nsub; m++) { + MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]); + discrete[ndiscrete][3] = 0; + discrete[ndiscrete][4] = 0; + discrete[ndiscrete][5] = 0; + discrete[ndiscrete][6] = 0; + ndiscrete++; + } + + // get the number of edges (vertices) + // and the index of the first edge of my body in the list + + ednum[i] = body_num_edges; + edfirst[i] = nedge; + + // grow the edge list if necessary + // the first 2 columns are for vertex indices within body, the last 3 for forces + + if (nedge + body_num_edges > edmax) { + edmax += DELTA; + memory->grow(edge,edmax,6,"pair:edge"); + } + + for (int m = 0; m < body_num_edges; m++) { + edge[nedge][0] = static_cast(edge_ends[2*m+0]); + edge[nedge][1] = static_cast(edge_ends[2*m+1]); + edge[nedge][2] = 0; + edge[nedge][3] = 0; + edge[nedge][4] = 0; + edge[nedge][5] = 0; + nedge++; + } + + // get the number of faces and the index of the first face + + facnum[i] = body_num_faces; + facfirst[i] = nface; + + // grow the face list if necessary + // the first 3 columns are for vertex indices within body, the last 3 for forces + + if (nface + body_num_faces > facmax) { + facmax += DELTA; + memory->grow(face,facmax,MAX_FACE_SIZE,"pair:face"); + } + + for (int m = 0; m < body_num_faces; m++) { + for (int k = 0; k < MAX_FACE_SIZE; k++) + face[nface][k] = static_cast(face_pts[MAX_FACE_SIZE*m+k]); + nface++; + } + + enclosing_radius[i] = eradius; + rounded_radius[i] = rradius; +} + +/* ---------------------------------------------------------------------- + Interaction between two spheres with different radii + according to the 2D model from Fraige et al. +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody, + int itype, int jtype, double delx, double dely, double delz, double rsq, + double** v, double** f, int evflag) +{ + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double rij,rsqinv,R,fx,fy,fz,fn[3],ft[3],fpair,shift,energy; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // relative translational velocity + + vr1 = v[ibody][0] - v[jbody][0]; + vr2 = v[ibody][1] - v[jbody][1]; + vr3 = v[ibody][2] - v[jbody][2]; + + // normal component + + rsqinv = 1.0/rsq; + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); +} + +/* ---------------------------------------------------------------------- + Interaction bt the edges of a polyhedron (ibody) and a sphere (jbody) +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody, + int itype, int jtype, double** x, double** v, double** f, double** torque, + double** angmom, int evflag) +{ + int ni,nei,ifirst,iefirst,npi1,npi2,ibonus; + double xi1[3],xi2[3],vti[3],h[3],fn[3],ft[3],d,t; + double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy; + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + nei = ednum[ibody]; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + for (ni = 0; ni < nei; ni++) { + + npi1 = static_cast(edge[iefirst+ni][0]); + npi2 = static_cast(edge[iefirst+ni][1]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0]; + xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1]; + xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2]; + + xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0]; + xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1]; + xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2]; + + // find the projection of the jbody's COM on the edge + + project_pt_line(x[jbody], xi1, xi2, h, d, t); + + if (d > contact_dist + cut_inner) continue; + if (t < 0 || t > 1) continue; + + if (fabs(t) < EPSILON) { + if (static_cast(discrete[ifirst+npi1][6]) == 1) + continue; + else { + h[0] = xi1[0]; + h[1] = xi1[1]; + h[2] = xi1[2]; + discrete[ifirst+npi1][6] = 1; + } + } + + if (fabs(t-1) < EPSILON) { + if (static_cast(discrete[ifirst+npi2][6]) == 1) + continue; + else { + h[0] = xi2[0]; + h[1] = xi2[1]; + h[2] = xi2[2]; + discrete[ifirst+npi2][6] = 1; + } + } + + delx = h[0] - x[jbody][0]; + dely = h[1] - x[jbody][1]; + delz = h[2] - x[jbody][2]; + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = (rsq == 0.0) ? 0.0 : 1.0/rsq; + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(h, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vti); + + // relative translational velocity + + vr1 = vti[0] - v[jbody][0]; + vr2 = vti[1] - v[jbody][1]; + vr3 = vti[2] - v[jbody][2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]); + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- + Interaction bt the faces of a polyhedron (ibody) and a sphere (jbody) +---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody, + int itype, int jtype, double** x, double** v, double** f, double** torque, + double** angmom, int evflag) +{ + int ni,nfi,inside,ifirst,iffirst,npi1,npi2,npi3,ibonus,tmp; + double xi1[3],xi2[3],xi3[3],ui[3],vi[3],vti[3],n[3],h[3],fn[3],ft[3],d; + double delx,dely,delz,rsq,rij,rsqinv,R,fx,fy,fz,fpair,shift,energy; + double rradi,rradj,contact_dist; + double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + nfi = facnum[ibody]; + + rradi = rounded_radius[ibody]; + rradj = rounded_radius[jbody]; + contact_dist = rradi + rradj; + + for (ni = 0; ni < nfi; ni++) { + + npi1 = static_cast(face[iffirst+ni][0]); + npi2 = static_cast(face[iffirst+ni][1]); + npi3 = static_cast(face[iffirst+ni][2]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = x[ibody][0] + discrete[ifirst+npi1][0]; + xi1[1] = x[ibody][1] + discrete[ifirst+npi1][1]; + xi1[2] = x[ibody][2] + discrete[ifirst+npi1][2]; + + xi2[0] = x[ibody][0] + discrete[ifirst+npi2][0]; + xi2[1] = x[ibody][1] + discrete[ifirst+npi2][1]; + xi2[2] = x[ibody][2] + discrete[ifirst+npi2][2]; + + xi3[0] = x[ibody][0] + discrete[ifirst+npi3][0]; + xi3[1] = x[ibody][1] + discrete[ifirst+npi3][1]; + xi3[2] = x[ibody][2] + discrete[ifirst+npi3][2]; + + // find the normal unit vector of the face + + MathExtra::sub3(xi2, xi1, ui); + MathExtra::sub3(xi3, xi1, vi); + MathExtra::cross3(ui, vi, n); + MathExtra::norm3(n); + + // skip if the COM of the two bodies are in the same side of the face + + if (opposite_sides(n, xi1, x[ibody], x[jbody]) == 0) continue; + + // find the projection of the sphere on the face + + project_pt_plane(x[jbody], xi1, xi2, xi3, h, d, inside); + + inside_polygon(ibody, ni, x[ibody], h, NULL, inside, tmp); + if (inside == 0) continue; + + delx = h[0] - x[jbody][0]; + dely = h[1] - x[jbody][1]; + delz = h[2] - x[jbody][2]; + rsq = delx*delx + dely*dely + delz*delz; + rij = sqrt(rsq); + R = rij - contact_dist; + + energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/rij; + fy = dely*fpair/rij; + fz = delz*fpair/rij; + + if (R <= 0) { // in contact + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(h, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vti); + + // relative translational velocity + + vr1 = vti[0] - v[jbody][0]; + vr2 = vti[1] - v[jbody][1]; + vr3 = vti[2] - v[jbody][2]; + + // normal component + + rsqinv = 1.0/rsq; + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact, + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + fx += fn[0] + ft[0]; + fy += fn[1] + ft[1]; + fz += fn[2] + ft[2]; + } + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], h, fx, fy, fz, torque[ibody]); + + if (newton_pair || jbody < nlocal) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + } + + if (evflag) ev_tally_xyz(ibody,jbody,nlocal,newton_pair, + energy,0.0,fx,fy,fz,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's edges against j's edges + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's edges and j's edges + Return: + +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_against_edge(int ibody, int jbody, + int itype, int jtype, double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc) +{ + int ni,nei,nj,nej,contact,interact; + double rradi,rradj,energy; + + nei = ednum[ibody]; + rradi = rounded_radius[ibody]; + nej = ednum[jbody]; + rradj = rounded_radius[jbody]; + + energy = 0; + interact = EE_NONE; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) { + + for (nj = 0; nj < nej; nj++) { + + // compute the distance between the edge nj to the edge ni + #ifdef _POLYHEDRON_DEBUG + printf("Compute interaction between edge %d of body %d " + "with edge %d of body %d:\n", + nj, jbody, ni, ibody); + #endif + + interact = interaction_edge_to_edge(ibody, ni, x[ibody], rradi, + jbody, nj, x[jbody], rradj, + itype, jtype, cut_inner, + contact_list, num_contacts, + energy, facc); + } + + } // end for looping through the edges of body i + + evdwl += energy; + + return interact; +} + +/* ---------------------------------------------------------------------- + Determine the interaction mode between i's edges against j's faces + + i = atom i (body i) + j = atom j (body j) + x = atoms' coordinates + f = atoms' forces + torque = atoms' torques + tag = atoms' tags + contact_list = list of contacts + num_contacts = number of contacts between i's edges and j's faces + Return: + +---------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody, + int itype, int jtype, double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc) +{ + int ni,nei,nj,nfj,contact,interact; + double rradi,rradj,energy; + + nei = ednum[ibody]; + rradi = rounded_radius[ibody]; + nfj = facnum[jbody]; + rradj = rounded_radius[jbody]; + + energy = 0; + interact = EF_NONE; + + // loop through body i's edges + + for (ni = 0; ni < nei; ni++) { + + // loop through body j's faces + + for (nj = 0; nj < nfj; nj++) { + + // compute the distance between the face nj to the edge ni + #ifdef _POLYHEDRON_DEBUG + printf("Compute interaction between face %d of body %d with " + "edge %d of body %d:\n", + nj, jbody, ni, ibody); + #endif + + interact = interaction_face_to_edge(jbody, nj, x[jbody], rradj, + ibody, ni, x[ibody], rradi, + itype, jtype, cut_inner, + contact_list, num_contacts, + energy, facc); + } + + } // end for looping through the edges of body i + + evdwl += energy; + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the distance between an edge of body i and an edge from + another body + Input: + ibody = body i (i.e. atom i) + face_index = face index of body i + xmi = atom i's coordinates (body i's center of mass) + rounded_radius_i = rounded radius of the body i + jbody = body i (i.e. atom j) + edge_index = coordinate of the tested edge from another body + xmj = atom j's coordinates (body j's center of mass) + rounded_radius_j = rounded radius of the body j + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + + contact = 0 no contact between the queried edge and the face + 1 contact detected + return + INVALID if the face index is invalid + NONE if there is no interaction +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody, + int edge_index_i, double *xmi, double rounded_radius_i, + int jbody, int edge_index_j, double *xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, double &energy, double* facc) +{ + int ifirst,iefirst,jfirst,jefirst,npi1,npi2,npj1,npj2,interact; + double xi1[3],xi2[3],xpj1[3],xpj2[3]; + double r,t1,t2,h1[3],h2[3]; + double contact_dist, shift; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + ifirst = dfirst[ibody]; + iefirst = edfirst[ibody]; + npi1 = static_cast(edge[iefirst+edge_index_i][0]); + npi2 = static_cast(edge[iefirst+edge_index_i][1]); + + // compute the space-fixed coordinates for the edge ends + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + // two ends of the edge from body j + + jfirst = dfirst[jbody]; + jefirst = edfirst[jbody]; + npj1 = static_cast(edge[jefirst+edge_index_j][0]); + npj2 = static_cast(edge[jefirst+edge_index_j][1]); + + xpj1[0] = xmj[0] + discrete[jfirst+npj1][0]; + xpj1[1] = xmj[1] + discrete[jfirst+npj1][1]; + xpj1[2] = xmj[2] + discrete[jfirst+npj1][2]; + + xpj2[0] = xmj[0] + discrete[jfirst+npj2][0]; + xpj2[1] = xmj[1] + discrete[jfirst+npj2][1]; + xpj2[2] = xmj[2] + discrete[jfirst+npj2][2]; + + contact_dist = rounded_radius_i + rounded_radius_j; + + int jflag = 1; + distance_bt_edges(xpj1, xpj2, xi1, xi2, h1, h2, t1, t2, r); + + #ifdef _POLYHEDRON_DEBUG + double ui[3],uj[3]; + MathExtra::sub3(xi1,xi2,ui); + MathExtra::norm3(ui); + MathExtra::sub3(xpj1,xpj2,uj); + MathExtra::norm3(uj); + double dot = MathExtra::dot3(ui, uj); + printf(" edge npi1 = %d (%f %f %f); npi2 = %d (%f %f %f) vs." + " edge npj1 = %d (%f %f %f); npj2 = %d (%f %f %f): " + "t1 = %f; t2 = %f; r = %f; dot = %f\n", + npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2], + npj1, xpj1[0], xpj1[1], xpj1[2], npj2, xpj2[0], xpj2[1], xpj2[2], + t1, t2, r, dot); + #endif + + interact = EE_NONE; + + // singularity case, ignore interactions + + if (r < EPSILON) return interact; + + // include the vertices for interactions + + if (t1 >= 0 && t1 <= 1 && t2 >= 0 && t2 <= 1 && + r < contact_dist + cut_inner) { + pair_force_and_torque(jbody, ibody, h1, h2, r, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + + interact = EE_INTERACT; + if (r <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = h2[0]; + contact_list[num_contacts].xi[1] = h2[1]; + contact_list[num_contacts].xi[2] = h2[2]; + contact_list[num_contacts].xj[0] = h1[0]; + contact_list[num_contacts].xj[1] = h1[1]; + contact_list[num_contacts].xj[2] = h1[2]; + contact_list[num_contacts].type = 1; + contact_list[num_contacts].separation = r - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + } else { + + } + + return interact; +} + +/* ------------------------------------------------------------------------- + Compute the interaction between a face of body i and an edge from + another body + Input: + ibody = body i (i.e. atom i) + face_index = face index of body i + xmi = atom i's coordinates (body i's center of mass) + rounded_radius_i = rounded radius of the body i + jbody = body i (i.e. atom j) + edge_index = coordinate of the tested edge from another body + xmj = atom j's coordinates (body j's center of mass) + rounded_radius_j = rounded radius of the body j + cut_inner = cutoff for vertex-vertex and vertex-edge interaction + Output: + d = Distance from a point x0 to an edge + hi = coordinates of the projection of x0 on the edge + + contact = 0 no contact between the queried edge and the face + 1 contact detected + return + INVALID if the face index is invalid + NONE if there is no interaction +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, + int face_index, double *xmi, double rounded_radius_i, + int jbody, int edge_index, double *xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, double &energy, double* facc) +{ + if (face_index >= facnum[ibody]) return EF_INVALID; + + int ifirst,iffirst,jfirst,npi1,npi2,npi3; + int jefirst,npj1,npj2; + double xi1[3],xi2[3],xi3[3],xpj1[3],xpj2[3],ui[3],vi[3],n[3]; + + double** x = atom->x; + double** v = atom->v; + double** f = atom->f; + double** torque = atom->torque; + double** angmom = atom->angmom; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + npi1 = static_cast(face[iffirst+face_index][0]); + npi2 = static_cast(face[iffirst+face_index][1]); + npi3 = static_cast(face[iffirst+face_index][2]); + + // compute the space-fixed coordinates for the vertices of the face + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + xi3[0] = xmi[0] + discrete[ifirst+npi3][0]; + xi3[1] = xmi[1] + discrete[ifirst+npi3][1]; + xi3[2] = xmi[2] + discrete[ifirst+npi3][2]; + + // find the normal unit vector of the face, ensure it point outward of the body + + MathExtra::sub3(xi2, xi1, ui); + MathExtra::sub3(xi3, xi1, vi); + MathExtra::cross3(ui, vi, n); + MathExtra::norm3(n); + + double xc[3], dot, ans[3]; + xc[0] = (xi1[0] + xi2[0] + xi3[0])/3.0; + xc[1] = (xi1[1] + xi2[1] + xi3[1])/3.0; + xc[2] = (xi1[2] + xi2[2] + xi3[2])/3.0; + MathExtra::sub3(xc, xmi, ans); + dot = MathExtra::dot3(ans, n); + if (dot < 0) MathExtra::negate3(n); + + // two ends of the edge from body j + + jfirst = dfirst[jbody]; + jefirst = edfirst[jbody]; + npj1 = static_cast(edge[jefirst+edge_index][0]); + npj2 = static_cast(edge[jefirst+edge_index][1]); + + xpj1[0] = xmj[0] + discrete[jfirst+npj1][0]; + xpj1[1] = xmj[1] + discrete[jfirst+npj1][1]; + xpj1[2] = xmj[2] + discrete[jfirst+npj1][2]; + + xpj2[0] = xmj[0] + discrete[jfirst+npj2][0]; + xpj2[1] = xmj[1] + discrete[jfirst+npj2][1]; + xpj2[2] = xmj[2] + discrete[jfirst+npj2][2]; + + // no interaction if two ends of the edge + // are on the same side with the COM wrt the face + + if (opposite_sides(n, xi1, xmi, xpj1) == 0 && + opposite_sides(n, xi1, xmi, xpj2) == 0) + return EF_NONE; + + // determine the intersection of the edge to the face + + double hi1[3], hi2[3], d1, d2, contact_dist, shift; + int inside1 = 0; + int inside2 = 0; + + // enum {EF_PARALLEL=0,EF_SAME_SIDE_OF_FACE, + // EF_INTERSECT_INSIDE,EF_INTERSECT_OUTSIDE}; + + int interact = edge_face_intersect(xi1, xi2, xi3, xpj1, xpj2, + hi1, hi2, d1, d2, inside1, inside2); + + inside_polygon(ibody, face_index, xmi, hi1, hi2, inside1, inside2); + + contact_dist = rounded_radius_i + rounded_radius_j; + + // both endpoints are on the same side of, or parallel to, the face + // and both are out of the interaction zone + + if (interact == EF_SAME_SIDE_OF_FACE || interact == EF_PARALLEL) { + + if (d1 > contact_dist + cut_inner && d2 > contact_dist + cut_inner) + return EF_NONE; + + int num_outside = 0; + int jflag = 1; + + #ifdef _POLYHEDRON_DEBUG + if (interact == EF_SAME_SIDE_OF_FACE) + printf(" - same side of face\n"); + else if (interact == EF_PARALLEL) + printf(" - parallel\n"); + printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", + xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]); + printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n", + xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]); + #endif + + // xpj1 is in the interaction zone + // and its projection on the face is inside the triangle + // compute vertex-face interaction and accumulate force/torque to both bodies + + if (d1 <= contact_dist + cut_inner) { + if (inside1) { + if (static_cast(discrete[jfirst+npj1][6]) == 0) { + pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + #ifdef _POLYHEDRON_DEBUG + printf(" - compute pair force between vertex %d from edge %d of body %d " + "with face %d of body %d: d1 = %f\n", + npj1, edge_index, jbody, face_index, ibody, d1); + #endif + + if (d1 <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = hi1[0]; + contact_list[num_contacts].xi[1] = hi1[1]; + contact_list[num_contacts].xi[2] = hi1[2]; + contact_list[num_contacts].xj[0] = xpj1[0]; + contact_list[num_contacts].xj[1] = xpj1[1]; + contact_list[num_contacts].xj[2] = xpj1[2]; + contact_list[num_contacts].type = 0; + contact_list[num_contacts].separation = d1 - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + + discrete[jfirst+npj1][6] = 1; + } + } else { + num_outside++; + } + } + + // xpj2 is in the interaction zone + // and its projection on the face is inside the triangle + // compute vertex-face interaction and accumulate force/torque to both bodies + + if (d2 <= contact_dist + cut_inner) { + if (inside2) { + if (static_cast(discrete[jfirst+npj2][6]) == 0) { + pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + #ifdef _POLYHEDRON_DEBUG + printf(" - compute pair force between vertex %d from edge %d of body %d " + "with face %d of body %d: d2 = %f\n", + npj2, edge_index, jbody, face_index, ibody, d2); + #endif + + if (d2 <= contact_dist) { + // store the contact info + contact_list[num_contacts].ibody = ibody; + contact_list[num_contacts].jbody = jbody; + contact_list[num_contacts].xi[0] = hi2[0]; + contact_list[num_contacts].xi[1] = hi2[1]; + contact_list[num_contacts].xi[2] = hi2[2]; + contact_list[num_contacts].xj[0] = xpj2[0]; + contact_list[num_contacts].xj[1] = xpj2[1]; + contact_list[num_contacts].xj[2] = xpj2[2]; + contact_list[num_contacts].type = 0; + contact_list[num_contacts].separation = d2 - contact_dist; + contact_list[num_contacts].unique = 1; + num_contacts++; + } + discrete[jfirst+npj2][6] = 1; + } + } else { + num_outside++; + } + } + + // both ends have projection outside of the face + // compute interaction between the edge with the three edges of the face + + if (num_outside == 2) { + + #ifdef _POLYHEDRON_DEBUG + printf(" - outside = 2\n"); + printf(" - compute pair force between edge %d of body %d " + "with 3 edges of face %d of body %d\n", + edge_index, jbody, face_index, ibody); + #endif + + interact = EF_INTERSECT_OUTSIDE; + + } + + } else if (interact == EF_INTERSECT_OUTSIDE) { + + // compute interaction between the edge with the three edges of the face + + #ifdef _POLYHEDRON_DEBUG + printf(" - intersect outside triangle\n"); + printf(" - compute pair force between edge %d of body %d " + "with face %d of body %d\n", edge_index, jbody, face_index, ibody); + printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", + xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]); + printf(" edge: xpj1 (%f %f %f) xpj2 (%f %f %f)\n", + xpj1[0], xpj1[1], xpj1[2], xpj2[0], xpj2[1], xpj2[2]); + + #endif + } else if (interact == EF_INTERSECT_INSIDE) { + // need to do something here to resolve overlap!! + // p is the intersection between the edge and the face + int jflag = 1; + if (d1 < d2) + pair_force_and_torque(jbody, ibody, xpj1, hi1, d1, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + else + pair_force_and_torque(jbody, ibody, xpj2, hi2, d2, contact_dist, + jtype, itype, x, v, f, torque, angmom, + jflag, energy, facc); + } + + return interact; +} + +/* ---------------------------------------------------------------------- + Compute forces and torques between two bodies caused by the interaction + between a pair of points on either bodies (similar to sphere-sphere) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::pair_force_and_torque(int ibody, int jbody, + double* pi, double* pj, double r, double contact_dist, + int itype, int jtype, double** x, + double** v, double** f, double** torque, double** angmom, + int jflag, double& energy, double* facc) +{ + double delx,dely,delz,R,fx,fy,fz,fpair; + + delx = pi[0] - pj[0]; + dely = pi[1] - pj[1]; + delz = pi[2] - pj[2]; + R = r - contact_dist; + + kernel_force(R, itype, jtype, energy, fpair); + + fx = delx*fpair/r; + fy = dely*fpair/r; + fz = delz*fpair/r; + + #ifdef _POLYHEDRON_DEBUG + printf(" - R = %f; r = %f; k_na = %f; shift = %f; fpair = %f;" + " energy = %f; jflag = %d\n", R, r, k_na, shift, fpair, + energy, jflag); + #endif + + if (R <= 0) { + + // contact: accumulate normal and tangential contact force components + + contact_forces(ibody, jbody, pi, pj, delx, dely, delz, fx, fy, fz, + x, v, angmom, f, torque, facc); + } else { + + // accumulate force and torque to both bodies directly + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], pi, fx, fy, fz, torque[ibody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + if (jflag) { + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], pj, -fx, -fy, -fz, torque[jbody]); + } + } +} + +/* ---------------------------------------------------------------------- + Kernel force is model-dependent and can be derived for other styles + here is the harmonic potential (linear piece-wise forces) in Wang et al. +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::kernel_force(double R, int itype, int jtype, + double& energy, double& fpair) +{ + double kn = k_n[itype][jtype]; + double kna = k_na[itype][jtype]; + double shift = kna * cut_inner; + double e = 0; + if (R <= 0) { // deformation occurs + fpair = -kn * R - shift; + e = (0.5 * kn * R + shift) * R; + } else if (R <= cut_inner) { // not deforming but cohesive ranges overlap + fpair = kna * R - shift; + e = (-0.5 * kna * R + shift) * R; + } else fpair = 0.0; + energy += e; +} + +/* ---------------------------------------------------------------------- + Compute contact forces between two bodies + modify the force stored at the vertex and edge in contact by j_a + sum forces and torque to the corresponding bodies + fx,fy,fz = unscaled cohesive forces + fn = normal friction component + ft = tangential friction component (-c_t * v_t) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::contact_forces(int ibody, int jbody, + double *xi, double *xj, double delx, double dely, double delz, + double fx, double fy, double fz, double** x, double** v, double** angmom, + double** f, double** torque, double* facc) +{ + int ibonus,jbonus; + double rsq,rsqinv,vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3; + double fn[3],ft[3],vi[3],vj[3]; + double *quat, *inertia; + AtomVecBody::Bonus *bonus; + + // compute the velocity of the vertex in the space-fixed frame + + ibonus = atom->body[ibody]; + bonus = &avec->bonus[ibonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xi, x[ibody], v[ibody], angmom[ibody], + inertia, quat, vi); + + // compute the velocity of the point on the edge in the space-fixed frame + + jbonus = atom->body[jbody]; + bonus = &avec->bonus[jbonus]; + quat = bonus->quat; + inertia = bonus->inertia; + total_velocity(xj, x[jbody], v[jbody], angmom[jbody], + inertia, quat, vj); + + // vector pointing from the contact point on ibody to that on jbody + + rsq = delx*delx + dely*dely + delz*delz; + rsqinv = 1.0/rsq; + + // relative translational velocity + + vr1 = vi[0] - vj[0]; + vr2 = vi[1] - vj[1]; + vr3 = vi[2] - vj[2]; + + // normal component + + vnnr = vr1*delx + vr2*dely + vr3*delz; + vn1 = delx*vnnr * rsqinv; + vn2 = dely*vnnr * rsqinv; + vn3 = delz*vnnr * rsqinv; + + // tangential component + + vt1 = vr1 - vn1; + vt2 = vr2 - vn2; + vt3 = vr3 - vn3; + + // normal friction term at contact + + fn[0] = -c_n * vn1; + fn[1] = -c_n * vn2; + fn[2] = -c_n * vn3; + + // tangential friction term at contact + // excluding the tangential deformation term for now + + ft[0] = -c_t * vt1; + ft[1] = -c_t * vt2; + ft[2] = -c_t * vt3; + + // these are contact forces (F_n, F_t and F_ne) only + // cohesive forces will be scaled by j_a after contact area is computed + // mu * fne = tangential friction deformation during gross sliding + // see Eq. 4, Fraige et al. + + fx = fn[0] + ft[0] + mu * fx; + fy = fn[1] + ft[1] + mu * fy; + fz = fn[2] + ft[2] + mu * fz; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]); + + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], xj, -fx, -fy, -fz, torque[jbody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + + #ifdef _POLYHEDRON_DEBUG + printf("contact ibody = %d: f = %f %f %f; torque = %f %f %f\n", ibody, + f[ibody][0], f[ibody][1], f[ibody][2], + torque[ibody][0], torque[ibody][1], torque[ibody][2]); + printf("contact jbody = %d: f = %f %f %f; torque = %f %f %f\n", jbody, + f[jbody][0], f[jbody][1], f[jbody][2], + torque[jbody][0], torque[jbody][1], torque[jbody][2]); + #endif +} + +/* ---------------------------------------------------------------------- + Rescale the forces and torques for all the contacts +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x, + double** f, double** torque, Contact* contact_list, int &num_contacts, + int itype, int jtype, double* facc) +{ + int m,ibody,jbody; + double delx,dely,delz,fx,fy,fz,R,fpair,r,contact_area; + + int num_unique_contacts = 0; + if (num_contacts == 1) { + num_unique_contacts = 1; + contact_area = 0; + } else if (num_contacts == 2) { + num_unique_contacts = 2; + contact_area = num_contacts * A_ua; + } else { + find_unique_contacts(contact_list, num_contacts); + + double xc[3],dx,dy,dz; + xc[0] = xc[1] = xc[2] = 0; + num_unique_contacts = 0; + for (int m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + xc[0] += contact_list[m].xi[0]; + xc[1] += contact_list[m].xi[1]; + xc[2] += contact_list[m].xi[2]; + num_unique_contacts++; + } + + xc[0] /= (double)num_unique_contacts; + xc[1] /= (double)num_unique_contacts; + xc[2] /= (double)num_unique_contacts; + + contact_area = 0.0; + for (int m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + dx = contact_list[m].xi[0] - xc[0]; + dy = contact_list[m].xi[1] - xc[1]; + dz = contact_list[m].xi[2] - xc[2]; + contact_area += (dx*dx + dy*dy + dz*dz); + } + contact_area *= (MY_PI/(double)num_unique_contacts); + } + + double j_a = contact_area / (num_unique_contacts * A_ua); + if (j_a < 1.0) j_a = 1.0; + for (m = 0; m < num_contacts; m++) { + if (contact_list[m].unique == 0) continue; + + ibody = contact_list[m].ibody; + jbody = contact_list[m].jbody; + + delx = contact_list[m].xi[0] - contact_list[m].xj[0]; + dely = contact_list[m].xi[1] - contact_list[m].xj[1]; + delz = contact_list[m].xi[2] - contact_list[m].xj[2]; + r = sqrt(delx*delx + dely*dely + delz*delz); + R = contact_list[m].separation; + + double energy = 0; + kernel_force(R, itype, jtype, energy, fpair); + + fpair *= j_a; + fx = delx*fpair/r; + fy = dely*fpair/r; + fz = delz*fpair/r; + + f[ibody][0] += fx; + f[ibody][1] += fy; + f[ibody][2] += fz; + sum_torque(x[ibody], contact_list[m].xi, fx, fy, fz, torque[ibody]); + + f[jbody][0] -= fx; + f[jbody][1] -= fy; + f[jbody][2] -= fz; + sum_torque(x[jbody], contact_list[m].xj, -fx, -fy, -fz, torque[jbody]); + + facc[0] += fx; facc[1] += fy; facc[2] += fz; + } +} + +/* ---------------------------------------------------------------------- + Accumulate torque to body from the force f=(fx,fy,fz) acting at point x +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sum_torque(double* xm, double *x, double fx, + double fy, double fz, double* torque) +{ + double rx = x[0] - xm[0]; + double ry = x[1] - xm[1]; + double rz = x[2] - xm[2]; + double tx = ry * fz - rz * fy; + double ty = rz * fx - rx * fz; + double tz = rx * fy - ry * fx; + torque[0] += tx; + torque[1] += ty; + torque[2] += tz; +} + +/* ---------------------------------------------------------------------- + Test if two points a and b are in opposite sides of a plane defined by + a normal vector n and a point x0 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::opposite_sides(double* n, double* x0, + double* a, double* b) +{ + double m_a = n[0]*(a[0] - x0[0])+n[1]*(a[1] - x0[1])+n[2]*(a[2] - x0[2]); + double m_b = n[0]*(b[0] - x0[0])+n[1]*(b[1] - x0[1])+n[2]*(b[2] - x0[2]); + // equal to zero when either a or b is on the plane + if (m_a * m_b <= 0) + return 1; + else + return 0; +} + +/* ---------------------------------------------------------------------- + Test if a line segment defined by two points a and b intersects with + a triangle defined by three points x1, x2 and x3 +------------------------------------------------------------------------- */ + +int PairBodyRoundedPolyhedron::edge_face_intersect(double* x1, double* x2, + double* x3, double* a, double* b, double* h_a, double* h_b, + double& d_a, double& d_b, int& inside_a, int& inside_b) +{ + double s[3], u[3], v[3], n[3]; + + // line director + + MathExtra::sub3(b, a, s); + + // plane normal vector + + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // find the projection of a and b to the plane and the corresponding distances + + project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a); + + project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b); + + // check if the line segment is parallel to the plane + + double dot = MathExtra::dot3(s, n); + if (fabs(dot) < EPSILON) return EF_PARALLEL; + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -s[0]; + m[0][1] = u[0]; + m[0][2] = v[0]; + + m[1][0] = -s[1]; + m[1][1] = u[1]; + m[1][2] = v[1]; + + m[2][0] = -s[2]; + m[2][1] = u[2]; + m[2][2] = v[2]; + + MathExtra::sub3(a, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + // p is reused for the intersection point + // s = b - a + + double t = ans[0]; + p[0] = a[0] + s[0] * t; + p[1] = a[1] + s[1] * t; + p[2] = a[2] + s[2] * t; + + // check if p is inside the triangle, excluding the edges and vertices + // the edge-edge and edge-vertices are handled separately + + int inside = 0; + if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1) + inside = 1; + + int interact; + if (t < 0 || t > 1) { + interact = EF_SAME_SIDE_OF_FACE; + } else { + if (inside == 1) + interact = EF_INTERSECT_INSIDE; + else + interact = EF_INTERSECT_OUTSIDE; + } + + return interact; +} + +/* ---------------------------------------------------------------------- + Find the projection of q on the plane defined by point p and the normal + unit vector n: q_proj = q - dot(q - p, n) * n + and the distance d from q to the plane +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_plane(const double* q, + const double* p, const double* n, + double* q_proj, double &d) +{ + double dot, ans[3], n_p[3]; + n_p[0] = n[0]; n_p[1] = n[1]; n_p[2] = n[2]; + MathExtra::sub3(q, p, ans); + dot = MathExtra::dot3(ans, n_p); + MathExtra::scale3(dot, n_p); + MathExtra::sub3(q, n_p, q_proj); + MathExtra::sub3(q, q_proj, ans); + d = MathExtra::len3(ans); +} + +/* ---------------------------------------------------------------------- + Check if points q1 and q2 are inside a convex polygon, i.e. a face of + a polyhedron + ibody = atom i's index + face_index = face index of the body + xmi = atom i's coordinates + q1 = tested point on the face (e.g. the projection of a point) + q2 = another point (can be NULL) for face-edge intersection + Output: + inside1 = 1 if q1 is inside the polygon, 0 otherwise + inside2 = 1 if q2 is inside the polygon, 0 otherwise +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::inside_polygon(int ibody, int face_index, + double* xmi, const double* q1, const double* q2, + int& inside1, int& inside2) + +{ + int i,n,ifirst,iffirst,npi1,npi2; + double xi1[3],xi2[3],u[3],v[3],costheta,anglesum1,anglesum2,magu,magv; + + ifirst = dfirst[ibody]; + iffirst = facfirst[ibody]; + anglesum1 = anglesum2 = 0;; + for (i = 0; i < MAX_FACE_SIZE; i++) { + npi1 = static_cast(face[iffirst+face_index][i]); + if (npi1 < 0) break; + n = i + 1; + if (n <= MAX_FACE_SIZE - 1) { + npi2 = static_cast(face[iffirst+face_index][n]); + if (npi2 < 0) npi2 = static_cast(face[iffirst+face_index][0]); + } else { + npi2 = static_cast(face[iffirst+face_index][0]); + } + + xi1[0] = xmi[0] + discrete[ifirst+npi1][0]; + xi1[1] = xmi[1] + discrete[ifirst+npi1][1]; + xi1[2] = xmi[2] + discrete[ifirst+npi1][2]; + + xi2[0] = xmi[0] + discrete[ifirst+npi2][0]; + xi2[1] = xmi[1] + discrete[ifirst+npi2][1]; + xi2[2] = xmi[2] + discrete[ifirst+npi2][2]; + + MathExtra::sub3(xi1,q1,u); + MathExtra::sub3(xi2,q1,v); + magu = MathExtra::len3(u); + magv = MathExtra::len3(v); + + // the point is at either vertices + + if (magu * magv < EPSILON) inside1 = 1; + else { + costheta = MathExtra::dot3(u,v)/(magu*magv); + anglesum1 += acos(costheta); + } + + if (q2 != NULL) { + MathExtra::sub3(xi1,q2,u); + MathExtra::sub3(xi2,q2,v); + magu = MathExtra::len3(u); + magv = MathExtra::len3(v); + if (magu * magv < EPSILON) inside2 = 1; + else { + costheta = MathExtra::dot3(u,v)/(magu*magv); + anglesum2 += acos(costheta); + } + } + } + + if (fabs(anglesum1 - MY_2PI) < EPSILON) inside1 = 1; + else inside1 = 0; + + if (q2 != NULL) { + if (fabs(anglesum2 - MY_2PI) < EPSILON) inside2 = 1; + else inside2 = 0; + } +} + +/* ---------------------------------------------------------------------- + Find the projection of q on the plane defined by 3 points x1, x2 and x3 + returns the distance d from q to the plane and whether the projected + point is inside the triangle defined by (x1, x2, x3) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_plane(const double* q, + const double* x1, const double* x2, const double* x3, double* q_proj, + double &d, int& inside) +{ + double u[3],v[3],n[3]; + + // plane normal vector + + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -n[0]; + m[0][1] = u[0]; + m[0][2] = v[0]; + + m[1][0] = -n[1]; + m[1][1] = u[1]; + m[1][2] = v[1]; + + m[2][0] = -n[2]; + m[2][1] = u[2]; + m[2][2] = v[2]; + + MathExtra::sub3(q, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + double t = ans[0]; + q_proj[0] = q[0] + n[0] * t; + q_proj[1] = q[1] + n[1] * t; + q_proj[2] = q[2] + n[2] * t; + + // check if the projection point is inside the triangle + // exclude the edges and vertices + // edge-sphere and sphere-sphere interactions are handled separately + + inside = 0; + if (ans[1] > 0 && ans[2] > 0 && ans[1] + ans[2] < 1) { + inside = 1; + } + + // distance from q to q_proj + + MathExtra::sub3(q, q_proj, ans); + d = MathExtra::len3(ans); +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::project_pt_line(const double* q, + const double* xi1, const double* xi2, double* h, double& d, double& t) +{ + double u[3],v[3],r[3],s; + + MathExtra::sub3(xi2, xi1, u); + MathExtra::norm3(u); + MathExtra::sub3(q, xi1, v); + + s = MathExtra::dot3(u, v); + h[0] = xi1[0] + s * u[0]; + h[1] = xi1[1] + s * u[1]; + h[2] = xi1[2] + s * u[2]; + + MathExtra::sub3(q, h, r); + d = MathExtra::len3(r); + + if (fabs(xi2[0] - xi1[0]) > 0) + t = (h[0] - xi1[0])/(xi2[0] - xi1[0]); + else if (fabs(xi2[1] - xi1[1]) > 0) + t = (h[1] - xi1[1])/(xi2[1] - xi1[1]); + else if (fabs(xi2[2] - xi1[2]) > 0) + t = (h[2] - xi1[2])/(xi2[2] - xi1[2]); +} + +/* ---------------------------------------------------------------------- + compute the shortest distance between two edges (line segments) + x1, x2: two endpoints of the first edge + x3, x4: two endpoints of the second edge + h1: the end point of the shortest segment perpendicular to both edges + on the line (x1;x2) + h2: the end point of the shortest segment perpendicular to both edges + on the line (x3;x4) + t1: fraction of h1 in the segment (x1,x2) + t2: fraction of h2 in the segment (x3,x4) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, + const double* x2, const double* x3, const double* x4, + double* h1, double* h2, double& t1, double& t2, double& r) +{ + double u[3],v[3],n[3],dot; + + // set the default returned values + + t1 = -2; + t2 = 2; + r = 0; + + // find the edge unit directors and their dot product + + MathExtra::sub3(x2, x1, u); + MathExtra::norm3(u); + MathExtra::sub3(x4, x3, v); + MathExtra::norm3(v); + dot = MathExtra::dot3(u,v); + dot = fabs(dot); + + // check if two edges are parallel + // find the two ends of the overlapping segment, if any + + if (fabs(dot - 1.0) < EPSILON) { + + double s1,s2,x13[3],x23[3],x13h[3]; + double t13,t23,t31,t41,x31[3],x41[3]; + t13=t23=t31=t41=0.0; + + MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3 + MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3 + + s1 = MathExtra::dot3(x13,v); + x13h[0] = x13[0] - s1*v[0]; + x13h[1] = x13[1] - s1*v[1]; + x13h[2] = x13[2] - s1*v[2]; + r = MathExtra::len3(x13h); + + // x13 is the projection of x1 on x3-x4 + + x13[0] = x3[0] + s1*v[0]; + x13[1] = x3[1] + s1*v[1]; + x13[2] = x3[2] + s1*v[2]; + + // x23 is the projection of x2 on x3-x4 + + s2 = MathExtra::dot3(x23,v); + x23[0] = x3[0] + s2*v[0]; + x23[1] = x3[1] + s2*v[1]; + x23[2] = x3[2] + s2*v[2]; + + // find the fraction of the projection points on the edges + + if (fabs(x4[0] - x3[0]) > 0) + t13 = (x13[0] - x3[0])/(x4[0] - x3[0]); + else if (fabs(x4[1] - x3[1]) > 0) + t13 = (x13[1] - x3[1])/(x4[1] - x3[1]); + else if (fabs(x4[2] - x3[2]) > 0) + t13 = (x13[2] - x3[2])/(x4[2] - x3[2]); + + if (fabs(x4[0] - x3[0]) > 0) + t23 = (x23[0] - x3[0])/(x4[0] - x3[0]); + else if (fabs(x4[1] - x3[1]) > 0) + t23 = (x23[1] - x3[1])/(x4[1] - x3[1]); + else if (fabs(x4[2] - x3[2]) > 0) + t23 = (x23[2] - x3[2])/(x4[2] - x3[2]); + + if (fabs(x23[0] - x13[0]) > 0) + t31 = (x3[0] - x13[0])/(x23[0] - x13[0]); + else if (fabs(x23[1] - x13[1]) > 0) + t31 = (x3[1] - x13[1])/(x23[1] - x13[1]); + else if (fabs(x23[2] - x13[2]) > 0) + t31 = (x3[2] - x13[2])/(x23[2] - x13[2]); + + // x31 is the projection of x3 on x1-x2 + + x31[0] = x1[0] + t31*(x2[0] - x1[0]); + x31[1] = x1[1] + t31*(x2[1] - x1[1]); + x31[2] = x1[2] + t31*(x2[2] - x1[2]); + + if (fabs(x23[0] - x13[0]) > 0) + t41 = (x4[0] - x13[0])/(x23[0] - x13[0]); + else if (fabs(x23[1] - x13[1]) > 0) + t41 = (x4[1] - x13[1])/(x23[1] - x13[1]); + else if (fabs(x23[2] - x13[2]) > 0) + t41 = (x4[2] - x13[2])/(x23[2] - x13[2]); + + // x41 is the projection of x4 on x1-x2 + + x41[0] = x1[0] + t41*(x2[0] - x1[0]); + x41[1] = x1[1] + t41*(x2[1] - x1[1]); + x41[2] = x1[2] + t41*(x2[2] - x1[2]); + + // determine two ends from the overlapping segments + + int n1 = 0; + int n2 = 0; + if (t13 >= 0 && t13 <= 1) { + h1[0] = x1[0]; + h1[1] = x1[1]; + h1[2] = x1[2]; + h2[0] = x13[0]; + h2[1] = x13[1]; + h2[2] = x13[2]; + t1 = 0; + t2 = t13; + n1++; + n2++; + } + if (t23 >= 0 && t23 <= 1) { + if (n1 == 0) { + h1[0] = x2[0]; + h1[1] = x2[1]; + h1[2] = x2[2]; + h2[0] = x23[0]; + h2[1] = x23[1]; + h2[2] = x23[2]; + t1 = 1; + t2 = t23; + n1++; + n2++; + } else { + h1[0] = (x1[0]+x2[0])/2; + h1[1] = (x1[1]+x2[1])/2; + h1[2] = (x1[2]+x2[2])/2; + h2[0] = (x13[0]+x23[0])/2; + h2[1] = (x13[1]+x23[1])/2; + h2[2] = (x13[2]+x23[2])/2; + t1 = 0.5; + t2 = (t13+t23)/2; + n1++; + n2++; + } + } + + if (n1 == 0 && n2 == 0) { + if (t31 >= 0 && t31 <= 1) { + h1[0] = x31[0]; + h1[1] = x31[1]; + h1[2] = x31[2]; + h2[0] = x3[0]; + h2[1] = x3[1]; + h2[2] = x3[2]; + t1 = t31; + t2 = 0; + n1++; + n2++; + } + if (t41 >= 0 && t41 <= 1) { + if (n1 == 0) { + h1[0] = x41[0]; + h1[1] = x41[1]; + h1[2] = x41[2]; + h2[0] = x4[0]; + h2[1] = x4[1]; + h2[2] = x4[2]; + t1 = t41; + t2 = 1; + n1++; + n2++; + } else { + h1[0] = (x31[0]+x41[0])/2; + h1[1] = (x31[1]+x41[1])/2; + h1[2] = (x31[2]+x41[2])/2; + h2[0] = (x3[0]+x4[0])/2; + h2[1] = (x3[1]+x4[1])/2; + h2[2] = (x3[2]+x4[2])/2; + t1 = (t31+t41)/2; + t2 = 0.5; + n1++; + n2++; + } + } + } + + // if n1 == 0 and n2 == 0 at this point, + // which means no overlapping segments bt two parallel edges, + // return the default values of t1 and t2 + + return; + + } + + // find the vector n perpendicular to both edges + + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); + + // find the intersection of the line (x3,x4) and the plane (x1,x2,n) + // s = director of the line (x3,x4) + // n_p = plane normal vector of the plane (x1,x2,n) + + double s[3], n_p[3]; + MathExtra::sub3(x4, x3, s); + MathExtra::sub3(x2, x1, u); + MathExtra::cross3(u, n, n_p); + MathExtra::norm3(n_p); + + // solve for the intersection between the line and the plane + + double m[3][3], invm[3][3], p[3], ans[3]; + m[0][0] = -s[0]; + m[0][1] = u[0]; + m[0][2] = n[0]; + + m[1][0] = -s[1]; + m[1][1] = u[1]; + m[1][2] = n[1]; + + m[2][0] = -s[2]; + m[2][1] = u[2]; + m[2][2] = n[2]; + + MathExtra::sub3(x3, x1, p); + MathExtra::invert3(m, invm); + MathExtra::matvec(invm, p, ans); + + t2 = ans[0]; + h2[0] = x3[0] + s[0] * t2; + h2[1] = x3[1] + s[1] * t2; + h2[2] = x3[2] + s[2] * t2; + + project_pt_plane(h2, x1, n, h1, r); + + if (fabs(x2[0] - x1[0]) > 0) + t1 = (h1[0] - x1[0])/(x2[0] - x1[0]); + else if (fabs(x2[1] - x1[1]) > 0) + t1 = (h1[1] - x1[1])/(x2[1] - x1[1]); + else if (fabs(x2[2] - x1[2]) > 0) + t1 = (h1[2] - x1[2])/(x2[2] - x1[2]); +} + +/* ---------------------------------------------------------------------- + Calculate the total velocity of a point (vertex, a point on an edge): + vi = vcm + omega ^ (p - xcm) +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::total_velocity(double* p, double *xcm, + double* vcm, double *angmom, double *inertia, double *quat, double* vi) +{ + double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3]; + r[0] = p[0] - xcm[0]; + r[1] = p[1] - xcm[1]; + r[2] = p[2] - xcm[2]; + MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space); + MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space, + inertia,omega); + vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0]; + vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1]; + vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2]; +} + +/* ---------------------------------------------------------------------- + Determine the length of the contact segment, i.e. the separation between + 2 contacts, should be extended for 3D models. +------------------------------------------------------------------------- */ + +double PairBodyRoundedPolyhedron::contact_separation(const Contact& c1, + const Contact& c2) +{ + double x1 = 0.5*(c1.xi[0] + c1.xj[0]); + double y1 = 0.5*(c1.xi[1] + c1.xj[1]); + double z1 = 0.5*(c1.xi[2] + c1.xj[2]); + double x2 = 0.5*(c2.xi[0] + c2.xj[0]); + double y2 = 0.5*(c2.xi[1] + c2.xj[1]); + double z2 = 0.5*(c2.xi[2] + c2.xj[2]); + double rsq = (x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1); + return rsq; +} + +/* ---------------------------------------------------------------------- + find the number of unique contacts +------------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list, + int& num_contacts) +{ + int n = num_contacts; + for (int i = 0; i < n - 1; i++) { + + for (int j = i + 1; j < n; j++) { + if (contact_list[i].unique == 0) continue; + double d = contact_separation(contact_list[i], contact_list[j]); + if (d < EPSILON) contact_list[j].unique = 0; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBodyRoundedPolyhedron::sanity_check() +{ + + double x1[3],x2[3],x3[3],x4[3],h_a[3],h_b[3],d_a,d_b,u[3],v[3],n[3]; + double a[3],b[3],t_a,t_b; + int inside_a, inside_b; + + x1[0] = 0; x1[1] = 3; x1[2] = 0; + x2[0] = 3; x2[1] = 0; x2[2] = 0; + x3[0] = 4; x3[1] = 3; x3[2] = 0; + x4[0] = 5; x4[1] = 3; x4[2] = 0; + + a[0] = 0; a[1] = 0; a[2] = 0; + b[0] = 4; b[1] = 0; b[2] = 0; + + project_pt_line(a, x1, x2, h_a, d_a, t_a); + project_pt_line(b, x1, x2, h_b, d_b, t_b); +/* + printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f; d_b = %f\n", + h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a, d_b); +*/ +/* + int mode = edge_face_intersect(x1, x2, x3, a, b, h_a, h_b, d_a, d_b, + inside_a, inside_b); + + MathExtra::sub3(x2, x1, u); + MathExtra::sub3(x3, x1, v); + MathExtra::cross3(u, v, n); + MathExtra::norm3(n); +*/ +/* + project_pt_plane(a, x1, x2, x3, h_a, d_a, inside_a); + printf("h_a: %f %f %f; d = %f: inside %d\n", + h_a[0], h_a[1], h_a[2], d_a, inside_a); + project_pt_plane(b, x1, x2, x3, h_b, d_b, inside_b); + printf("h_b: %f %f %f; d = %f: inside %d\n", + h_b[0], h_b[1], h_b[2], d_b, inside_b); +*/ +/* + distance_bt_edges(x1, x2, x3, x4, h_a, h_b, t_a, t_b, d_a); + printf("h_a: %f %f %f; h_b: %f %f %f; t_a = %f; t_b = %f; d = %f\n", + h_a[0], h_a[1], h_a[2], h_b[0], h_b[1], h_b[2], t_a, t_b, d_a); +*/ +} + diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h new file mode 100644 index 0000000000000000000000000000000000000000..71c04ff9665aa0b24b7e7f4069cc4f4f4766bf4d --- /dev/null +++ b/src/BODY/pair_body_rounded_polyhedron.h @@ -0,0 +1,200 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(body/rounded/polyhedron,PairBodyRoundedPolyhedron) + +#else + +#ifndef LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H +#define LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairBodyRoundedPolyhedron : public Pair { + public: + PairBodyRoundedPolyhedron(class LAMMPS *); + ~PairBodyRoundedPolyhedron(); + void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + + virtual void kernel_force(double R, int itype, int jtype, + double& energy, double& fpair); + + struct Contact { + int ibody, jbody; // body (i.e. atom) indices (not tags) + int type; // 0 = VERTEX-FACE; 1 = EDGE-EDGE + double fx,fy,fz; // unscaled cohesive forces at contact + double xi[3]; // coordinates of the contact point on ibody + double xj[3]; // coordinates of the contact point on jbody + double separation; // contact surface separation + int unique; + }; + + protected: + double **k_n; // normal repulsion strength + double **k_na; // normal attraction strength + double c_n; // normal damping coefficient + double c_t; // tangential damping coefficient + double mu; // normal friction coefficient during gross sliding + double A_ua; // characteristic contact area + double cut_inner; // cutoff for interaction between vertex-edge surfaces + + class AtomVecBody *avec; + class BodyRoundedPolyhedron *bptr; + + double **discrete; // list of all sub-particles for all bodies + int ndiscrete; // number of discretes in list + int dmax; // allocated size of discrete list + int *dnum; // number of discretes per line, 0 if uninit + int *dfirst; // index of first discrete per each line + int nmax; // allocated size of dnum,dfirst vectors + + double **edge; // list of all edge for all bodies + int nedge; // number of edge in list + int edmax; // allocated size of edge list + int *ednum; // number of edges per line, 0 if uninit + int *edfirst; // index of first edge per each line + int ednummax; // allocated size of ednum,edfirst vectors + + double **face; // list of all edge for all bodies + int nface; // number of faces in list + int facmax; // allocated size of face list + int *facnum; // number of faces per line, 0 if uninit + int *facfirst; // index of first face per each line + int facnummax; // allocated size of facnum,facfirst vectors + + double *enclosing_radius; // enclosing radii for all bodies + double *rounded_radius; // rounded radii for all bodies + double *maxerad; // per-type maximum enclosing radius + + void allocate(); + void body2space(int); + + // sphere-sphere interaction + void sphere_against_sphere(int ibody, int jbody, int itype, int jtype, + double delx, double dely, double delz, double rsq, + double** v, double** f, int evflag); + // sphere-edge interaction + void sphere_against_edge(int ibody, int jbody, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int evflag); + // sphere-face interaction + void sphere_against_face(int ibody, int jbody, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int evflag); + // edge-edge interactions + int edge_against_edge(int ibody, int jbody, int itype, int jtype, + double** x,Contact* contact_list, int &num_contacts, + double &evdwl, double* facc); + // edge-face interactions + int edge_against_face(int ibody, int jbody, int itype, int jtype, + double** x, Contact* contact_list, int &num_contacts, + double &evdwl, double* facc); + + // a face vs. a single edge + int interaction_face_to_edge(int ibody, int face_index, double* xmi, + double rounded_radius_i, int jbody, int edge_index, + double* xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, + double& energy, double* facc); + // an edge vs. an edge from another body + int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi, + double rounded_radius_i, int jbody, int edge_index_j, + double* xmj, double rounded_radius_j, + int itype, int jtype, double cut_inner, + Contact* contact_list, int &num_contacts, + double& energy, double* facc); + + // compute contact forces if contact points are detected + void contact_forces(int ibody, int jbody, double *xi, double *xj, + double delx, double dely, double delz, double fx, double fy, double fz, + double** x, double** v, double** angmom, double** f, double** torque, + double* facc); + + // compute force and torque between two bodies given a pair of interacting points + void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj, + double r, double contact_dist, int itype, int jtype, + double** x, double** v, double** f, double** torque, + double** angmom, int jflag, double& energy, double* facc); + + // rescale the cohesive forces if a contact area is detected + void rescale_cohesive_forces(double** x, double** f, double** torque, + Contact* contact_list, int &num_contacts, + int itype, int jtype, double* facc); + + // compute the separation between two contacts + double contact_separation(const Contact& c1, const Contact& c2); + + // detect the unique contact points (as there may be double counts) + void find_unique_contacts(Contact* contact_list, int& num_contacts); + + // accumulate torque to a body given a force at a given point + void sum_torque(double* xm, double *x, double fx, double fy, double fz, double* torque); + + // find the intersection point (if any) between an edge and a face + int edge_face_intersect(double* x1, double* x2, double* x3, double* a, double* b, + double* hi1, double* hi2, double& d1, double& d2, + int& inside_a, int& inside_b); + // helper functions + int opposite_sides(double* n, double* x0, double* a, double* b); + void project_pt_plane(const double* q, const double* p, + const double* n, double* q_proj, double &d); + void project_pt_plane(const double* q, const double* x1, const double* x2, + const double* x3, double* q_proj, double &d, int& inside); + void project_pt_line(const double* q, const double* xi1, const double* xi2, + double* h, double& d, double& t); + void inside_polygon(int ibody, int face_index, double* xmi, + const double* q1, const double* q2, int& inside1, int& inside2); + + void distance_bt_edges(const double* x1, const double* x2, + const double* x3, const double* x4, + double* h1, double* h2, double& t1, double& t2, double& r); + void total_velocity(double* p, double *xcm, double* vcm, double *angmom, + double *inertia, double *quat, double* vi); + void sanity_check(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair body/rounded/polyhedron requires atom style body rounded/polyhedron + +Self-explanatory. + +E: Pair body requires body style rounded/polyhedron + +This pair style is specific to the rounded/polyhedron body style. + +*/ diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index a850a9b2b350c7a8c9de4b88fb9fda912f564a4c..20429009db948c5cf89b006c4b1807cb24f376f9 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -35,8 +35,12 @@ action pair_beck_gpu.cpp action pair_beck_gpu.h action pair_born_coul_long_gpu.cpp pair_born_coul_long.cpp action pair_born_coul_long_gpu.h pair_born_coul_long.cpp +action pair_born_coul_long_cs_gpu.cpp pair_born_coul_long_cs.cpp +action pair_born_coul_long_cs_gpu.h pair_born_coul_long_cs.cpp action pair_born_coul_wolf_gpu.cpp action pair_born_coul_wolf_gpu.h +action pair_born_coul_wolf_cs_gpu.cpp pair_born_coul_wolf_cs.cpp +action pair_born_coul_wolf_cs_gpu.h pair_born_coul_wolf_cs.cpp action pair_born_gpu.cpp action pair_born_gpu.h action pair_buck_coul_cut_gpu.cpp pair_buck_coul_cut.cpp @@ -55,6 +59,8 @@ action pair_coul_dsf_gpu.cpp action pair_coul_dsf_gpu.h action pair_coul_long_gpu.cpp pair_coul_long.cpp action pair_coul_long_gpu.h pair_coul_long.cpp +action pair_coul_long_cs_gpu.cpp pair_coul_long_cs.cpp +action pair_coul_long_cs_gpu.h pair_coul_long_cs.cpp action pair_dpd_gpu.cpp action pair_dpd_gpu.h action pair_dpd_tstat_gpu.cpp @@ -97,6 +103,8 @@ action pair_lj_cut_gpu.cpp action pair_lj_cut_gpu.h action pair_lj_expand_gpu.cpp action pair_lj_expand_gpu.h +action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp +action pair_lj_expand_coul_long_gpu.h pair_lj_expand_coul_long.cpp action pair_lj_gromacs_gpu.cpp action pair_lj_gromacs_gpu.h action pair_lj_sdk_coul_long_gpu.cpp pair_lj_sdk_coul_long.cpp diff --git a/src/GPU/gpu_extra.h b/src/GPU/gpu_extra.h index 56a4f15f1bff5a18ee050badf8acfb420c97b28b..111d13c563a2fc129c1d6e816f38dd7479c8c97a 100644 --- a/src/GPU/gpu_extra.h +++ b/src/GPU/gpu_extra.h @@ -58,6 +58,9 @@ namespace GPU_EXTRA { else if (all_success == -11) error->all(FLERR, "Invalid custom OpenCL parameter string."); + else if (all_success == -12) + error->all(FLERR, + "Invalid OpenCL platform ID."); else error->all(FLERR,"Unknown error in GPU library"); } diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp new file mode 100644 index 0000000000000000000000000000000000000000..13cf5f643abf8bb1b7003a64910ad6dc70fd371d --- /dev/null +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -0,0 +1,340 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Dac Nguyen (Northwestern) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_born_coul_long_cs_gpu.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "integrate.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "neigh_request.h" +#include "universe.h" +#include "update.h" +#include "domain.h" +#include "kspace.h" +#include "gpu_extra.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 +#define EWALD_P 9.95473818e-1 +#define B0 -0.1335096380159268 +#define B1 -2.57839507e-1 +#define B2 -1.37203639e-1 +#define B3 -8.88822059e-3 +#define B4 -5.80844129e-3 +#define B5 1.14652755e-1 + +#define EPSILON 1.0e-20 +#define EPS_EWALD 1.0e-6 +#define EPS_EWALD_SQR 1.0e-12 + +// External functions from cuda library for atom decomposition + +int bornclcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, + double **host_born3, double **host_a, + double **host_c, double **host_d, + double **sigma, double **offset, double *special_lj, + const int inum, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, + int &gpu_mode, FILE *screen, double **host_cut_ljsq, + double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +void bornclcs_gpu_clear(); +int** bornclcs_gpu_compute_n(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, double *sublo, + double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd); +void bornclcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd); +double bornclcs_gpu_bytes(); + +/* ---------------------------------------------------------------------- */ + +PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) : + PairBornCoulLongCS(lmp), gpu_mode(GPU_FORCE) +{ + respa_enable = 0; + reinitflag = 0; + cpu_time = 0.0; + GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairBornCoulLongCSGPU::~PairBornCoulLongCSGPU() +{ + bornclcs_gpu_clear(); +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulLongCSGPU::compute(int eflag, int vflag) +{ + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + int nall = atom->nlocal + atom->nghost; + int inum, host_start; + + bool success = true; + int *ilist, *numneigh, **firstneigh; + if (gpu_mode != GPU_FORCE) { + inum = atom->nlocal; + firstneigh = bornclcs_gpu_compute_n(neighbor->ago, inum, nall, atom->x, + atom->type, domain->sublo, domain->subhi, + atom->tag, atom->nspecial, atom->special, + eflag, vflag, eflag_atom, vflag_atom, + host_start, &ilist, &numneigh, cpu_time, + success, atom->q, domain->boxlo, + domain->prd); + } else { + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + bornclcs_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, + vflag_atom, host_start, cpu_time, success, atom->q, + atom->nlocal, domain->boxlo, domain->prd); + } + if (!success) + error->one(FLERR,"Insufficient memory on accelerator"); + + if (host_startq_flag) + error->all(FLERR, + "Pair style born/coul/long/cs/gpu requires atom attribute q"); + if (force->newton_pair) + error->all(FLERR, + "Cannot use newton pair with born/coul/long/cs/gpu pair style"); + + // Repeat cutsq calculation because done after call to init_style + double maxcut = -1.0; + double cut; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + cut = init_one(i,j); + cut *= cut; + if (cut > maxcut) + maxcut = cut; + cutsq[i][j] = cutsq[j][i] = cut; + } else + cutsq[i][j] = cutsq[j][i] = 0.0; + } + } + double cell_size = sqrt(maxcut) + neighbor->skin; + + cut_coulsq = cut_coul * cut_coul; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + int maxspecial=0; + if (atom->molecular) + maxspecial=atom->maxspecial; + int success = bornclcs_gpu_init(atom->ntypes+1, cutsq, rhoinv, + born1, born2, born3, a, c, d, sigma, + offset, force->special_lj, atom->nlocal, + atom->nlocal+atom->nghost, 300, maxspecial, + cell_size, gpu_mode, screen, cut_ljsq, + cut_coulsq, force->special_coul, + force->qqrd2e, g_ewald); + + GPU_EXTRA::check_flag(success,error,world); + + if (gpu_mode == GPU_FORCE) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairBornCoulLongCSGPU::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes + bornclcs_gpu_bytes(); +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulLongCSGPU::cpu_compute(int start, int inum, int eflag, + int vflag, int *ilist, int *numneigh, + int **firstneigh) +{ + int i,j,ii,jj,jnum,itable,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double fraction,table; + double r,rsq,rexp,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double grij,expm2,prefactor,t,erfc,u; + int *jlist; + + evdwl = ecoul = 0.0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + double qqrd2e = force->qqrd2e; + + // loop over neighbors of my atoms + + for (ii = start; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq) { + rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond; + r2inv = 1.0/rsq; + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + prefactor = qqrd2e * qtmp*q[j]; + if (factor_coul < 1.0) { + // When bonded parts are being calculated a minimal distance (EPS_EWALD) + // has to be added to the prefactor and erfc in order to make the + // used approximation functions for the Ewald correction valid + grij = g_ewald * (r+EPS_EWALD); + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + u = 1.0 - t; + erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; + prefactor /= (r+EPS_EWALD); + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul)); + // Additionally r2inv needs to be accordingly modified since the later + // scaling of the overall force shall be consistent + r2inv = 1.0/(rsq + EPS_EWALD_SQR); + } else { + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + u = 1.0 - t; + erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; + prefactor /= r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + } + } else { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + itable = rsq_lookup.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + + forcecoul *= r2inv; + + } else forcecoul = 0; + + r2inv = 1.0/rsq; + r = sqrt(rsq); + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = forcecoul + factor_lj*forceborn * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = prefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz); + } + } + } +} diff --git a/src/GPU/pair_born_coul_long_cs_gpu.h b/src/GPU/pair_born_coul_long_cs_gpu.h new file mode 100644 index 0000000000000000000000000000000000000000..65c80157f2a6c334e229d4d072cb3acfa02d5d75 --- /dev/null +++ b/src/GPU/pair_born_coul_long_cs_gpu.h @@ -0,0 +1,66 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(born/coul/long/cs/gpu,PairBornCoulLongCSGPU) + +#else + +#ifndef LMP_PAIR_BORN_COUL_LONG_CS_GPU_H +#define LMP_PAIR_BORN_COUL_LONG_CS_GPU_H + +#include "pair_born_coul_long_cs.h" + +namespace LAMMPS_NS { + +class PairBornCoulLongCSGPU : public PairBornCoulLongCS { + public: + PairBornCoulLongCSGPU(LAMMPS *lmp); + ~PairBornCoulLongCSGPU(); + void cpu_compute(int, int, int, int, int *, int *, int **); + void compute(int, int); + void init_style(); + double memory_usage(); + + enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH }; + + private: + int gpu_mode; + double cpu_time; +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Insufficient memory on accelerator + +There is insufficient memory on one of the devices specified for the gpu +package + +E: Pair style born/coul/long/cs/gpu requires atom attribute q + +The atom style defined does not have this attribute. + +E: Cannot use newton pair with born/coul/long/cs/gpu pair style + +Self-explanatory. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +*/ diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp new file mode 100644 index 0000000000000000000000000000000000000000..90ddf825a96c42859d1876a4e502a1c5cf60ac61 --- /dev/null +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -0,0 +1,295 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Trung Dac Nguyen (Northwestern) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_born_coul_wolf_cs_gpu.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "integrate.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "neigh_request.h" +#include "universe.h" +#include "update.h" +#include "domain.h" +#include "gpu_extra.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EPSILON 1.0e-20 + +// External functions from cuda library for atom decomposition + +int borncwcs_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv, + double **host_born1, double **host_born2, + double **host_born3, double **host_a, double **host_c, + double **host_d, double **sigma, double **offset, + double *special_lj, const int inum, + const int nall, const int max_nbors, const int maxspecial, + const double cell_size, int &gpu_mode, FILE *screen, + double **host_cut_ljsq, double host_cut_coulsq, + double *host_special_coul, const double qqrd2e, + const double alf, const double e_shift, const double f_shift); +void borncwcs_gpu_clear(); +int ** borncwcs_gpu_compute_n(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, double *sublo, + double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success, double *host_q, double *boxlo, + double *prd); +void borncwcs_gpu_compute(const int ago, const int inum_full, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd); +double borncwcs_gpu_bytes(); + +/* ---------------------------------------------------------------------- */ + +PairBornCoulWolfCSGPU::PairBornCoulWolfCSGPU(LAMMPS *lmp) : PairBornCoulWolfCS(lmp), + gpu_mode(GPU_FORCE) +{ + respa_enable = 0; + reinitflag = 0; + cpu_time = 0.0; + GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairBornCoulWolfCSGPU::~PairBornCoulWolfCSGPU() +{ + borncwcs_gpu_clear(); +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulWolfCSGPU::compute(int eflag, int vflag) +{ + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + int nall = atom->nlocal + atom->nghost; + int inum, host_start; + + bool success = true; + int *ilist, *numneigh, **firstneigh; + if (gpu_mode != GPU_FORCE) { + inum = atom->nlocal; + firstneigh = borncwcs_gpu_compute_n(neighbor->ago, inum, nall, + atom->x, atom->type, domain->sublo, + domain->subhi, atom->tag, atom->nspecial, + atom->special, eflag, vflag, eflag_atom, + vflag_atom, host_start, + &ilist, &numneigh, cpu_time, success, + atom->q, domain->boxlo, domain->prd); + } else { + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + borncwcs_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, + vflag_atom, host_start, cpu_time, success, atom->q, + atom->nlocal, domain->boxlo, domain->prd); + } + if (!success) + error->one(FLERR,"Insufficient memory on accelerator"); + + if (host_startnewton_pair) + error->all(FLERR, + "Cannot use newton pair with born/coul/wolf/cs/gpu pair style"); + + // Repeat cutsq calculation because done after call to init_style + double maxcut = -1.0; + double cut; + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + cut = init_one(i,j); + cut *= cut; + if (cut > maxcut) + maxcut = cut; + cutsq[i][j] = cutsq[j][i] = cut; + } else + cutsq[i][j] = cutsq[j][i] = 0.0; + } + } + double cell_size = sqrt(maxcut) + neighbor->skin; + + cut_coulsq = cut_coul * cut_coul; + + double e_shift = erfc(alf*cut_coul)/cut_coul; + double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / + cut_coul; + + int maxspecial=0; + if (atom->molecular) + maxspecial=atom->maxspecial; + int success = borncwcs_gpu_init(atom->ntypes+1, cutsq, rhoinv, + born1, born2, born3, a, c, d, sigma, offset, + force->special_lj, atom->nlocal, + atom->nlocal+atom->nghost, 300, maxspecial, + cell_size, gpu_mode, screen, cut_ljsq, + cut_coulsq, force->special_coul, force->qqrd2e, + alf, e_shift, f_shift); + GPU_EXTRA::check_flag(success,error,world); + + if (gpu_mode == GPU_FORCE) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +double PairBornCoulWolfCSGPU::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes + borncwcs_gpu_bytes(); +} + +/* ---------------------------------------------------------------------- */ + +void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag, int vflag, + int *ilist, int *numneigh, + int **firstneigh) { + int i,j,ii,jj,jnum,itype,jtype; + double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; + double erfcc,erfcd,v_sh,dvdrr,e_self,qisq; + double prefactor; + double r,rexp; + int *jlist; + + evdwl = ecoul = 0.0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + double qqrd2e = force->qqrd2e; + + double e_shift = erfc(alf*cut_coul)/cut_coul; + double f_shift = -(e_shift+ 2.0*alf/MY_PIS * exp(-alf*alf*cut_coul*cut_coul)) / + cut_coul; + + // loop over neighbors of my atoms + + for (ii = start; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + qisq = qtmp*qtmp; + e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e; + if (evflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + rsq += EPSILON; // Add EPISLON for case: r = 0; Interaction must be removed by special bond + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + prefactor = qqrd2e*qtmp*q[j]/r; + erfcc = erfc(alf*r); + erfcd = exp(-alf*alf*r*r); + v_sh = (erfcc - e_shift*r) * prefactor; + dvdrr = (erfcc/rsq + 2.0*alf/MY_PIS * erfcd/r) + f_shift; + forcecoul = dvdrr*rsq*prefactor; + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]); + forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv + + born3[itype][jtype]*r2inv*r6inv; + } else forceborn = 0.0; + + fpair = (factor_coul*forcecoul + factor_lj*forceborn) * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) { + if (rsq < cut_coulsq) { + ecoul = v_sh; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv + + d[itype][jtype]*r6inv*r2inv - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz); + } + } + } +} diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.h b/src/GPU/pair_born_coul_wolf_cs_gpu.h new file mode 100644 index 0000000000000000000000000000000000000000..5f4f4ea35c4e867c18cb52d3aacc7f901df7544d --- /dev/null +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.h @@ -0,0 +1,58 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(born/coul/wolf/cs/gpu,PairBornCoulWolfCSGPU) + +#else + +#ifndef LMP_PAIR_BORN_COUL_WOLF_CS_GPU_H +#define LMP_PAIR_BORN_COUL_WOLF_CS_GPU_H + +#include "pair_born_coul_wolf_cs.h" + +namespace LAMMPS_NS { + +class PairBornCoulWolfCSGPU : public PairBornCoulWolfCS { + public: + PairBornCoulWolfCSGPU(LAMMPS *lmp); + ~PairBornCoulWolfCSGPU(); + void cpu_compute(int, int, int, int, int *, int *, int **); + void compute(int, int); + void init_style(); + double memory_usage(); + + enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH }; + + private: + int gpu_mode; + double cpu_time; +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Insufficient memory on accelerator + +There is insufficient memory on one of the devices specified for the gpu +package + +E: Cannot use newton pair with born/coul/wolf/cs/gpu pair style + +Self-explanatory. + +*/ diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp new file mode 100644 index 0000000000000000000000000000000000000000..cbb9c73ceb0fa0cc371d62781647a427b338a130 --- /dev/null +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -0,0 +1,320 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Trung Nguyen (Northwestern) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_coul_long_cs_gpu.h" +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "integrate.h" +#include "memory.h" +#include "error.h" +#include "neigh_request.h" +#include "universe.h" +#include "update.h" +#include "domain.h" +#include "kspace.h" +#include "gpu_extra.h" + +using namespace LAMMPS_NS; + +#define EWALD_F 1.12837917 +#define EWALD_P 9.95473818e-1 +#define B0 -0.1335096380159268 +#define B1 -2.57839507e-1 +#define B2 -1.37203639e-1 +#define B3 -8.88822059e-3 +#define B4 -5.80844129e-3 +#define B5 1.14652755e-1 + +#define EPSILON 1.0e-20 +#define EPS_EWALD 1.0e-6 +#define EPS_EWALD_SQR 1.0e-12 + +// External functions from cuda library for atom decomposition + +int clcs_gpu_init(const int ntypes, double **scale, + const int nlocal, const int nall, const int max_nbors, + const int maxspecial, const double cell_size, int &gpu_mode, + FILE *screen, double host_cut_coulsq, double *host_special_coul, + const double qqrd2e, const double g_ewald); +void clcs_gpu_reinit(const int ntypes, double **scale); +void clcs_gpu_clear(); +int ** clcs_gpu_compute_n(const int ago, const int inum, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, + int **nspecial, tagint **special, const bool eflag, + const bool vflag, const bool eatom, const bool vatom, + int &host_start, int **ilist, int **jnum, + const double cpu_time, bool &success, double *host_q, + double *boxlo, double *prd); +void clcs_gpu_compute(const int ago, const int inum, const int nall, + double **host_x, int *host_type, int *ilist, int *numj, + int **firstneigh, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + const double cpu_time, bool &success, double *host_q, + const int nlocal, double *boxlo, double *prd); +double clcs_gpu_bytes(); + +/* ---------------------------------------------------------------------- */ + +PairCoulLongCSGPU::PairCoulLongCSGPU(LAMMPS *lmp) : + PairCoulLongCS(lmp), gpu_mode(GPU_FORCE) +{ + respa_enable = 0; + cpu_time = 0.0; + GPU_EXTRA::gpu_ready(lmp->modify, lmp->error); +} + +/* ---------------------------------------------------------------------- + free all arrays +------------------------------------------------------------------------- */ + +PairCoulLongCSGPU::~PairCoulLongCSGPU() +{ + clcs_gpu_clear(); +} + +/* ---------------------------------------------------------------------- */ + +void PairCoulLongCSGPU::compute(int eflag, int vflag) +{ + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + int nall = atom->nlocal + atom->nghost; + int inum, host_start; + + bool success = true; + int *ilist, *numneigh, **firstneigh; + if (gpu_mode != GPU_FORCE) { + inum = atom->nlocal; + firstneigh = clcs_gpu_compute_n(neighbor->ago, inum, nall, atom->x, + atom->type, domain->sublo, domain->subhi, + atom->tag, atom->nspecial, atom->special, + eflag, vflag, eflag_atom, vflag_atom, + host_start, &ilist, &numneigh, cpu_time, + success, atom->q, domain->boxlo, + domain->prd); + } else { + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + clcs_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, + ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, + vflag_atom, host_start, cpu_time, success, atom->q, + atom->nlocal, domain->boxlo, domain->prd); + } + if (!success) + error->one(FLERR,"Insufficient memory on accelerator"); + + if (host_startq_flag) + error->all(FLERR,"Pair style coul/long/cs/gpu requires atom attribute q"); + if (force->newton_pair) + error->all(FLERR,"Cannot use newton pair with coul/long/cs/gpu pair style"); + + // Call init_one calculation make sure scale is correct + for (int i = 1; i <= atom->ntypes; i++) { + for (int j = i; j <= atom->ntypes; j++) { + if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { + double cut = init_one(i,j); + } + } + } + double cell_size = cut_coul + neighbor->skin; + + cut_coulsq = cut_coul * cut_coul; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + // setup force tables + + if (ncoultablebits) init_tables(cut_coul,cut_respa); + + int maxspecial=0; + if (atom->molecular) + maxspecial=atom->maxspecial; + int success = clcs_gpu_init(atom->ntypes+1, scale, + atom->nlocal, atom->nlocal+atom->nghost, 300, + maxspecial, cell_size, gpu_mode, screen, cut_coulsq, + force->special_coul, force->qqrd2e, g_ewald); + + GPU_EXTRA::check_flag(success,error,world); + + if (gpu_mode == GPU_FORCE) { + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + } +} + +/* ---------------------------------------------------------------------- */ + +void PairCoulLongCSGPU::reinit() +{ + Pair::reinit(); + + clcs_gpu_reinit(atom->ntypes+1, scale); +} + +/* ---------------------------------------------------------------------- */ + +double PairCoulLongCSGPU::memory_usage() +{ + double bytes = Pair::memory_usage(); + return bytes + clcs_gpu_bytes(); +} + +/* ---------------------------------------------------------------------- */ + +void PairCoulLongCSGPU::cpu_compute(int start, int inum, int eflag, + int vflag, int *ilist, int *numneigh, + int **firstneigh) +{ + int i,j,ii,jj,jnum,itable,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; + double fraction,table; + double r,r2inv,forcecoul,factor_coul; + double grij,expm2,prefactor,t,erfc,u; + int *jlist; + double rsq; + + ecoul = 0.0; + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + double *special_coul = force->special_coul; + double qqrd2e = force->qqrd2e; + + // loop over neighbors of my atoms + + for (ii = start; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cut_coulsq) { + rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond; + r2inv = 1.0/rsq; + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j]; + if (factor_coul < 1.0) { + // When bonded parts are being calculated a minimal distance (EPS_EWALD) + // has to be added to the prefactor and erfc in order to make the + // used approximation functions for the Ewald correction valid + grij = g_ewald * (r+EPS_EWALD); + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + u = 1.0 - t; + erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; + prefactor /= (r+EPS_EWALD); + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul)); + // Additionally r2inv needs to be accordingly modified since the later + // scaling of the overall force shall be consistent + r2inv = 1.0/(rsq + EPS_EWALD_SQR); + } else { + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + u = 1.0 - t; + erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2; + prefactor /= r; + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + } + } else { + union_int_float_t rsq_lookup; + rsq_lookup.f = rsq; + itable = rsq_lookup.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = scale[itype][jtype] * qtmp*q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = scale[itype][jtype] * qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + + fpair = forcecoul * r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + + if (eflag) { + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + ecoul = prefactor*erfc; + else { + table = etable[itable] + fraction*detable[itable]; + ecoul = scale[itype][jtype] * qtmp*q[j] * table; + } + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + } + + if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz); + } + } + } +} diff --git a/src/GPU/pair_coul_long_cs_gpu.h b/src/GPU/pair_coul_long_cs_gpu.h new file mode 100644 index 0000000000000000000000000000000000000000..95ed8d018227aa1246d85f3764b22cd38642059a --- /dev/null +++ b/src/GPU/pair_coul_long_cs_gpu.h @@ -0,0 +1,67 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(coul/long/cs/gpu,PairCoulLongCSGPU) + +#else + +#ifndef LMP_PAIR_COUL_LONG_CS_GPU_H +#define LMP_PAIR_COUL_LONG_CS_GPU_H + +#include "pair_coul_long_cs.h" + +namespace LAMMPS_NS { + +class PairCoulLongCSGPU : public PairCoulLongCS { + public: + PairCoulLongCSGPU(LAMMPS *lmp); + ~PairCoulLongCSGPU(); + void cpu_compute(int, int, int, int, int *, int *, int **); + void compute(int, int); + void init_style(); + void reinit(); + double memory_usage(); + + enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH }; + + private: + int gpu_mode; + double cpu_time; +}; + +} +#endif +#endif + +/* ERROR/WARNING messages: + +E: Insufficient memory on accelerator + +There is insufficient memory on one of the devices specified for the gpu +package + +E: Pair style coul/long/cs/gpu requires atom attribute q + +The atom style defined does not have these attributes. + +E: Cannot use newton pair with coul/long/cs/gpu pair style + +Self-explanatory. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +*/ diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 203128471d4cfaeaea3010513d89c03f31c64856..49e8be5879e3e607c6505982dc6e90d5436f2816 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -223,8 +223,9 @@ void PairLJExpandCoulLongGPU::cpu_compute(int start, int inum, int eflag, double fraction,table; double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; double grij,expm2,prefactor,t,erfc; + double rsq,rshift,rshiftsq,rshift2inv; + int *jlist; - double rsq; evdwl = ecoul = 0.0; @@ -290,11 +291,16 @@ void PairLJExpandCoulLongGPU::cpu_compute(int start, int inum, int eflag, } else forcecoul = 0.0; if (rsq < cut_ljsq[itype][jtype]) { - r6inv = r2inv*r2inv*r2inv; + r = sqrt(rsq); + rshift = r - shift[itype][jtype]; + rshiftsq = rshift*rshift; + rshift2inv = 1.0/rshiftsq; + r6inv = rshift2inv*rshift2inv*rshift2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + forcelj = factor_lj*forcelj/rshift/r; } else forcelj = 0.0; - fpair = (forcecoul + factor_lj*forcelj) * r2inv; + fpair = forcecoul*r2inv + forcelj; f[i][0] += delx*fpair; f[i][1] += dely*fpair; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 679690ea82215c9a389ff9b417c74385a35a163e..347177b7f454bc03abfd739e8d51f218065b24de 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -148,7 +148,7 @@ void FixNHKokkos::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 70055bf8c9df4fd0f70f32b83e012e9eec0132c9..99e51ebe38e0a154683ff6b5476a467e3fba4941 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -157,7 +157,6 @@ void FixShardlowKokkos::init() k_pairDPDE->k_cutsq.template sync(); d_cutsq = k_pairDPDE->k_cutsq.template view(); - const double boltz2 = 2.0*force->boltz; for (int i = 1; i <= ntypes; i++) { for (int j = i; j <= ntypes; j++) { F_FLOAT cutone = k_pairDPDE->cut[i][j]; @@ -165,7 +164,7 @@ void FixShardlowKokkos::init() else k_params.h_view(i,j).cutinv = FLT_MAX; k_params.h_view(i,j).halfsigma = 0.5*k_pairDPDE->sigma[i][j]; k_params.h_view(i,j).kappa = k_pairDPDE->kappa[i][j]; - k_params.h_view(i,j).alpha = sqrt(boltz2*k_pairDPDE->kappa[i][j]); + k_params.h_view(i,j).alpha = k_pairDPDE->alpha[i][j]; k_params.h_view(j,i) = k_params.h_view(i,j); diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 7ff536f8dd792c77515ec0e0f55a569d1f4763ef..038d95394ac6947036e44e39c0f684251e5ddd31 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -591,7 +591,7 @@ void PairDPDfdtEnergyKokkos::operator()(TagPairDPDfdtEnergyComputeNo // Compute uCond randnum = rand_gen.normal(); kappa_ij = STACKPARAMS?m_params[itype][jtype].kappa:params(itype,jtype).kappa; - alpha_ij = sqrt(2.0*boltz*kappa_ij); + alpha_ij = STACKPARAMS?m_params[itype][jtype].alpha:params(itype,jtype).alpha; randPair = alpha_ij*wr*randnum*dtinvsqrt; uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd; @@ -676,6 +676,7 @@ double PairDPDfdtEnergyKokkos::init_one(int i, int j) k_params.h_view(i,j).a0 = a0[i][j]; k_params.h_view(i,j).sigma = sigma[i][j]; k_params.h_view(i,j).kappa = kappa[i][j]; + k_params.h_view(i,j).alpha = alpha[i][j]; k_params.h_view(j,i) = k_params.h_view(i,j); if(i::init_md() swa = control->nonb_low; swb = control->nonb_cut; + enobondsflag = control->enobondsflag; if (fabs(swa) > 0.01 ) error->warning(FLERR,"Warning: non-zero lower Taper-radius cutoff"); @@ -2272,12 +2273,12 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) e_lp = p_lp2 * d_Delta_lp[i] * inv_expvd2; const F_FLOAT dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * d_Delta_lp[i] * expvd2 * inv_expvd2*inv_expvd2; const F_FLOAT CElp = dElp * d_dDelta_lp[i]; - if (numbonds > 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) a_CdDelta[i] += CElp; if (eflag) ev.ereax[0] += e_lp; @@ -2314,7 +2315,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8; if (eflag) ev.ereax[2] += e_un; @@ -2334,7 +2335,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeMulti2 0 || control->enobondsflag) + if (numbonds > 0 || enobondsflag) a_CdDelta[i] += CEunder3; const int j_start = d_bo_first[i]; diff --git a/src/KOKKOS/pair_reaxc_kokkos.h b/src/KOKKOS/pair_reaxc_kokkos.h index 5175e274a8998f45ee6d8f40116f1bf47f671af3..5c96d44618361ca3828ba26ceb1738a1dac4de51 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.h +++ b/src/KOKKOS/pair_reaxc_kokkos.h @@ -427,7 +427,7 @@ class PairReaxCKokkos : public PairReaxC { friend void pair_virial_fdotr_compute(PairReaxCKokkos*); - int bocnt,hbcnt; + int bocnt,hbcnt,enobondsflag; typedef LR_lookup_table_kk LR_lookup_table_kk_DT; diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index c2bfa1a5a1f1ba6500b4da5baa4633833abb6d1b..18502dd0138d56fc6ebe73fa1f37461e5357c848 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -37,11 +37,18 @@ using namespace FixConst; extern "C" { void latte(int *, int *, double *, int *, int *, double *, double *, double *, double *, - double *, double *, double *, int*, - double *, double *, double *, double *, bool *); + double *, double *, double *, int *, + double *, double *, double *, double *, int * , bool *); int latte_abiversion(); } +// the ABIVERSION number here must be kept consistent +// with its counterpart in the LATTE library and the +// prototype above. We want to catch mismatches with +// a meaningful error messages, as they can cause +// difficult to debug crashes or memory corruption. + +#define LATTE_ABIVERSION 20180622 #define INVOKED_PERATOM 8 /* ---------------------------------------------------------------------- */ @@ -55,7 +62,7 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) : if (comm->nprocs != 1) error->all(FLERR,"Fix latte currently runs only in serial"); - if (20180207 != latte_abiversion()) + if (LATTE_ABIVERSION != latte_abiversion()) error->all(FLERR,"LAMMPS is linked against incompatible LATTE library"); if (narg != 4) error->all(FLERR,"Illegal fix latte command"); @@ -191,14 +198,18 @@ void FixLatte::init_list(int id, NeighList *ptr) void FixLatte::setup(int vflag) { + newsystem = 1; post_force(vflag); + newsystem = 0; } /* ---------------------------------------------------------------------- */ void FixLatte::min_setup(int vflag) { + newsystem = 1; post_force(vflag); + newsystem = 0; } /* ---------------------------------------------------------------------- */ @@ -288,10 +299,10 @@ void FixLatte::post_force(int vflag) if (coulomb) forces = &flatte[0][0]; else forces = &atom->f[0][0]; int maxiter = -1; - + latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy, &domain->xz,&domain->yz,forces,&maxiter,&latte_energy, - &atom->v[0][0],&update->dt,virial,&latteerror); + &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); if (latteerror) error->all(FLERR,"Internal LATTE problem"); diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 46c65b201696d2acdcb257d2182690e710a14115..6d30ced0a075c7a162b0865c0668f9f51485cada 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -48,7 +48,7 @@ class FixLatte : public Fix { int coulomb,pbcflag,pe_peratom,virial_global,virial_peratom,neighflag; int eflag_caller; - int nmax; + int nmax,newsystem; double *qpotential; double **flatte; double latte_energy; diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl new file mode 100644 index 0000000000000000000000000000000000000000..0f5087618ba749169e73a7ff45178f8d660f840b --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl @@ -0,0 +1,121 @@ +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +#export OMPI_CXX = armclang++ +CC = mpicxx +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl new file mode 100644 index 0000000000000000000000000000000000000000..c303a97e177109b3e73f2d85cb2112199c028c7a --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl @@ -0,0 +1,120 @@ +# arm_serial = Arm armclang compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = armclang++ +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = armclang++ +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl new file mode 100644 index 0000000000000000000000000000000000000000..b3cc1f48a3887bf0a54838ea460a4a712e5c36af --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl @@ -0,0 +1,121 @@ +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +export OMPI_CXX = g++ +CC = mpicxx +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl new file mode 100644 index 0000000000000000000000000000000000000000..45c0bb162b2ff714cbae797ba7cd570ea9bf44f8 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl @@ -0,0 +1,120 @@ +# g++_serial = GNU g++ compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = g++ +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = g++ +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.theta b/src/MAKE/MACHINES/Makefile.theta new file mode 100644 index 0000000000000000000000000000000000000000..cad5a03b420274d6f99eed1f2a730ee671638eb9 --- /dev/null +++ b/src/MAKE/MACHINES/Makefile.theta @@ -0,0 +1,133 @@ +# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT +# module load perftools-base perftools +# make theta -j 8 +# pat_build -g mpi -u ./lmp_theta + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = CC -mkl +#OPTFLAGS = -O0 +OPTFLAGS = -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits +CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \ + -fno-alias -ansi-alias -restrict $(OPTFLAGS) +#CCFLAGS += -DLMP_INTEL_NO_TBB +#CCFLAGS += -DLAMMPS_BIGBIG +#CCFLAGS += -D_USE_PAPI +#CCFLAGS += -D_USE_CRAYPAT_API +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = $(CC) +LINKFLAGS = -g -qopenmp $(OPTFLAGS) +LINKFLAGS += -dynamic +LIB = +#LIB += -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc +LIB += -ltbbmalloc +#LIB += /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP #-DLAMMPS_JPEG + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_MKL -DFFT_SINGLE +FFT_PATH = +FFT_LIB = -L$(MKLROOT)/lib/intel64/ -Wl,--start-group -lmkl_intel_ilp64 \ + -lmkl_intel_thread -lmkl_core -Wl,--end-group + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + icc -O -o $@ $< + +sinclude .depend diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp new file mode 100644 index 0000000000000000000000000000000000000000..66ebad6244a9d16b939bfb61c63862742e709cc8 --- /dev/null +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -0,0 +1,677 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Alexander Stukowski + Technical University of Darmstadt, + Germany Department of Materials Science +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_eam_cd.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define ASSERT(cond) +#define MAXLINE 1024 // This sets the maximum line length in EAM input files. + +PairEAMCD::PairEAMCD(LAMMPS *lmp, int _cdeamVersion) + : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion) +{ + single_enable = 0; + restartinfo = 0; + + rhoB = NULL; + D_values = NULL; + hcoeff = NULL; + + // Set communication buffer sizes needed by this pair style. + + if (cdeamVersion == 1) { + comm_forward = 4; + comm_reverse = 3; + } else if (cdeamVersion == 2) { + comm_forward = 3; + comm_reverse = 2; + } else { + error->all(FLERR,"Invalid eam/cd potential version."); + } +} + +PairEAMCD::~PairEAMCD() +{ + memory->destroy(rhoB); + memory->destroy(D_values); + if (hcoeff) delete[] hcoeff; +} + +void PairEAMCD::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,rhoip,rhojp,recip,phi; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + + // Grow per-atom arrays if necessary + + if (atom->nmax > nmax) { + memory->destroy(rho); + memory->destroy(fp); + memory->destroy(rhoB); + memory->destroy(D_values); + nmax = atom->nmax; + memory->create(rho,nmax,"pair:rho"); + memory->create(rhoB,nmax,"pair:rhoB"); + memory->create(fp,nmax,"pair:fp"); + memory->create(D_values,nmax,"pair:D_values"); + } + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // Zero out per-atom arrays. + + int m = nlocal + atom->nghost; + for (i = 0; i < m; i++) { + rho[i] = 0.0; + rhoB[i] = 0.0; + D_values[i] = 0.0; + } + + // Stage I + + // Compute rho and rhoB at each local atom site. + + // Additionally calculate the D_i values here if we are using the + // one-site formulation. For the two-site formulation we have to + // calculate the D values in an extra loop (Stage II). + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + jtype = type[j]; + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + double localrho = RhoOfR(index, jtype, itype); + rho[i] += localrho; + if (jtype == speciesB) rhoB[i] += localrho; + if (newton_pair || j < nlocal) { + localrho = RhoOfR(index, itype, jtype); + rho[j] += localrho; + if (itype == speciesB) rhoB[j] += localrho; + } + + if (cdeamVersion == 1 && itype != jtype) { + + // Note: if the i-j interaction is not concentration dependent (because either + // i or j are not species A or B) then its contribution to D_i and D_j should + // be ignored. + // This if-clause is only required for a ternary. + + if ((itype == speciesA && jtype == speciesB) + || (jtype == speciesA && itype == speciesB)) { + double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); + D_values[i] += Phi_AB; + if (newton_pair || j < nlocal) + D_values[j] += Phi_AB; + } + } + } + } + } + + // Communicate and sum densities. + + if (newton_pair) { + communicationStage = 1; + comm->reverse_comm_pair(this); + } + + // fp = derivative of embedding energy at each atom + // phi = embedding energy at each atom + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + EAMTableIndex index = rhoToTableIndex(rho[i]); + fp[i] = FPrimeOfRho(index, type[i]); + if (eflag) { + phi = FofRho(index, type[i]); + if (eflag_global) eng_vdwl += phi; + if (eflag_atom) eatom[i] += phi; + } + } + + // Communicate derivative of embedding function and densities + // and D_values (this for one-site formulation only). + + communicationStage = 2; + comm->forward_comm_pair(this); + + // The electron densities may not drop to zero because then the + // concentration would no longer be defined. But the concentration + // is not needed anyway if there is no interaction with another atom, + // which is the case if the electron density is exactly zero. + // That's why the following lines have been commented out. + // + //for (i = 0; i < nlocal + atom->nghost; i++) { + // if (rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB)) + // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density."); + //} + + // Stage II + // This is only required for the original two-site formulation of the CD-EAM potential. + + if (cdeamVersion == 2) { + + // Compute intermediate value D_i for each atom. + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // This code line is required for ternary alloys. + + if (itype != speciesA && itype != speciesB) continue; + + double x_i = rhoB[i] / rho[i]; // Concentration at atom i. + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + if (itype == jtype) continue; + + // This code line is required for ternary alloys. + + if (jtype != speciesA && jtype != speciesB) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + + // The concentration independent part of the cross pair potential. + + double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); + + // Average concentration of two sites + + double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]); + + // Calculate derivative of h(x_ij) polynomial function. + + double h_prime = evalHprime(x_ij); + + D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]); + if (newton_pair || j < nlocal) + D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]); + } + } + } + + // Communicate and sum D values. + + if (newton_pair) { + communicationStage = 3; + comm->reverse_comm_pair(this); + } + communicationStage = 4; + comm->forward_comm_pair(this); + } + + // Stage III + + // Compute force acting on each atom. + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // Concentration at site i + // The value -1 indicates: no concentration dependence for all interactions of atom i. + // It will be replaced by the concentration at site i if atom i is either A or B. + + double x_i = -1.0; + double D_i, h_prime_i; + + // This if-clause is only required for ternary alloys. + + if ((itype == speciesA || itype == speciesB) && rho[i] != 0.0) { + + // Compute local concentration at site i. + + x_i = rhoB[i]/rho[i]; + ASSERT(x_i >= 0 && x_i<=1.0); + + if (cdeamVersion == 1) { + + // Calculate derivative of h(x_i) polynomial function. + + h_prime_i = evalHprime(x_i); + D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]); + } else if (cdeamVersion == 2) { + D_i = D_values[i]; + } else { + ASSERT(false); + } + } + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutforcesq) { + jtype = type[j]; + double r = sqrt(rsq); + const EAMTableIndex index = radiusToTableIndex(r); + + // rhoip = derivative of (density at atom j due to atom i) + // rhojp = derivative of (density at atom i due to atom j) + // psip needs both fp[i] and fp[j] terms since r_ij appears in two + // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) + // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip + + rhoip = RhoPrimeOfR(index, itype, jtype); + rhojp = RhoPrimeOfR(index, jtype, itype); + fpair = fp[i]*rhojp + fp[j]*rhoip; + recip = 1.0/r; + + // The value -1 indicates: no concentration dependence for this + // i-j pair because atom j is not of species A nor B. + + double x_j = -1; + + // This code line is required for ternary alloy. + + if (jtype == speciesA || jtype == speciesB) { + ASSERT(rho[i] != 0.0); + ASSERT(rho[j] != 0.0); + + // Compute local concentration at site j. + + x_j = rhoB[j]/rho[j]; + ASSERT(x_j >= 0 && x_j<=1.0); + + double D_j=0.0; + if (cdeamVersion == 1) { + + // Calculate derivative of h(x_j) polynomial function. + + double h_prime_j = evalHprime(x_j); + D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]); + } else if (cdeamVersion == 2) { + D_j = D_values[j]; + } else { + ASSERT(false); + } + double t2 = -rhoB[j]; + if (itype == speciesB) t2 += rho[j]; + fpair += D_j * rhoip * t2; + } + + // This if-clause is only required for a ternary alloy. + // Actually we don't need it at all because D_i should be zero + // anyway if atom i has no concentration dependent interactions + // (because it is not species A or B). + + if (x_i != -1.0) { + double t1 = -rhoB[i]; + if (jtype == speciesB) t1 += rho[i]; + fpair += D_i * rhojp * t1; + } + + double phip; + double phi = PhiOfR(index, itype, jtype, recip, phip); + if (itype == jtype || x_i == -1.0 || x_j == -1.0) { + + // Case of no concentration dependence. + + fpair += phip; + } else { + + // We have a concentration dependence for the i-j interaction. + + double h=0.0; + if (cdeamVersion == 1) { + + // Calculate h(x_i) polynomial function. + + double h_i = evalH(x_i); + + // Calculate h(x_j) polynomial function. + + double h_j = evalH(x_j); + h = 0.5 * (h_i + h_j); + } else if (cdeamVersion == 2) { + + // Average concentration. + + double x_ij = 0.5 * (x_i + x_j); + + // Calculate h(x_ij) polynomial function. + + h = evalH(x_ij); + } else { + ASSERT(false); + } + fpair += h * phip; + phi *= h; + } + + // Divide by r_ij and negate to get forces from gradient. + + fpair /= -r; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) evdwl = phi; + if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::coeff(int narg, char **arg) +{ + PairEAMAlloy::coeff(narg, arg); + + // Make sure the EAM file is a CD-EAM binary alloy. + + if (setfl->nelements < 2) + error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style."); + + // Read in the coefficients of the h polynomial from the end of the EAM file. + + read_h_coeff(arg[2]); + + // Determine which atom type is the A species and which is the B + // species in the alloy. By default take the first element (index 0) + // in the EAM file as the A species and the second element (index 1) + // in the EAM file as the B species. + + speciesA = -1; + speciesB = -1; + for (int i = 1; i <= atom->ntypes; i++) { + if (map[i] == 0) { + if (speciesA >= 0) + error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type."); + speciesA = i; + } + if (map[i] == 1) { + if (speciesB >= 0) + error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type."); + speciesB = i; + } + } + if (speciesA < 0) + error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type."); + if (speciesB < 0) + error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type."); +} + +/* ---------------------------------------------------------------------- + Reads in the h(x) polynomial coefficients +------------------------------------------------------------------------- */ + +void PairEAMCD::read_h_coeff(char *filename) +{ + if (comm->me == 0) { + + // Open potential file + + FILE *fptr; + char line[MAXLINE]; + char nextline[MAXLINE]; + fptr = force->open_potential(filename); + if (fptr == NULL) { + char str[128]; + sprintf(str,"Cannot open EAM potential file %s", filename); + error->one(FLERR,str); + } + + // h coefficients are stored at the end of the file. + // Skip to last line of file. + + while(fgets(nextline, MAXLINE, fptr) != NULL) { + strcpy(line, nextline); + } + char* ptr = strtok(line, " \t\n\r\f"); + int degree = atoi(ptr); + nhcoeff = degree+1; + hcoeff = new double[nhcoeff]; + int i = 0; + while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) { + hcoeff[i++] = atof(ptr); + } + if (i != nhcoeff || nhcoeff < 1) + error->one(FLERR,"Failed to read h(x) function coefficients from EAM file."); + + // Close the potential file. + + fclose(fptr); + } + + MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world); + if (comm->me != 0) hcoeff = new double[nhcoeff]; + MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world); +} + + +/* ---------------------------------------------------------------------- */ + +int PairEAMCD::pack_forward_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + + m = 0; + if (communicationStage == 2) { + if (cdeamVersion == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = fp[j]; + buf[m++] = rho[j]; + buf[m++] = rhoB[j]; + buf[m++] = D_values[j]; + } + return m; + } else if (cdeamVersion == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = fp[j]; + buf[m++] = rho[j]; + buf[m++] = rhoB[j]; + } + return m; + } else { ASSERT(false); return 0; } + } else if (communicationStage == 4) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = D_values[j]; + } + return m; + } else return 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + if (communicationStage == 2) { + if (cdeamVersion == 1) { + for (i = first; i < last; i++) { + fp[i] = buf[m++]; + rho[i] = buf[m++]; + rhoB[i] = buf[m++]; + D_values[i] = buf[m++]; + } + } else if (cdeamVersion == 2) { + for (i = first; i < last; i++) { + fp[i] = buf[m++]; + rho[i] = buf[m++]; + rhoB[i] = buf[m++]; + } + } else { + ASSERT(false); + } + } else if (communicationStage == 4) { + for (i = first; i < last; i++) { + D_values[i] = buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- */ +int PairEAMCD::pack_reverse_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + if (communicationStage == 1) { + if (cdeamVersion == 1) { + for (i = first; i < last; i++) { + buf[m++] = rho[i]; + buf[m++] = rhoB[i]; + buf[m++] = D_values[i]; + } + return m; + } else if (cdeamVersion == 2) { + for (i = first; i < last; i++) { + buf[m++] = rho[i]; + buf[m++] = rhoB[i]; + } + return m; + } else { ASSERT(false); return 0; } + } else if (communicationStage == 3) { + for (i = first; i < last; i++) { + buf[m++] = D_values[i]; + } + return m; + } else return 0; +} + +/* ---------------------------------------------------------------------- */ + +void PairEAMCD::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + if (communicationStage == 1) { + if (cdeamVersion == 1) { + for (i = 0; i < n; i++) { + j = list[i]; + rho[j] += buf[m++]; + rhoB[j] += buf[m++]; + D_values[j] += buf[m++]; + } + } else if (cdeamVersion == 2) { + for (i = 0; i < n; i++) { + j = list[i]; + rho[j] += buf[m++]; + rhoB[j] += buf[m++]; + } + } else { + ASSERT(false); + } + } else if (communicationStage == 3) { + for (i = 0; i < n; i++) { + j = list[i]; + D_values[j] += buf[m++]; + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ +double PairEAMCD::memory_usage() +{ + double bytes = 2 * nmax * sizeof(double); + return PairEAMAlloy::memory_usage() + bytes; +} diff --git a/src/USER-MISC/pair_cdeam.h b/src/MANYBODY/pair_eam_cd.h similarity index 93% rename from src/USER-MISC/pair_cdeam.h rename to src/MANYBODY/pair_eam_cd.h index 934b7601a4bfac37bbad057f94ed8a373a6848fe..ee84fb09c53f9fed5c2808f8e784340b705b7679 100644 --- a/src/USER-MISC/pair_cdeam.h +++ b/src/MANYBODY/pair_eam_cd.h @@ -13,26 +13,26 @@ #ifdef PAIR_CLASS -PairStyle(eam/cd,PairCDEAM_OneSite) -PairStyle(eam/cd/old,PairCDEAM_TwoSite) +PairStyle(eam/cd,PairEAMCD_OneSite) +PairStyle(eam/cd/old,PairEAMCD_TwoSite) #else -#ifndef LMP_PAIR_CDEAM_H -#define LMP_PAIR_CDEAM_H +#ifndef LMP_PAIR_EAM_CD_H +#define LMP_PAIR_EAM_CD_H #include "pair_eam_alloy.h" namespace LAMMPS_NS { -class PairCDEAM : public PairEAMAlloy +class PairEAMCD : public PairEAMAlloy { public: /// Constructor. - PairCDEAM(class LAMMPS*, int cdeamVersion); + PairEAMCD(class LAMMPS*, int cdeamVersion); /// Destructor. - virtual ~PairCDEAM(); + virtual ~PairEAMCD(); /// Calculates the energies and forces for all atoms in the system. virtual void compute(int, int); @@ -211,19 +211,19 @@ public: }; /// The one-site concentration formulation of CD-EAM. - class PairCDEAM_OneSite : public PairCDEAM + class PairEAMCD_OneSite : public PairEAMCD { public: /// Constructor. - PairCDEAM_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 1) {} + PairEAMCD_OneSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 1) {} }; /// The two-site concentration formulation of CD-EAM. - class PairCDEAM_TwoSite : public PairCDEAM + class PairEAMCD_TwoSite : public PairEAMCD { public: /// Constructor. - PairCDEAM_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairCDEAM(lmp, 2) {} + PairEAMCD_TwoSite(class LAMMPS* lmp) : PairEAM(lmp), PairEAMCD(lmp, 2) {} }; } diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index 6221e6d52c26b359d9efd7d87460a1ed3ceacaf3..b40ce6a1b3342bf185846a37b7caa0ca8c6a0c10 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -1589,6 +1589,7 @@ void FixGCMC::attempt_atomic_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); if (random_equal->uniform() < @@ -1607,6 +1608,7 @@ void FixGCMC::attempt_atomic_deletion_full() if (q_flag) atom->q[i] = q_tmp; } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); energy_stored = energy_before; } update_gas_atoms_list(); @@ -1700,6 +1702,7 @@ void FixGCMC::attempt_atomic_insertion_full() comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); if (energy_after < MAXENERGYTEST && @@ -1712,6 +1715,7 @@ void FixGCMC::attempt_atomic_insertion_full() atom->natoms--; if (proc_flag) atom->nlocal--; if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); energy_stored = energy_before; } update_gas_atoms_list(); @@ -1949,6 +1953,7 @@ void FixGCMC::attempt_molecule_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); // energy_before corrected by energy_intra @@ -1981,6 +1986,7 @@ void FixGCMC::attempt_molecule_deletion_full() } } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); } update_gas_atoms_list(); delete[] tmpmask; @@ -2151,6 +2157,7 @@ void FixGCMC::attempt_molecule_insertion_full() comm->borders(); if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); double energy_after = energy_full(); // energy_after corrected by energy_intra @@ -2181,6 +2188,7 @@ void FixGCMC::attempt_molecule_insertion_full() } else i++; } if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); } update_gas_atoms_list(); } diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index 83d734de0f4e492f8ffdadf2c771aaaaf250b248..a778d7a5b6c839f4bce0dcf1f08af09be831e56e 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -282,10 +282,12 @@ double PairNMCut::init_one(int i, int j) double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * - (rr1*pow(cut[i][j],p1)-rr2*pow(cut[i][j],p2)); - ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * - nn[i][j]*mm[i][j]*(rrr1*pow(cut[i][j],p1)-rrr2*pow(cut[i][j],p2)); + double cut3 = cut[i][j]*cut[i][j]*cut[i][j]; + ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut3 * + (pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3)); + etail_ij = 2.*MY_PI*all[0]*all[1]*e0nm[i][j]*cut3 * + (mm[i][j]*pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - nn[i][j]*pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3)); + } return cut[i][j]; diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index 0c9a43f4dc94fc5b4a8e9d2c705be0bad3cc2438..b807bc972bfd9c5ab9e620b2c8e88e763ecd1135 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -332,10 +332,11 @@ double PairNMCutCoulCut::init_one(int i, int j) double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * - (rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2)); - ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * - nn[i][j]*mm[i][j]*(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2)); + double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 * + (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); + etail_ij = 2.*MY_PI*all[0]*all[1]*e0nm[i][j]*cut_lj3 * + (mm[i][j]*pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - nn[i][j]*pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); } diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 3296f8fd92b62ae567c7790ffbf0d98c62cd021a..325f3da0033c78dafd85e759112ccd0056dec4d6 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -379,10 +379,12 @@ double PairNMCutCoulLong::init_one(int i, int j) double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] * - (rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2)); - ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j]*nn[i][j]*mm[i][j] * - (rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2)); + double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 * + (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); + etail_ij = 2.*MY_PI*all[0]*all[1]*e0nm[i][j]*cut_lj3 * + (mm[i][j]*pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - nn[i][j]*pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); + } return cut; diff --git a/src/Makefile b/src/Makefile index d17a2ccbd99ecf0ff2c29b1626ebe1bdd3da39dc..948d203cfe078a51e70ca617375e0b90b44a3257 100644 --- a/src/Makefile +++ b/src/Makefile @@ -18,7 +18,7 @@ OBJDIR = Obj_$@ OBJSHDIR = Obj_shared_$@ SRC = $(wildcard *.cpp) -INC = $(wildcard *.h) +INC = $(filter-out lmpinstalledpkgs.h,$(wildcard *.h)) OBJ = $(SRC:.cpp=.o) SRCLIB = $(filter-out main.cpp,$(SRC)) @@ -55,7 +55,7 @@ endif PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ granular kim kokkos kspace latte manybody mc meam misc \ molecule mpiio mscg opt peri poems \ - python qeq reax replica rigid shock snap srd voronoi + python qeq reax replica rigid shock snap spin srd voronoi PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ @@ -150,6 +150,21 @@ help: for file in $$files; do head -1 $$file; done @echo '' + +lmpinstalledpkgs.h: $(SRC) $(INC) + @echo 'Gathering installed package information (may take a little while)' + @echo '#ifndef LMP_INSTALLED_PKGS_H' > lmpinstalledpkgs.tmp + @echo '#define LMP_INSTALLED_PKGS_H' >> lmpinstalledpkgs.tmp + @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> lmpinstalledpkgs.tmp + @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ + [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> lmpinstalledpkgs.tmp || :; done + @echo ' NULL };' >> lmpinstalledpkgs.tmp + @echo '#endif' >> lmpinstalledpkgs.tmp + @if [ -f lmpinstalledpkgs.h ]; \ + then test "`diff --brief lmpinstalledpkgs.tmp lmpinstalledpkgs.h`" != "" && \ + mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h || rm lmpinstalledpkgs.tmp ; \ + else mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h ; fi + # Build LAMMPS in one of 4 modes # exe = exe with static compile in Obj_machine (default) # shexe = exe with shared compile in Obj_shared_machine @@ -163,6 +178,8 @@ help: -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi @$(SHELL) Make.sh style + @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h + @echo 'Compiling LAMMPS for machine $@' @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi @if [ -f MAKE/OPTIONS/Makefile.$@ ]; \ diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index 9f018ad6029e4b30789037d3e05ff88912440dd6..cc5edaf3f52ebd4b248e81c696e559d8def017ae 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -344,7 +344,7 @@ void PythonImpl::invoke_function(int ifunc, char *result) } else if (otype == DOUBLE) { sprintf(result,"%.15g",PyFloat_AsDouble(pValue)); } else if (otype == STRING) { - char *pystr = PY_STRING_AS_STRING(pValue); + const char *pystr = PY_STRING_AS_STRING(pValue); if (pfuncs[ifunc].longstr) strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr); else strncpy(result,pystr,VALUELENGTH-1); diff --git a/src/Purge.list b/src/Purge.list index 2e854ead3d577e4d6cb1a968e814f1cbdb954e65..cb98636b1c17860fab98343824d10bf5f2063bbf 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -1,6 +1,7 @@ # auto-generated style files style_angle.h style_atom.h +style_body.h style_bond.h style_command.h style_compute.h @@ -12,10 +13,23 @@ style_integrate.h style_kspace.h style_minimize.h style_pair.h +style_reader.h style_region.h style_neigh_bin.h style_neigh_pair.h style_neigh_stencil.h +style_nbin.h +style_npair.h +style_nstencil.h +style_ntopo.h +# other auto-generated files +lmpinstalledpkgs.h +# renamed on 31 July 2018 +pair_cdeam.h +pair_cdeam.cpp +# renamed on 20 July 2018 +pair_body.h +pair_body.cpp # deleted on 4 April 2018 pair_kim_version.h # deleted on 15 December 2017 diff --git a/src/SPIN/README b/src/SPIN/README new file mode 100644 index 0000000000000000000000000000000000000000..e371e3976746e4b900fca5d135e6dda30831aedd --- /dev/null +++ b/src/SPIN/README @@ -0,0 +1,25 @@ +The SPIN package enables coupled spin dynamics and molecular +dynamics simulations. + +The package provides the following features: + +* defining a classical magnetic atomic spin associated to each magnetic +atom in the system +* integrating the equations of motion for the coupled spin-lattice system +* implementing magnetic pair interactions and magnetic forces +* thermostating and applying a transverse damping to the magnetic spins +* computing and outputing magnetic quantities + +The different options provided by this package are explained in the +LAMMPS documentation. + +Once you have successfully built LAMMPS with this package, you can test +it using one of the input files provided from the examples/SPIN dir: + +./lmp_serial < lammps/examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp + + +== Credits and license == + +The person who created this package is Julien Tranchida (jtranch at +sandia.gov). You can contact him if you have questions. diff --git a/src/SPIN/atom_vec_spin.cpp b/src/SPIN/atom_vec_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6460a6185fb72d0635b623dbd7e8a2e7a2d27ba6 --- /dev/null +++ b/src/SPIN/atom_vec_spin.cpp @@ -0,0 +1,952 @@ +/* ---------------------------------------------------------------------- + + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "atom.h" +#include "atom_vec_spin.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "memory.h" +#include "modify.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp) +{ + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = 0; + comm_f_only = 0; + size_forward = 7; + size_reverse = 6; + size_border = 10; + size_velocity = 3; + size_data_atom = 9; + size_data_vel = 4; + xcol_data = 4; + + atom->sp_flag = 1; +} + + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecSpin::grow(int n) +{ + if (n == 0) grow_nmax(); + else nmax = n; + atom->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + tag = memory->grow(atom->tag,nmax,"atom:tag"); + type = memory->grow(atom->type,nmax,"atom:type"); + mask = memory->grow(atom->mask,nmax,"atom:mask"); + image = memory->grow(atom->image,nmax,"atom:image"); + + // allocating mech. quantities + + x = memory->grow(atom->x,nmax,3,"atom:x"); + v = memory->grow(atom->v,nmax,3,"atom:v"); + f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f"); + + // allocating mag. quantities + + sp = memory->grow(atom->sp,nmax,4,"atom:sp"); + fm = memory->grow(atom->fm,nmax*comm->nthreads,3,"atom:fm"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecSpin::grow_reset() +{ + tag = atom->tag; type = atom->type; + mask = atom->mask; image = atom->image; + x = atom->x; v = atom->v; f = atom->f; + sp = atom->sp; fm = atom->fm; +} + + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecSpin::copy(int i, int j, int delflag) +{ + tag[j] = tag[i]; + type[j] = type[i]; + mask[j] = mask[i]; + image[j] = image[i]; + x[j][0] = x[i][0]; + x[j][1] = x[i][1]; + x[j][2] = x[i][2]; + v[j][0] = v[i][0]; + v[j][1] = v[i][1]; + v[j][2] = v[i][2]; + + sp[j][0] = sp[i][0]; + sp[j][1] = sp[i][1]; + sp[j][2] = sp[i][2]; + sp[j][3] = sp[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz; + dy = pbc[1]*domain->yprd + pbc[3]*domain->yz; + dz = pbc[2]*domain->zprd; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } + } + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_comm_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_comm_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_comm_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_reverse(int n, int first, double *buf) +{ + int i,m,last; + m = 0; + last = first + n; + for (i = first; i < last; i++) { + buf[m++] = f[i][0]; + buf[m++] = f[i][1]; + buf[m++] = f[i][2]; + buf[m++] = fm[i][0]; + buf[m++] = fm[i][1]; + buf[m++] = fm[i][2]; + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_reverse(int n, int *list, double *buf) +{ + int i,j,m; + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + f[j][0] += buf[m++]; + f[j][1] += buf[m++]; + f[j][2] += buf[m++]; + fm[j][0] += buf[m++]; + fm[j][1] += buf[m++]; + fm[j][2] += buf[m++]; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0]; + buf[m++] = x[j][1]; + buf[m++] = x[j][2]; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = x[j][0] + dx; + buf[m++] = x[j][1] + dy; + buf[m++] = x[j][2] + dz; + buf[m++] = ubuf(tag[j]).d; + buf[m++] = ubuf(type[j]).d; + buf[m++] = ubuf(mask[j]).d; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + if (mask[i] & deform_groupbit) { + buf[m++] = v[j][0] + dvx; + buf[m++] = v[j][1] + dvy; + buf[m++] = v[j][2] + dvz; + } else { + buf[m++] = v[j][0]; + buf[m++] = v[j][1]; + buf[m++] = v[j][2]; + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::pack_border_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = sp[j][0]; + buf[m++] = sp[j][1]; + buf[m++] = sp[j][2]; + buf[m++] = sp[j][3]; + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpin::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + x[i][0] = buf[m++]; + x[i][1] = buf[m++]; + x[i][2] = buf[m++]; + tag[i] = (tagint) ubuf(buf[m++]).i; + type[i] = (int) ubuf(buf[m++]).i; + mask[i] = (int) ubuf(buf[m++]).i; + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + v[i][0] = buf[m++]; + v[i][1] = buf[m++]; + v[i][2] = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); + +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_border_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + sp[i][0] = buf[m++]; + sp[i][1] = buf[m++]; + sp[i][2] = buf[m++]; + sp[i][3] = buf[m++]; + } + + return m; +} + +/* ---------------------------------------------------------------------- + pack all atom quantities for shipping to another proc + xyz must be 1st 3 values, so that comm::exchange can test on them +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + + buf[m++] = sp[i][0]; + buf[m++] = sp[i][1]; + buf[m++] = sp[i][2]; + buf[m++] = sp[i][3]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + + sp[nlocal][0] = buf[m++]; + sp[nlocal][1] = buf[m++]; + sp[nlocal][2] = buf[m++]; + sp[nlocal][3] = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecSpin::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 15 * nlocal; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_restart(int i, double *buf) +{ + int m = 1; + + buf[m++] = x[i][0]; + buf[m++] = x[i][1]; + buf[m++] = x[i][2]; + buf[m++] = ubuf(tag[i]).d; + buf[m++] = ubuf(type[i]).d; + buf[m++] = ubuf(mask[i]).d; + buf[m++] = ubuf(image[i]).d; + buf[m++] = v[i][0]; + buf[m++] = v[i][1]; + buf[m++] = v[i][2]; + + buf[m++] = sp[i][0]; + buf[m++] = sp[i][1]; + buf[m++] = sp[i][2]; + buf[m++] = sp[i][3]; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecSpin::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + int m = 1; + x[nlocal][0] = buf[m++]; + x[nlocal][1] = buf[m++]; + x[nlocal][2] = buf[m++]; + tag[nlocal] = (tagint) ubuf(buf[m++]).i; + type[nlocal] = (int) ubuf(buf[m++]).i; + mask[nlocal] = (int) ubuf(buf[m++]).i; + image[nlocal] = (imageint) ubuf(buf[m++]).i; + v[nlocal][0] = buf[m++]; + v[nlocal][1] = buf[m++]; + v[nlocal][2] = buf[m++]; + + sp[nlocal][0] = buf[m++]; + sp[nlocal][1] = buf[m++]; + sp[nlocal][2] = buf[m++]; + sp[nlocal][3] = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecSpin::create_atom(int itype, double *coord) +{ + + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = 0; + type[nlocal] = itype; + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + mask[nlocal] = 1; + image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + sp[nlocal][0] = 0.0; + sp[nlocal][1] = 0.0; + sp[nlocal][2] = 0.0; + sp[nlocal][3] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecSpin::data_atom(double *coord, imageint imagetmp, char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + tag[nlocal] = ATOTAGINT(values[0]); + type[nlocal] = atoi(values[1]); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + x[nlocal][0] = coord[0]; + x[nlocal][1] = coord[1]; + x[nlocal][2] = coord[2]; + + sp[nlocal][3] = atof(values[2]); + sp[nlocal][0] = atof(values[6]); + sp[nlocal][1] = atof(values[7]); + sp[nlocal][2] = atof(values[8]); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + + image[nlocal] = imagetmp; + + mask[nlocal] = 1; + v[nlocal][0] = 0.0; + v[nlocal][1] = 0.0; + v[nlocal][2] = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecSpin::data_atom_hybrid(int nlocal, char **values) +{ + + sp[nlocal][0] = atof(values[0]); + sp[nlocal][1] = atof(values[1]); + sp[nlocal][2] = atof(values[2]); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + sp[nlocal][3] = atof(values[3]); + + return 4; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpin::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = ubuf(tag[i]).d; + buf[i][1] = ubuf(type[i]).d; + buf[i][2] = sp[i][3]; + buf[i][3] = x[i][0]; + buf[i][4] = x[i][1]; + buf[i][5] = x[i][2]; + buf[i][6] = sp[i][0]; + buf[i][7] = sp[i][1]; + buf[i][8] = sp[i][2]; + buf[i][9] = ubuf((image[i] & IMGMASK) - IMGMAX).d; + buf[i][10] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d; + buf[i][11] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecSpin::pack_data_hybrid(int i, double *buf) +{ + buf[0] = sp[i][0]; + buf[1] = sp[i][1]; + buf[2] = sp[i][2]; + buf[3] = sp[i][3]; + return 4; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpin::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,TAGINT_FORMAT \ + " %d %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e " + "%-1.16e %d %d %d\n", + (tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i, + buf[i][2],buf[i][3],buf[i][4], + buf[i][5],buf[i][6],buf[i][7],buf[i][8], + (int) ubuf(buf[i][9]).i,(int) ubuf(buf[i][10]).i, + (int) ubuf(buf[i][11]).i); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecSpin::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3],buf[4]); + return 4; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +bigint AtomVecSpin::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3); + + if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4); + if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3); + + return bytes; +} + +void AtomVecSpin::force_clear(int n, size_t nbytes) +{ + memset(&atom->f[0][0],0,3*nbytes); + memset(&atom->fm[0][0],0,3*nbytes); +} + + diff --git a/src/SPIN/atom_vec_spin.h b/src/SPIN/atom_vec_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..34bc55b99f771792d9285758dbbc0d270698ee5b --- /dev/null +++ b/src/SPIN/atom_vec_spin.h @@ -0,0 +1,93 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(spin,AtomVecSpin) + +#else + +#ifndef LMP_ATOM_VEC_SPIN_H +#define LMP_ATOM_VEC_SPIN_H + +#include "atom_vec.h" + +namespace LAMMPS_NS { + +class AtomVecSpin : public AtomVec { + public: + AtomVecSpin(class LAMMPS *); + void grow(int); + void grow_reset(); + void copy(int, int, int); + int pack_comm(int, int *, double *, int, int *); + int pack_comm_vel(int, int *, double *, int, int *); + int pack_comm_hybrid(int, int *, double *); + void unpack_comm(int, int, double *); + void unpack_comm_vel(int, int, double *); + int unpack_comm_hybrid(int, int, double *); + int pack_reverse(int, int, double *); + void unpack_reverse(int, int *, double *); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + bigint memory_usage(); + + // clear magnetic and mechanic forces + + void force_clear(int, size_t); + + + private: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; // lattice quantities + double **sp,**fm; // spin quantities + // sp[i][0-2] direction of the spin i + // sp[i][3] atomic magnetic moment of the spin i + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +*/ diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..dc16190c98763053d76fb84e5a423eca570f860d --- /dev/null +++ b/src/SPIN/compute_spin.cpp @@ -0,0 +1,154 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include "atom.h" +#include "compute_spin.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "math_special.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathSpecial; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +ComputeSpin::ComputeSpin(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg) +{ + if ((narg != 3) && (narg != 4)) error->all(FLERR,"Illegal compute compute/spin command"); + + vector_flag = 1; + size_vector = 6; + extvector = 0; + + init(); + + allocate(); + +} + +/* ---------------------------------------------------------------------- */ + +ComputeSpin::~ComputeSpin() +{ + memory->destroy(vector); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSpin::init() +{ + hbar = force->hplanck/MY_2PI; + kb = force->boltz; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeSpin::compute_vector() +{ + int i; + int countsp, countsptot; + double mag[4], magtot[4]; + double magenergy, magenergytot; + double tempnum, tempnumtot; + double tempdenom, tempdenomtot; + double spintemperature; + + invoked_vector = update->ntimestep; + + countsp = countsptot = 0.0; + mag[0] = mag[1] = mag[2] = mag[3] = 0.0; + magtot[0] = magtot[1] = magtot[2] = magtot[3] = 0.0; + magenergy = magenergytot = 0.0; + tempnum = tempnumtot = 0.0; + tempdenom = tempdenomtot = 0.0; + spintemperature = 0.0; + + int *mask = atom->mask; + double **sp = atom->sp; + double **fm = atom->fm; + double tx,ty,tz; + + int nlocal = atom->nlocal; + + // compute total magnetization and magnetic energy + // compute spin temperature (Nurdin et al., Phys. Rev. E 61, 2000) + + for (i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (atom->sp_flag) { + mag[0] += sp[i][0]; + mag[1] += sp[i][1]; + mag[2] += sp[i][2]; + magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]); + tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1]; + ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2]; + tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0]; + tempnum += tx*tx+ty*ty+tz*tz; + tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2]; + countsp++; + } + } + else error->all(FLERR,"Compute compute/spin requires atom/spin style"); + } + + MPI_Allreduce(mag,magtot,4,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&magenergy,&magenergytot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&tempnum,&tempnumtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&tempdenom,&tempdenomtot,1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(&countsp,&countsptot,1,MPI_INT,MPI_SUM,world); + + double scale = 1.0/countsptot; + magtot[0] *= scale; + magtot[1] *= scale; + magtot[2] *= scale; + magtot[3] = sqrt((magtot[0]*magtot[0])+(magtot[1]*magtot[1])+(magtot[2]*magtot[2])); + spintemperature = hbar*tempnumtot; + spintemperature /= (kb*tempdenomtot); + + vector[0] = magtot[0]; + vector[1] = magtot[1]; + vector[2] = magtot[2]; + vector[3] = magtot[3]; + vector[4] = magenergytot*hbar; + vector[5] = spintemperature; + +} + +/* ---------------------------------------------------------------------- + free and reallocate arrays +------------------------------------------------------------------------- */ + +void ComputeSpin::allocate() +{ + memory->create(vector,6,"compute/spin:vector"); +} + diff --git a/src/SPIN/compute_spin.h b/src/SPIN/compute_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..59f0ce2876d3e718d08c88bece84475a74dc04ef --- /dev/null +++ b/src/SPIN/compute_spin.h @@ -0,0 +1,62 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMPUTE_CLASS + +ComputeStyle(compute/spin,ComputeSpin) + +#else + +#ifndef LMP_COMPUTE_SPIN_H +#define LMP_COMPUTE_SPIN_H + +#include "compute.h" + +namespace LAMMPS_NS { + +class ComputeSpin : public Compute { + public: + ComputeSpin(class LAMMPS *, int, char **); + ~ComputeSpin(); + void init(); + void compute_vector(); + + private: + double kb,hbar; + int usecenter; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Chunk/atom compute does not exist for compute compute/spin + +Self-explanatory. + +E: Compute compute/spin does not use chunk/atom compute + +The style of the specified compute is not chunk/atom. + +*/ diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..cb344654826883c41b7d6fcf8802d5ebacdccd0d --- /dev/null +++ b/src/SPIN/fix_langevin_spin.cpp @@ -0,0 +1,199 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "atom.h" +#include "atom_vec_ellipsoid.h" +#include "comm.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix_langevin_spin.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "math_const.h" +#include "math_extra.h" +#include "memory.h" +#include "modify.h" +#include "random_mars.h" +#include "random_park.h" +#include "region.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), id_temp(NULL), random(NULL) +{ + if (narg != 6) error->all(FLERR,"Illegal langevin/spin command"); + + dynamic_group_allow = 1; + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + nevery = 1; + + temp = force->numeric(FLERR,arg[3]); + alpha_t = force->numeric(FLERR,arg[4]); + seed = force->inumeric(FLERR,arg[5]); + + if (alpha_t < 0.0) { + error->all(FLERR,"Illegal langevin/spin command"); + } else if (alpha_t == 0.0) { + tdamp_flag = 0; + } else { + tdamp_flag = 1; + } + + if (temp < 0.0) { + error->all(FLERR,"Illegal langevin/spin command"); + } else if (temp == 0.0) { + temp_flag = 0; + } else { + temp_flag = 1; + } + + // initialize Marsaglia RNG with processor-unique seed + + random = new RanPark(lmp,seed + comm->me); + +} + +/* ---------------------------------------------------------------------- */ + +FixLangevinSpin::~FixLangevinSpin() +{ + memory->destroy(spi); + memory->destroy(fmi); + delete random; +} + +/* ---------------------------------------------------------------------- */ + +int FixLangevinSpin::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= POST_FORCE_RESPA; + mask |= END_OF_STEP; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::init() +{ + // fix_langevin_spin has to be the last defined fix + + int flag_force = 0; + int flag_lang = 0; + for (int i = 0; i < modify->nfix; i++) { + if (strcmp("precession/spin",modify->fix[i]->style)==0) flag_force = MAX(flag_force,i); + if (strcmp("langevin/spin",modify->fix[i]->style)==0) flag_lang = i; + } + if (flag_force >= flag_lang) error->all(FLERR,"Fix langevin/spin has to come after all other spin fixes"); + + memory->create(spi,3,"langevin:spi"); + memory->create(fmi,3,"langevin:fmi"); + + gil_factor = 1.0/(1.0+(alpha_t)*(alpha_t)); + dts = update->dt; + + double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + double kb = force->boltz; // eV/K + D = (MY_2PI*alpha_t*gil_factor*kb*temp); + D /= (hbar*dts); + sigma = sqrt(2.0*D); +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); + post_force_respa(vflag,nlevels_respa-1,0); + ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3]) +{ + double cpx = fmi[1]*spi[2] - fmi[2]*spi[1]; + double cpy = fmi[2]*spi[0] - fmi[0]*spi[2]; + double cpz = fmi[0]*spi[1] - fmi[1]*spi[0]; + + // adding the transverse damping + + fmi[0] -= alpha_t*cpx; + fmi[1] -= alpha_t*cpy; + fmi[2] -= alpha_t*cpz; +} + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::add_temperature(double fmi[3]) +{ + + double rx = sigma*(2.0*random->uniform() - 1.0); + double ry = sigma*(2.0*random->uniform() - 1.0); + double rz = sigma*(2.0*random->uniform() - 1.0); + + // adding the random field + + fmi[0] += rx; + fmi[1] += ry; + fmi[2] += rz; + + // adding gilbert's prefactor + + fmi[0] *= gil_factor; + fmi[1] *= gil_factor; + fmi[2] *= gil_factor; + +} + + +/* ---------------------------------------------------------------------- */ + +void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int iloop) +{ + if (ilevel == nlevels_respa-1) post_force(vflag); +} + diff --git a/src/SPIN/fix_langevin_spin.h b/src/SPIN/fix_langevin_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..5358438396b661562bc06376698696bea318bd38 --- /dev/null +++ b/src/SPIN/fix_langevin_spin.h @@ -0,0 +1,108 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(langevin/spin,FixLangevinSpin) + +#else + +#ifndef LMP_FIX_LANGEVIN_SPIN_H +#define LMP_FIX_LANGEVIN_SPIN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixLangevinSpin : public Fix { + public: + FixLangevinSpin(class LAMMPS *, int, char **); + virtual ~FixLangevinSpin(); + int setmask(); + void init(); + void setup(int); + void post_force_respa(int, int, int); + void add_tdamping(double spi[3], double fmi[3]); // add transverse damping + void add_temperature(double fmi[3]); // add temperature + int tdamp_flag, ldamp_flag, temp_flag; // damping and temperature flags + + protected: + double *spi, *fmi; + double alpha_t; // transverse mag. damping + double dts; // magnetic timestep + double temp; // spin bath temperature + double D,sigma; // bath intensity var. + double gil_factor; // gilbert's prefactor + + char *id_temp; + class Compute *temperature; + + int nlevels_respa; + class RanPark *random; + int seed; + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal langevin/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix langevin period must be > 0.0 + +The time window for temperature relaxation must be > 0 + +W: Energy tally does not account for 'zero yes' + +The energy removed by using the 'zero yes' flag is not accounted +for in the energy tally and thus energy conservation cannot be +monitored in this case. + + +E: Variable for fix langevin is invalid style + +It must be an equal-style variable. + + +E: Cannot zero Langevin force of 0 atoms + +The group has zero atoms, so you cannot request its force +be zeroed. + +E: Fix langevin variable returned negative temperature + +Self-explanatory. + +E: Could not find fix_modify temperature ID + +The compute ID for computing temperature does not exist. + +E: Fix_modify temperature ID does not compute temperature + +The compute ID assigned to the fix must compute temperature. + +W: Group for fix_modify temp != fix group + +The fix_modify command is specifying a temperature computation that +computes a temperature on a different group of atoms than the fix +itself operates on. This is probably not what you want to do. + +*/ diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..b75f03212a143e0e5ebab08afd6d026834a6f210 --- /dev/null +++ b/src/SPIN/fix_nve_spin.cpp @@ -0,0 +1,642 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "atom_vec.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix_precession_spin.h" +#include "fix_nve_spin.h" +#include "fix_langevin_spin.h" +#include "force.h" +#include "math_vector.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_spin.h" +#include "respa.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; +using namespace MathExtra; + +static const char cite_fix_nve_spin[] = + "fix nve/spin command:\n\n" + "@article{tranchida2018massively,\n" + "title={Massively parallel symplectic algorithm for coupled magnetic spin " + "dynamics and molecular dynamics},\n" + "author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n" + "journal={Journal of Computational Physics},\n" + "year={2018},\n" + "publisher={Elsevier}\n" + "}\n\n"; + +enum{NONE}; + +/* ---------------------------------------------------------------------- */ + +FixNVESpin::FixNVESpin(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + pair(NULL), spin_pairs(NULL), + rsec(NULL), stack_head(NULL), stack_foot(NULL), + backward_stacks(NULL), forward_stacks(NULL) +{ + if (lmp->citeme) lmp->citeme->add(cite_fix_nve_spin); + + if (narg < 4) error->all(FLERR,"Illegal fix/NVE/spin command"); + + time_integrate = 1; + sector_flag = NONE; + lattice_flag = 1; + nlocal_max = 0; + npairs = 0; + npairspin = 0; + + + // checking if map array or hash is defined + + if (atom->map_style == 0) + error->all(FLERR,"Fix NVE/spin requires an atom map, see atom_modify"); + + // defining sector_flag + + int nprocs_tmp = comm->nprocs; + if (nprocs_tmp == 1) { + sector_flag = 0; + } else if (nprocs_tmp >= 1) { + sector_flag = 1; + } else error->all(FLERR,"Illegal fix/NVE/spin command"); + + // defining lattice_flag + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"lattice") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix/NVE/spin command"); + if (strcmp(arg[iarg+1],"no") == 0) lattice_flag = 0; + else if (strcmp(arg[iarg+1],"yes") == 0) lattice_flag = 1; + else error->all(FLERR,"Illegal fix/NVE/spin command"); + iarg += 2; + } else error->all(FLERR,"Illegal fix/NVE/spin command"); + } + + // check if the atom/spin style is defined + + if (!atom->sp_flag) + error->all(FLERR,"Fix NVE/spin requires atom/spin style"); + + // check if sector_flag is correctly defined + + if (sector_flag == 0 && nprocs_tmp > 1) + error->all(FLERR,"Illegal fix/NVE/spin command"); + + // initialize the magnetic interaction flags + + pair_spin_flag = 0; + precession_spin_flag = 0; + maglangevin_flag = 0; + tdamp_flag = temp_flag = 0; + +} + +/* ---------------------------------------------------------------------- */ + +FixNVESpin::~FixNVESpin() +{ + memory->destroy(rsec); + memory->destroy(stack_head); + memory->destroy(stack_foot); + memory->destroy(forward_stacks); + memory->destroy(backward_stacks); + delete [] spin_pairs; +} + +/* ---------------------------------------------------------------------- */ + +int FixNVESpin::setmask() +{ + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= PRE_NEIGHBOR; + mask |= FINAL_INTEGRATE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::init() +{ + + // set timesteps + + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + dts = 0.25 * update->dt; + npairs = npairspin = 0; + + // set ptrs on Pair/Spin styles + + // loop 1: obtain # of Pairs, and # of Pair/Spin styles + + if (force->pair_match("spin",0,0)) { // only one Pair/Spin style + pair = force->pair_match("spin",0,0); + npairs = pair->instance_total; + npairspin = 1; + } else if (force->pair_match("spin",0,1)) { // more than one Pair/Spin style + pair = force->pair_match("spin",0,1); + npairs = pair->instance_total; + for (int i = 0; ipair_match("spin",0,i)) { + npairspin ++; + } + } + } + + // init length of vector of ptrs to Pair/Spin styles + + if (npairspin > 0) { + spin_pairs = new PairSpin*[npairspin]; + } + + // loop 2: fill vector with ptrs to Pair/Spin styles + + int count = 0; + if (npairspin == 1) { + count = 1; + spin_pairs[0] = (PairSpin *) force->pair_match("spin",0,0); + } else if (npairspin > 1) { + for (int i = 0; ipair_match("spin",0,i)) { + spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); + count++; + } + } + } + + if (count != npairspin) + error->all(FLERR,"Incorrect number of spin pairs"); + + if (npairspin >= 1) pair_spin_flag = 1; + + // ptrs FixPrecessionSpin classes + + int iforce; + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"precession/spin")) { + precession_spin_flag = 1; + lockprecessionspin = (FixPrecessionSpin *) modify->fix[iforce]; + } + } + + // ptrs on the FixLangevinSpin class + + for (iforce = 0; iforce < modify->nfix; iforce++) { + if (strstr(modify->fix[iforce]->style,"langevin/spin")) { + maglangevin_flag = 1; + locklangevinspin = (FixLangevinSpin *) modify->fix[iforce]; + } + } + + if (maglangevin_flag) { + if (locklangevinspin->tdamp_flag == 1) tdamp_flag = 1; + if (locklangevinspin->temp_flag == 1) temp_flag = 1; + } + + // setting the sector variables/lists + + nsectors = 0; + memory->create(rsec,3,"NVE/spin:rsec"); + + // perform the sectoring operation + + if (sector_flag) sectoring(); + + // init. size of stacking lists (sectoring) + + nlocal_max = atom->nlocal; + stack_head = memory->grow(stack_head,nsectors,"NVE/spin:stack_head"); + stack_foot = memory->grow(stack_foot,nsectors,"NVE/spin:stack_foot"); + backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); + if (nlocal_max == 0) + error->all(FLERR,"Incorrect value of nlocal_max"); + +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::initial_integrate(int vflag) +{ + double dtfm; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + int *type = atom->type; + int *mask = atom->mask; + + // update half v for all atoms + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + } + + // update half s for all atoms + + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_foot[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } + } + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_head[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } + } + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + } else error->all(FLERR,"Illegal fix NVE/spin command"); + + // update x for all particles + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + x[i][0] += dtv * v[i][0]; + x[i][1] += dtv * v[i][1]; + x[i][2] += dtv * v[i][2]; + } + } + } + + // update half s for all particles + + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_foot[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = forward_stacks[i]; + } + } + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + comm->forward_comm(); + int i = stack_head[j]; + while (i >= 0) { + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + i = backward_stacks[i]; + } + } + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal-1 + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal-1 + ComputeInteractionsSpin(i); + AdvanceSingleSpin(i); + } + } else error->all(FLERR,"Illegal fix NVE/spin command"); + +} + +/* ---------------------------------------------------------------------- + setup pre_neighbor() +---------------------------------------------------------------------- */ + +void FixNVESpin::setup_pre_neighbor() +{ + pre_neighbor(); +} + +/* ---------------------------------------------------------------------- + store in two linked lists the advance order of the spins (sectoring) +---------------------------------------------------------------------- */ + +void FixNVESpin::pre_neighbor() +{ + double **x = atom->x; + int nlocal = atom->nlocal; + + if (nlocal_max < nlocal) { // grow linked lists if necessary + nlocal_max = nlocal; + backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); + forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); + } + + for (int j = 0; j < nsectors; j++) { + stack_head[j] = -1; + stack_foot[j] = -1; + } + + int nseci; + for (int j = 0; j < nsectors; j++) { // stacking backward order + for (int i = 0; i < nlocal; i++) { + nseci = coords2sector(x[i]); + if (j != nseci) continue; + backward_stacks[i] = stack_head[j]; + stack_head[j] = i; + } + } + for (int j = nsectors-1; j >= 0; j--) { // stacking forward order + for (int i = nlocal-1; i >= 0; i--) { + nseci = coords2sector(x[i]); + if (j != nseci) continue; + forward_stacks[i] = stack_foot[j]; + stack_foot[j] = i; + } + } + +} + +/* ---------------------------------------------------------------------- + compute the magnetic torque for the spin ii +---------------------------------------------------------------------- */ + +void FixNVESpin::ComputeInteractionsSpin(int i) +{ + double spi[3], fmi[3]; + + double **sp = atom->sp; + double **fm = atom->fm; + + // force computation for spin i + + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + fmi[0] = fmi[1] = fmi[2] = 0.0; + + // update magnetic pair interactions + + if (pair_spin_flag) { + for (int k = 0; k < npairspin; k++) { + spin_pairs[k]->compute_single_pair(i,fmi); + } + } + + // update magnetic precession interactions + + if (precession_spin_flag) { + lockprecessionspin->compute_single_precession(i,spi,fmi); + } + + // update langevin damping and random force + + if (maglangevin_flag) { // mag. langevin + if (tdamp_flag) { // transverse damping + locklangevinspin->add_tdamping(spi,fmi); + } + if (temp_flag) { // spin temperature + locklangevinspin->add_temperature(fmi); + } + } + + // replace the magnetic force fm[i] by its new value fmi + + fm[i][0] = fmi[0]; + fm[i][1] = fmi[1]; + fm[i][2] = fmi[2]; + +} + +/* ---------------------------------------------------------------------- + divide each domain into 8 sectors +---------------------------------------------------------------------- */ + +void FixNVESpin::sectoring() +{ + int sec[3]; + double sublo[3],subhi[3]; + double* sublotmp = domain->sublo; + double* subhitmp = domain->subhi; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]; + subhi[dim]=subhitmp[dim]; + } + + const double rsx = subhi[0] - sublo[0]; + const double rsy = subhi[1] - sublo[1]; + const double rsz = subhi[2] - sublo[2]; + + // extract larger cutoff from PairSpin styles + + double rv, cutoff; + rv = cutoff = 0.0; + int dim = 0; + for (int i = 0; i < npairspin ; i++) { + cutoff = *((double *) spin_pairs[i]->extract("cut",dim)); + rv = MAX(rv,cutoff); + } + + if (rv == 0.0) + error->all(FLERR,"Illegal sectoring operation"); + + double rax = rsx/rv; + double ray = rsy/rv; + double raz = rsz/rv; + + sec[0] = 1; + sec[1] = 1; + sec[2] = 1; + if (rax >= 2.0) sec[0] = 2; + if (ray >= 2.0) sec[1] = 2; + if (raz >= 2.0) sec[2] = 2; + + nsectors = sec[0]*sec[1]*sec[2]; + + if (sector_flag == 1 && nsectors != 8) + error->all(FLERR,"Illegal sectoring operation"); + + rsec[0] = rsx; + rsec[1] = rsy; + rsec[2] = rsz; + if (sec[0] == 2) rsec[0] = rsx/2.0; + if (sec[1] == 2) rsec[1] = rsy/2.0; + if (sec[2] == 2) rsec[2] = rsz/2.0; + +} + +/* ---------------------------------------------------------------------- + define sector for an atom at a position x[i] +---------------------------------------------------------------------- */ + +int FixNVESpin::coords2sector(double *x) +{ + int nseci; + int seci[3]; + double sublo[3]; + double* sublotmp = domain->sublo; + for (int dim = 0 ; dim<3 ; dim++) { + sublo[dim]=sublotmp[dim]; + } + + seci[0] = x[0] > (sublo[0] + rsec[0]); + seci[1] = x[1] > (sublo[1] + rsec[1]); + seci[2] = x[2] > (sublo[2] + rsec[2]); + + nseci = (seci[0] + 2*seci[1] + 4*seci[2]); + + return nseci; +} + +/* ---------------------------------------------------------------------- + advance the spin i of a timestep dts +---------------------------------------------------------------------- */ + +void FixNVESpin::AdvanceSingleSpin(int i) +{ + int j=0; + int *sametag = atom->sametag; + double **sp = atom->sp; + double **fm = atom->fm; + double msq,scale,fm2,energy,dts2; + double cp[3],g[3]; + + cp[0] = cp[1] = cp[2] = 0.0; + g[0] = g[1] = g[2] = 0.0; + fm2 = (fm[i][0]*fm[i][0])+(fm[i][1]*fm[i][1])+(fm[i][2]*fm[i][2]); + energy = (sp[i][0]*fm[i][0])+(sp[i][1]*fm[i][1])+(sp[i][2]*fm[i][2]); + dts2 = dts*dts; + + cp[0] = fm[i][1]*sp[i][2]-fm[i][2]*sp[i][1]; + cp[1] = fm[i][2]*sp[i][0]-fm[i][0]*sp[i][2]; + cp[2] = fm[i][0]*sp[i][1]-fm[i][1]*sp[i][0]; + + g[0] = sp[i][0]+cp[0]*dts; + g[1] = sp[i][1]+cp[1]*dts; + g[2] = sp[i][2]+cp[2]*dts; + + g[0] += (fm[i][0]*energy-0.5*sp[i][0]*fm2)*0.5*dts2; + g[1] += (fm[i][1]*energy-0.5*sp[i][1]*fm2)*0.5*dts2; + g[2] += (fm[i][2]*energy-0.5*sp[i][2]*fm2)*0.5*dts2; + + g[0] /= (1+0.25*fm2*dts2); + g[1] /= (1+0.25*fm2*dts2); + g[2] /= (1+0.25*fm2*dts2); + + sp[i][0] = g[0]; + sp[i][1] = g[1]; + sp[i][2] = g[2]; + + // renormalization (check if necessary) + + msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; + scale = 1.0/sqrt(msq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][2] *= scale; + + // comm. sp[i] to atoms with same tag (for serial algo) + + if (sector_flag == 0) { + if (sametag[i] >= 0) { + j = sametag[i]; + while (j >= 0) { + sp[j][0] = sp[i][0]; + sp[j][1] = sp[i][1]; + sp[j][2] = sp[i][2]; + j = sametag[j]; + } + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void FixNVESpin::final_integrate() +{ + double dtfm; + + double **v = atom->v; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; + int *type = atom->type; + int *mask = atom->mask; + + // update half v for all particles + + if (lattice_flag) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + if (rmass) dtfm = dtf / rmass[i]; + else dtfm = dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + v[i][1] += dtfm * f[i][1]; + v[i][2] += dtfm * f[i][2]; + } + } + } + +} diff --git a/src/SPIN/fix_nve_spin.h b/src/SPIN/fix_nve_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..afc1db14d698ba238655f793da953b9918f4cc23 --- /dev/null +++ b/src/SPIN/fix_nve_spin.h @@ -0,0 +1,112 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(nve/spin,FixNVESpin) + +#else + +#ifndef LMP_FIX_NVE_SPIN_H +#define LMP_FIX_NVE_SPIN_H + +#include "fix.h" +#include "pair.h" +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class FixNVESpin : public Fix { +friend class PairSpin; + public: + FixNVESpin(class LAMMPS *, int, char **); + virtual ~FixNVESpin(); + int setmask(); + void init(); + virtual void initial_integrate(int); + virtual void final_integrate(); + + void ComputeInteractionsSpin(int); // compute and advance single spin functions + void AdvanceSingleSpin(int); + + void sectoring(); // sectoring operation functions + int coords2sector(double *); + + void setup_pre_neighbor(); + void pre_neighbor(); + + int lattice_flag; // lattice_flag = 0 if spins only + // lattice_flag = 1 if spin-lattice calc. + + + protected: + int sector_flag; // sector_flag = 0 if serial algorithm + // sector_flag = 1 if parallel algorithm + + double dtv, dtf, dts; // velocity, force, and spin timesteps + + int nlocal_max; // max value of nlocal (for lists size) + + int pair_spin_flag; // magnetic pair flags + int precession_spin_flag; // magnetic precession flags + int maglangevin_flag; // magnetic langevin flags + int tdamp_flag, temp_flag; + + // pointers to magnetic fixes + + class FixPrecessionSpin *lockprecessionspin; + class FixLangevinSpin *locklangevinspin; + + // pointers to magnetic pair styles + + int npairs, npairspin; // # of pairs, and # of spin pairs + class Pair *pair; + class PairSpin **spin_pairs; // vector of spin pairs + + // sectoring variables + + int nsectors; + double *rsec; + + // stacking variables for sectoring algorithm + + int *stack_head; // index of first atom in backward_stacks + int *stack_foot; // index of first atom in forward_stacks + int *backward_stacks; // index of next atom in backward stack + int *forward_stacks; // index of next atom in forward stack + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal fix NVE/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Pair spin requires atom attribute spin + +An atom/spin style with this attribute is needed. + +E: Illegal sectoring operation + +The number of processes does not match the size of the system. +See the documentation of the sectoring method. + +*/ diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..b908478952941416546c4b083833f59dd9729a1c --- /dev/null +++ b/src/SPIN/fix_precession_spin.cpp @@ -0,0 +1,282 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "fix_precession_spin.h" +#include "force.h" +#include "input.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include "variable.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{CONSTANT,EQUAL}; + +/* ---------------------------------------------------------------------- */ + +FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) +{ + if (narg < 7) error->all(FLERR,"Illegal precession/spin command"); + + // magnetic interactions coded for cartesian coordinates + + hbar = force->hplanck/MY_2PI; + + dynamic_group_allow = 1; + scalar_flag = 1; + global_freq = 1; + extscalar = 1; + respa_level_support = 1; + ilevel_respa = 0; + + magstr = NULL; + magfieldstyle = CONSTANT; + + H_field = 0.0; + nhx = nhy = nhz = 0.0; + hx = hy = hz = 0.0; + Ka = 0.0; + nax = nay = naz = 0.0; + Kax = Kay = Kaz = 0.0; + + zeeman_flag = aniso_flag = 0; + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"zeeman") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + zeeman_flag = 1; + H_field = force->numeric(FLERR,arg[iarg+1]); + nhx = force->numeric(FLERR,arg[iarg+2]); + nhy = force->numeric(FLERR,arg[iarg+3]); + nhz = force->numeric(FLERR,arg[iarg+4]); + iarg += 5; + } else if (strcmp(arg[iarg],"anisotropy") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal fix precession/spin command"); + aniso_flag = 1; + Ka = force->numeric(FLERR,arg[iarg+1]); + nax = force->numeric(FLERR,arg[iarg+2]); + nay = force->numeric(FLERR,arg[iarg+3]); + naz = force->numeric(FLERR,arg[iarg+4]); + iarg += 5; + } else error->all(FLERR,"Illegal precession/spin command"); + } + + degree2rad = MY_PI/180.0; + time_origin = update->ntimestep; + + eflag = 0; + emag = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +FixPrecessionSpin::~FixPrecessionSpin() +{ + delete [] magstr; +} + +/* ---------------------------------------------------------------------- */ + +int FixPrecessionSpin::setmask() +{ + int mask = 0; + mask |= POST_FORCE; + mask |= THERMO_ENERGY; + mask |= POST_FORCE_RESPA; + return mask; +} + + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::init() +{ + const double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + const double mub = 5.78901e-5; // in eV/T + const double gyro = mub/hbar; // in rad.THz/T + + H_field *= gyro; // in rad.THz + Ka /= hbar; // in rad.THz + + if (strstr(update->integrate_style,"respa")) { + ilevel_respa = ((Respa *) update->integrate)->nlevels-1; + if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); + } + + if (magstr) { + magvar = input->variable->find(magstr); + if (magvar < 0) + error->all(FLERR,"Illegal precession/spin command"); + if (!input->variable->equalstyle(magvar)) + error->all(FLERR,"Illegal precession/spin command"); + } + + varflag = CONSTANT; + if (magfieldstyle != CONSTANT) varflag = EQUAL; + + // set magnetic field components + + if (varflag == CONSTANT) set_magneticprecession(); + +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::setup(int vflag) +{ + if (strstr(update->integrate_style,"verlet")) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa); + post_force_respa(vflag,ilevel_respa,0); + ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa); + } +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::post_force(int vflag) +{ + // update mag field with time (potential improvement) + + if (varflag != CONSTANT) { + modify->clearstep_compute(); + modify->addstep_compute(update->ntimestep + 1); + set_magneticprecession(); // update mag. field if time-dep. + } + + double **sp = atom->sp; + double **fm = atom->fm; + double spi[3], fmi[3]; + const int nlocal = atom->nlocal; + + eflag = 0; + emag = 0.0; + + for (int i = 0; i < nlocal; i++) { + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + if (zeeman_flag) { // compute Zeeman interaction + compute_zeeman(i,fmi); + emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + } + + if (aniso_flag) { // compute magnetic anisotropy + compute_anisotropy(spi,fmi); + emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + } + + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + } + emag *= hbar; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double fmi[3]) +{ + if (zeeman_flag) { + compute_zeeman(i,fmi); + } + if (aniso_flag) { + compute_anisotropy(spi,fmi); + } +} + + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_zeeman(int i, double fmi[3]) +{ + double **sp = atom->sp; + fmi[0] -= sp[i][3]*hx; + fmi[1] -= sp[i][3]*hy; + fmi[2] -= sp[i][3]*hz; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::compute_anisotropy(double spi[3], double fmi[3]) +{ + double scalar = nax*spi[0] + nay*spi[1] + naz*spi[2]; + fmi[0] += scalar*Kax; + fmi[1] += scalar*Kay; + fmi[2] += scalar*Kaz; +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::post_force_respa(int vflag, int ilevel, int iloop) +{ + if (ilevel == ilevel_respa) post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::set_magneticprecession() +{ + if (zeeman_flag) { + hx = H_field*nhx; + hy = H_field*nhy; + hz = H_field*nhz; + } + if (aniso_flag) { + Kax = 2.0*Ka*nax; + Kay = 2.0*Ka*nay; + Kaz = 2.0*Ka*naz; + } +} + +/* ---------------------------------------------------------------------- + potential energy in magnetic field +------------------------------------------------------------------------- */ + +double FixPrecessionSpin::compute_scalar() +{ + // only sum across procs one time + + if (eflag == 0) { + MPI_Allreduce(&emag,&emag_all,1,MPI_DOUBLE,MPI_SUM,world); + eflag = 1; + } + return emag_all; +} diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..53ae4ba1245f989741354e4949b35169911dc878 --- /dev/null +++ b/src/SPIN/fix_precession_spin.h @@ -0,0 +1,92 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(precession/spin,FixPrecessionSpin) + +#else + +#ifndef LMP_FIX_PRECESSION_SPIN_H +#define LMP_FIX_PRECESSION_SPIN_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixPrecessionSpin : public Fix { + friend class FixPour; + + public: + FixPrecessionSpin(class LAMMPS *, int, char **); + ~FixPrecessionSpin(); + int setmask(); + void init(); + void setup(int); + virtual void post_force(int); + virtual void post_force_respa(int, int, int); + double compute_scalar(); + + int zeeman_flag, aniso_flag; + void compute_single_precession(int, double *, double *); + void compute_zeeman(int, double *); + void compute_anisotropy(double *, double *); + + protected: + int style; // style of the magnetic precession + + double degree2rad; + double hbar; + int ilevel_respa; + int time_origin; + int eflag; + double emag, emag_all; + + int varflag; + int magfieldstyle; + int magvar; + char *magstr; + + // zeeman field intensity and direction + + double H_field; + double nhx, nhy, nhz; + double hx, hy, hz; // temp. force variables + + // magnetic anisotropy intensity and direction + + double Ka; + double nax, nay, naz; + double Kax, Kay, Kaz; // temp. force variables + + void set_magneticprecession(); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal precession/spin command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +precession/spin fix command has 7 arguments: +fix ID group precession/spin magnitude (T or eV) style (zeeman or anisotropy) +direction (3 cartesian coordinates) +*/ diff --git a/src/SPIN/pair_spin.cpp b/src/SPIN/pair_spin.cpp new file mode 100644 index 0000000000000000000000000000000000000000..398206b26ee3233b42707585d4bb2dd7dac0c4c6 --- /dev/null +++ b/src/SPIN/pair_spin.cpp @@ -0,0 +1,96 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair.h" +#include "pair_hybrid.h" +#include "pair_hybrid_overlay.h" +#include "pair_spin.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpin::PairSpin(LAMMPS *lmp) : Pair(lmp) +{ + hbar = force->hplanck/MY_2PI; + single_enable = 0; + no_virial_fdotr_compute = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairSpin::~PairSpin() {} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpin::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + // pair/spin need the metal unit style + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"pair/spin style requires metal units"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpin::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); +} diff --git a/src/SPIN/pair_spin.h b/src/SPIN/pair_spin.h new file mode 100644 index 0000000000000000000000000000000000000000..100eec17325ce94f187a1bbec2ff3f664bc0fa63 --- /dev/null +++ b/src/SPIN/pair_spin.h @@ -0,0 +1,70 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(pair/spin,PairSpin) + +#else + +#ifndef LMP_PAIR_SPIN_H +#define LMP_PAIR_SPIN_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairSpin : public Pair { +friend class FixNVESpin; + public: + PairSpin(class LAMMPS *); + virtual ~PairSpin(); + virtual void settings(int, char **); + virtual void coeff(int, char **) {} + virtual void init_style(); + virtual double init_one(int, int) {return 0.0;} + virtual void *extract(const char *, int &) {return NULL;} + + virtual void compute(int, int) {} + virtual void compute_single_pair(int, double *) {} + + protected: + double hbar; // Planck constant (eV.ps.rad-1) + + virtual void allocate() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp new file mode 100644 index 0000000000000000000000000000000000000000..08e2c63e7f6ba147c6062da17f92a68b2a5d090a --- /dev/null +++ b/src/SPIN/pair_spin_dmi.cpp @@ -0,0 +1,565 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_dmi.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinDmi::PairSpinDmi(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinDmi::~PairSpinDmi() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_dmi); + memory->destroy(DM); + memory->destroy(v_dmx); + memory->destroy(v_dmy); + memory->destroy(v_dmz); + memory->destroy(vmech_dmx); + memory->destroy(vmech_dmy); + memory->destroy(vmech_dmz); + memory->destroy(cutsq); + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinDmi::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair/spin/dmi command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_dmi_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i+1; j <= atom->ntypes; j++) { + if (setflag[i][j]) { + cut_spin_dmi[i][j] = cut_spin_dmi_global; + } + } + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinDmi::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"dmi") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 8) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double dm = (force->numeric(FLERR,arg[4])); + double dmx = force->numeric(FLERR,arg[5]); + double dmy = force->numeric(FLERR,arg[6]); + double dmz = force->numeric(FLERR,arg[7]); + + double inorm = 1.0/(dmx*dmx+dmy*dmy+dmz*dmz); + dmx *= inorm; + dmy *= inorm; + dmz *= inorm; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_dmi[i][j] = rij; + DM[i][j] = dm; + v_dmx[i][j] = dmx * dm / hbar; + v_dmy[i][j] = dmy * dm / hbar; + v_dmz[i][j] = dmz * dm / hbar; + vmech_dmx[i][j] = dmx * dm; + vmech_dmy[i][j] = dmy * dm; + vmech_dmz[i][j] = dmz * dm; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinDmi::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinDmi::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + DM[j][i] = DM[i][j]; + v_dmx[j][i] = v_dmx[i][j]; + v_dmy[j][i] = v_dmy[i][j]; + v_dmz[j][i] = v_dmz[i][j]; + vmech_dmx[j][i] = vmech_dmx[i][j]; + vmech_dmy[j][i] = vmech_dmy[i][j]; + vmech_dmz[j][i] = vmech_dmz[i][j]; + cut_spin_dmi[j][i] = cut_spin_dmi[i][j]; + + return cut_spin_dmi_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinDmi::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_dmi_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinDmi::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // dmi computation + // loop over all atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; + + // compute dmi interaction + + if (rsq <= local_cut2) { + compute_dmi(i,j,eij,fmi,spj); + if (lattice_flag) { + compute_dmi_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinDmi::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], eij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; + + if (rsq <= local_cut2) { + compute_dmi(i,j,eij,fmi,spj); + } + + } + +} + +/* ---------------------------------------------------------------------- + compute the dmi interaction between spin i and spin j +------------------------------------------------------------------------- */ + +void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double dmix, dmiy, dmiz; + itype = type[i]; + jtype = type[j]; + + dmix = eij[1]*v_dmz[itype][jtype] - eij[2]*v_dmy[itype][jtype]; + dmiy = eij[2]*v_dmx[itype][jtype] - eij[0]*v_dmz[itype][jtype]; + dmiz = eij[0]*v_dmy[itype][jtype] - eij[1]*v_dmx[itype][jtype]; + + fmi[0] -= (spj[1]*dmiz - spj[2]*dmiy); + fmi[1] -= (spj[2]*dmix - spj[0]*dmiz); + fmi[2] -= (spj[0]*dmiy - spj[1]*dmix); +} + +/* ---------------------------------------------------------------------- + compute the mechanical force due to the dmi interaction between atom i and atom j +------------------------------------------------------------------------- */ + +void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double eij[3], + double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double dmix,dmiy,dmiz; + itype = type[i]; + jtype = type[j]; + double csx,csy,csz,cdmx,cdmy,cdmz,irij; + + irij = 1.0/sqrt(rsq); + + dmix = vmech_dmx[itype][jtype]; + dmiy = vmech_dmy[itype][jtype]; + dmiz = vmech_dmz[itype][jtype]; + + csx = (spi[1]*spj[2] - spi[2]*spj[1]); + csy = (spi[2]*spj[0] - spi[0]*spj[2]); + csz = (spi[0]*spj[1] - spi[1]*spj[0]); + + cdmx = (dmiy*csz - dmiz*csy); + cdmy = (dmiz*csx - dmix*csz); + cdmz = (dmix*csy - dmiy*csz); + + fi[0] += irij*cdmx; + fi[1] += irij*cdmy; + fi[2] += irij*cdmz; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinDmi::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_dmi,n+1,n+1,"pair:cut_spin_dmi"); + memory->create(DM,n+1,n+1,"pair:DM"); + memory->create(v_dmx,n+1,n+1,"pair:DM_vector_x"); + memory->create(v_dmy,n+1,n+1,"pair:DM_vector_y"); + memory->create(v_dmz,n+1,n+1,"pair:DM_vector_z"); + memory->create(vmech_dmx,n+1,n+1,"pair:DMmech_vector_x"); + memory->create(vmech_dmy,n+1,n+1,"pair:DMmech_vector_y"); + memory->create(vmech_dmz,n+1,n+1,"pair:DMmech_vector_z"); + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinDmi::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&DM[i][j],sizeof(double),1,fp); + fwrite(&v_dmx[i][j],sizeof(double),1,fp); + fwrite(&v_dmy[i][j],sizeof(double),1,fp); + fwrite(&v_dmz[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmx[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmy[i][j],sizeof(double),1,fp); + fwrite(&vmech_dmz[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_dmi[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinDmi::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&DM[i][j],sizeof(double),1,fp); + fread(&v_dmx[i][j],sizeof(double),1,fp); + fread(&v_dmy[i][j],sizeof(double),1,fp); + fread(&v_dmz[i][j],sizeof(double),1,fp); + fread(&vmech_dmx[i][j],sizeof(double),1,fp); + fread(&vmech_dmy[i][j],sizeof(double),1,fp); + fread(&vmech_dmz[i][j],sizeof(double),1,fp); + fread(&cut_spin_dmi[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&DM[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmx[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmy[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_dmz[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmx[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmy[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&vmech_dmz[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_dmi[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinDmi::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_dmi_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinDmi::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_dmi_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_dmi_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_dmi.h b/src/SPIN/pair_spin_dmi.h new file mode 100644 index 0000000000000000000000000000000000000000..68e42e879dfe15577d6bf73fe8f80a5593530dfd --- /dev/null +++ b/src/SPIN/pair_spin_dmi.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/dmi,PairSpinDmi) + +#else + +#ifndef LMP_PAIR_SPIN_DMI_H +#define LMP_PAIR_SPIN_DMI_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinDmi : public PairSpin { + public: + PairSpinDmi(class LAMMPS *); + virtual ~PairSpinDmi(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_dmi(int, int, double *, double *, double *); + void compute_dmi_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_dmi_global; // short range pair cutoff + + protected: + double **DM; // dmi coeff in eV + double **v_dmx, **v_dmy, **v_dmz; // dmi direction + double **vmech_dmx, **vmech_dmy, **vmech_dmz; // dmi mech direction + double **cut_spin_dmi; // cutoff distance dmi + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp new file mode 100644 index 0000000000000000000000000000000000000000..cc074bb97d9b9dd91d2bfcc8e378d7cd56a7ba5e --- /dev/null +++ b/src/SPIN/pair_spin_exchange.cpp @@ -0,0 +1,530 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_exchange.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinExchange::PairSpinExchange(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinExchange::~PairSpinExchange() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_exchange); + memory->destroy(J1_mag); + memory->destroy(J1_mech); + memory->destroy(J2); + memory->destroy(J3); + memory->destroy(cutsq); // to be implemented + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinExchange::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_exchange_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_spin_exchange[i][j] = cut_spin_exchange_global; + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinExchange::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"exchange") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 7) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // get exchange arguments from input command + + const double rc = force->numeric(FLERR,arg[3]); + const double j1 = force->numeric(FLERR,arg[4]); + const double j2 = force->numeric(FLERR,arg[5]); + const double j3 = force->numeric(FLERR,arg[6]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_exchange[i][j] = rc; + J1_mag[i][j] = j1/hbar; + J1_mech[i][j] = j1; + J2[i][j] = j2; + J3[i][j] = j3; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinExchange::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinExchange::init_one(int i, int j) +{ + + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + J1_mag[j][i] = J1_mag[i][j]; + J1_mech[j][i] = J1_mech[i][j]; + J2[j][i] = J2[i][j]; + J3[j][i] = J3[i][j]; + cut_spin_exchange[j][i] = cut_spin_exchange[i][j]; + + return cut_spin_exchange_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinExchange::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_exchange_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinExchange::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // computation of the exchange interaction + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; + + // compute exchange interaction + + if (rsq <= local_cut2) { + compute_exchange(i,j,rsq,fmi,spj); + if (lattice_flag) { + compute_exchange_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- + update the pair interactions fmi acting on the spin ii +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_single_pair(int ii, double fmi[3]) +{ + + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], rij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= local_cut2) { + compute_exchange(i,j,rsq,fmi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- + compute exchange interaction between spins i and j +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double Jex, ra; + itype = type[i]; + jtype = type[j]; + + ra = rsq/J3[itype][jtype]/J3[itype][jtype]; + Jex = 4.0*J1_mag[itype][jtype]*ra; + Jex *= (1.0-J2[itype][jtype]*ra); + Jex *= exp(-ra); + + fmi[0] += Jex*spj[0]; + fmi[1] += Jex*spj[1]; + fmi[2] += Jex*spj[2]; +} + +/* ---------------------------------------------------------------------- + compute the mechanical force due to the exchange interaction between atom i and atom j +------------------------------------------------------------------------- */ + +void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3], + double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double Jex, Jex_mech, ra, rr, iJ3; + itype = type[i]; + jtype = type[j]; + + Jex = J1_mech[itype][jtype]; + iJ3 = 1.0/(J3[itype][jtype]*J3[itype][jtype]); + + ra = rsq*iJ3; + rr = sqrt(rsq)*iJ3; + + Jex_mech = 1.0-ra-J2[itype][jtype]*ra*(2.0-ra); + Jex_mech *= 8.0*Jex*rr*exp(-ra); + Jex_mech *= (spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]); + + fi[0] -= Jex_mech*eij[0]; + fi[1] -= Jex_mech*eij[1]; + fi[2] -= Jex_mech*eij[2]; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinExchange::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_exchange,n+1,n+1,"pair/spin/exchange:cut_spin_exchange"); + memory->create(J1_mag,n+1,n+1,"pair/spin/exchange:J1_mag"); + memory->create(J1_mech,n+1,n+1,"pair/spin/exchange:J1_mech"); + memory->create(J2,n+1,n+1,"pair/spin/exchange:J2"); + memory->create(J3,n+1,n+1,"pair/spin/exchange:J3"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinExchange::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&J1_mag[i][j],sizeof(double),1,fp); + fwrite(&J1_mech[i][j],sizeof(double),1,fp); + fwrite(&J2[i][j],sizeof(double),1,fp); + fwrite(&J3[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_exchange[i][j],sizeof(double),1,fp); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinExchange::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&J1_mag[i][j],sizeof(double),1,fp); + fread(&J1_mech[i][j],sizeof(double),1,fp); + fread(&J2[i][j],sizeof(double),1,fp); + fread(&J2[i][j],sizeof(double),1,fp); + fread(&cut_spin_exchange[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&J1_mag[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&J3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_exchange[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinExchange::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_exchange_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinExchange::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_exchange_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_exchange_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + diff --git a/src/SPIN/pair_spin_exchange.h b/src/SPIN/pair_spin_exchange.h new file mode 100644 index 0000000000000000000000000000000000000000..b524a513eb3229e755a94fbbcdcfb485dc92cf00 --- /dev/null +++ b/src/SPIN/pair_spin_exchange.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/exchange,PairSpinExchange) + +#else + +#ifndef LMP_PAIR_SPIN_EXCHANGE_H +#define LMP_PAIR_SPIN_EXCHANGE_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinExchange : public PairSpin { + public: + PairSpinExchange(class LAMMPS *); + virtual ~PairSpinExchange(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_exchange(int, int, double, double *, double *); + void compute_exchange_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_exchange_global; // global exchange cutoff distance + + protected: + double **J1_mag; // exchange coeffs in eV + double **J1_mech; // mech exchange coeffs in + double **J2, **J3; // J1 in eV, J2 adim, J3 in Ang + double **cut_spin_exchange; // cutoff distance exchange + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6bc1f71947333ac405e29d6342696165b47379ab --- /dev/null +++ b/src/SPIN/pair_spin_magelec.cpp @@ -0,0 +1,543 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_magelec.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinMagelec::PairSpinMagelec(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinMagelec::~PairSpinMagelec() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_magelec); + memory->destroy(ME); + memory->destroy(ME_mech); + memory->destroy(v_mex); + memory->destroy(v_mey); + memory->destroy(v_mez); + memory->destroy(cutsq); // to be deteled + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinMagelec::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_magelec_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_spin_magelec[i][j] = cut_spin_magelec_global; + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinMagelec::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"magelec") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 8) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double magelec = (force->numeric(FLERR,arg[4])); + double mex = force->numeric(FLERR,arg[5]); + double mey = force->numeric(FLERR,arg[6]); + double mez = force->numeric(FLERR,arg[7]); + + double inorm = 1.0/(mex*mex+mey*mey+mez*mez); + mex *= inorm; + mey *= inorm; + mez *= inorm; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_magelec[i][j] = rij; + ME[i][j] = magelec/hbar; + ME_mech[i][j] = magelec; + v_mex[i][j] = mex; + v_mey[i][j] = mey; + v_mez[i][j] = mez; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinMagelec::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinMagelec::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + ME[j][i] = ME[i][j]; + ME_mech[j][i] = ME_mech[i][j]; + v_mex[j][i] = v_mex[i][j]; + v_mey[j][i] = v_mey[i][j]; + v_mez[j][i] = v_mez[i][j]; + cut_spin_magelec[j][i] = cut_spin_magelec[i][j]; + + return cut_spin_magelec_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinMagelec::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_magelec_global; + return NULL; +} + + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl, ecoul; + double xi[3], eij[3]; + double delx,dely,delz; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // magneto-electric computation + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; + + // compute me interaction + + if (rsq <= local_cut2) { + compute_magelec(i,j,rsq,eij,fmi,spj); + if (lattice_flag) { + compute_magelec_mech(i,j,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + double xi[3], eij[3]; + double delx,dely,delz; + double spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + if (rsq <= local_cut2) { + compute_magelec(i,j,rsq,eij,fmi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_magelec(int i, int j, double rsq, double eij[3], double fmi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + double meix,meiy,meiz; + double vx,vy,vz; + itype = type[i]; + jtype = type[j]; + + vx = v_mex[itype][jtype]; + vy = v_mey[itype][jtype]; + vz = v_mez[itype][jtype]; + + meix = vy*eij[2] - vz*eij[1]; + meiy = vz*eij[0] - vx*eij[2]; + meiz = vx*eij[1] - vy*eij[0]; + + meix *= ME[itype][jtype]; + meiy *= ME[itype][jtype]; + meiz *= ME[itype][jtype]; + + fmi[0] += spj[1]*meiz - spj[2]*meiy; + fmi[1] += spj[2]*meix - spj[0]*meiz; + fmi[2] += spj[0]*meiy - spj[1]*meix; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double meix,meiy,meiz; + double vx, vy, vz; + + vx = v_mex[itype][jtype]; + vy = v_mey[itype][jtype]; + vz = v_mez[itype][jtype]; + + meix = spi[1]*spi[2] - spi[2]*spj[1]; + meiy = spi[2]*spi[0] - spi[0]*spj[2]; + meiz = spi[0]*spi[1] - spi[1]*spj[0]; + + meix *= ME_mech[itype][jtype]; + meiy *= ME_mech[itype][jtype]; + meiz *= ME_mech[itype][jtype]; + + fi[0] += meiy*vz - meiz*vy; + fi[1] += meiz*vx - meix*vz; + fi[2] += meix*vy - meiy*vx; + +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinMagelec::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_magelec,n+1,n+1,"pair/spin/me:cut_spin_magelec"); + memory->create(ME,n+1,n+1,"pair/spin/me:ME"); + memory->create(ME_mech,n+1,n+1,"pair/spin/me:ME_mech"); + memory->create(v_mex,n+1,n+1,"pair/spin/me:ME_vector_x"); + memory->create(v_mey,n+1,n+1,"pair/spin/me:ME_vector_y"); + memory->create(v_mez,n+1,n+1,"pair/spin/me:ME_vector_z"); + memory->create(cutsq,n+1,n+1,"pair:cutsq"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinMagelec::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&ME[i][j],sizeof(double),1,fp); + fwrite(&v_mex[i][j],sizeof(double),1,fp); + fwrite(&v_mey[i][j],sizeof(double),1,fp); + fwrite(&v_mez[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_magelec[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinMagelec::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&ME[i][j],sizeof(double),1,fp); + fread(&v_mex[i][j],sizeof(double),1,fp); + fread(&v_mey[i][j],sizeof(double),1,fp); + fread(&v_mez[i][j],sizeof(double),1,fp); + fread(&cut_spin_magelec[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&ME[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mex[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mey[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&v_mez[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_magelec[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinMagelec::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_magelec_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinMagelec::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_magelec_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_magelec_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h new file mode 100644 index 0000000000000000000000000000000000000000..ce1347627186877ec7774626741096b4841f3127 --- /dev/null +++ b/src/SPIN/pair_spin_magelec.h @@ -0,0 +1,84 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/magelec,PairSpinMagelec) + +#else + +#ifndef LMP_PAIR_SPIN_MAGELEC_H +#define LMP_PAIR_SPIN_MAGELEC_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinMagelec : public PairSpin { + public: + PairSpinMagelec(class LAMMPS *); + virtual ~PairSpinMagelec(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_magelec(int, int, double, double *, double *, double *); + void compute_magelec_mech(int, int, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_magelec_global; // global me cutoff + + protected: + double **ME, **ME_mech; // magelec coeff in eV + double **v_mex, **v_mey, **v_mez; // magelec direction + double **cut_spin_magelec; // magelec cutoff distance + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp new file mode 100644 index 0000000000000000000000000000000000000000..55f537cf4fe1c4b2af7de3dc3a1945cca14b4f0e --- /dev/null +++ b/src/SPIN/pair_spin_neel.cpp @@ -0,0 +1,722 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "fix.h" +#include "fix_nve_spin.h" +#include "force.h" +#include "pair_hybrid.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "modify.h" +#include "pair_spin_neel.h" +#include "update.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairSpinNeel::PairSpinNeel(LAMMPS *lmp) : PairSpin(lmp), +lockfixnvespin(NULL) +{ + single_enable = 0; + no_virial_fdotr_compute = 1; + lattice_flag = 0; +} + +/* ---------------------------------------------------------------------- */ + +PairSpinNeel::~PairSpinNeel() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cut_spin_neel); + memory->destroy(g1); + memory->destroy(g1_mech); + memory->destroy(g2); + memory->destroy(g3); + memory->destroy(q1); + memory->destroy(q1_mech); + memory->destroy(q2); + memory->destroy(q3); + memory->destroy(cutsq); // to be deleted + } +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairSpinNeel::settings(int narg, char **arg) +{ + if (narg < 1 || narg > 2) + error->all(FLERR,"Incorrect number of args in pair_style pair/spin command"); + + if (strcmp(update->unit_style,"metal") != 0) + error->all(FLERR,"Spin simulations require metal unit style"); + + cut_spin_neel_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i+1; j <= atom->ntypes; j++) { + if (setflag[i][j]) { + cut_spin_neel[i][j] = cut_spin_neel_global; + } + } + } + } + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type spin pairs (only one for now) +------------------------------------------------------------------------- */ + +void PairSpinNeel::coeff(int narg, char **arg) +{ + if (!allocated) allocate(); + + // check if args correct + + if (strcmp(arg[2],"neel") != 0) + error->all(FLERR,"Incorrect args in pair_style command"); + if (narg != 10) + error->all(FLERR,"Incorrect args in pair_style command"); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + const double rij = force->numeric(FLERR,arg[3]); + const double k1 = force->numeric(FLERR,arg[4]); + const double k2 = force->numeric(FLERR,arg[5]); + const double k3 = force->numeric(FLERR,arg[6]); + const double l1 = force->numeric(FLERR,arg[7]); + const double l2 = force->numeric(FLERR,arg[8]); + const double l3 = force->numeric(FLERR,arg[9]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut_spin_neel[i][j] = rij; + g1[i][j] = k1/hbar; + q1[i][j] = l1/hbar; + g1_mech[i][j] = k1; + q1_mech[i][j] = l1; + g2[i][j] = k2; + g3[i][j] = k3; + q2[i][j] = l2; + q3[i][j] = l3; + setflag[i][j] = 1; + count++; + } + } + if (count == 0) + error->all(FLERR,"Incorrect args in pair_style command"); + +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairSpinNeel::init_style() +{ + if (!atom->sp_flag) + error->all(FLERR,"Pair spin requires atom/spin style"); + + // need a full neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + + // checking if nve/spin is a listed fix + + int ifix = 0; + while (ifix < modify->nfix) { + if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; + ifix++; + } + if (ifix == modify->nfix) + error->all(FLERR,"pair/spin style requires nve/spin"); + + // get the lattice_flag from nve/spin + + for (int i = 0; i < modify->nfix; i++) { + if (strcmp(modify->fix[i]->style,"nve/spin") == 0) { + lockfixnvespin = (FixNVESpin *) modify->fix[i]; + lattice_flag = lockfixnvespin->lattice_flag; + } + } + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairSpinNeel::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + g1[j][i] = g1[i][j]; + g1_mech[j][i] = g1_mech[i][j]; + g2[j][i] = g2[i][j]; + g3[j][i] = g3[i][j]; + q1[j][i] = q1[i][j]; + q1_mech[j][i] = q1_mech[i][j]; + q2[j][i] = q2[i][j]; + q3[j][i] = q3[i][j]; + + return cut_spin_neel_global; +} + +/* ---------------------------------------------------------------------- + extract the larger cutoff +------------------------------------------------------------------------- */ + +void *PairSpinNeel::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut") == 0) return (void *) &cut_spin_neel_global; + return NULL; +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double evdwl,ecoul; + double xi[3], rij[3], eij[3]; + double spi[3], spj[3]; + double fi[3], fmi[3]; + double local_cut2; + double rsq, inorm; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = 0; + + double **x = atom->x; + double **f = atom->f; + double **fm = atom->fm; + double **sp = atom->sp; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // computation of the neel interaction + // loop over atoms and their neighbors + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + itype = type[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + // loop on neighbors + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + evdwl = 0.0; + + fi[0] = fi[1] = fi[2] = 0.0; + fmi[0] = fmi[1] = fmi[2] = 0.0; + rij[0] = rij[1] = rij[2] = 0.0; + + rij[0] = x[j][0] - xi[0]; + rij[1] = x[j][1] - xi[1]; + rij[2] = x[j][2] - xi[2]; + rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + inorm = 1.0/sqrt(rsq); + eij[0] = rij[0]*inorm; + eij[1] = rij[1]*inorm; + eij[2] = rij[2]*inorm; + + itype = type[i]; + jtype = type[j]; + + local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; + + // compute neel interaction + + if (rsq <= local_cut2) { + compute_neel(i,j,rsq,eij,fmi,spi,spj); + if (lattice_flag) { + compute_neel_mech(i,j,rsq,eij,fi,spi,spj); + } + } + + f[i][0] += fi[0]; + f[i][1] += fi[1]; + f[i][2] += fi[2]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; + fm[i][2] += fmi[2]; + + if (newton_pair || j < nlocal) { + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; + f[j][2] -= fi[2]; + } + + if (eflag) { + evdwl = (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; + } else evdwl = 0.0; + + if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, + evdwl,ecoul,fi[0],fi[1],fi[2],rij[0],rij[1],rij[2]); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_single_pair(int ii, double fmi[3]) +{ + int *type = atom->type; + double **x = atom->x; + double **sp = atom->sp; + double local_cut2; + + double xi[3], rij[3], eij[3]; + double spi[3], spj[3]; + + int i,j,jnum,itype,jtype; + int *ilist,*jlist,*numneigh,**firstneigh; + + double rsq, inorm; + + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + i = ilist[ii]; + itype = type[i]; + + spi[0] = sp[i][0]; + spi[1] = sp[i][1]; + spi[2] = sp[i][2]; + + xi[0] = x[i][0]; + xi[1] = x[i][1]; + xi[2] = x[i][2]; + + eij[0] = eij[1] = eij[2] = 0.0; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + rij[0] = x[j][0] - xi[0]; + rij[1] = x[j][1] - xi[1]; + rij[2] = x[j][2] - xi[2]; + rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + inorm = 1.0/sqrt(rsq); + eij[0] = inorm*rij[0]; + eij[1] = inorm*rij[1]; + eij[2] = inorm*rij[2]; + + if (rsq <= local_cut2) { + compute_neel(i,j,rsq,eij,fmi,spi,spj); + } + } + +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_neel(int i, int j, double rsq, double eij[3], double fmi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double gij, q1ij, q2ij, ra; + double pdx, pdy, pdz; + double pq1x, pq1y, pq1z; + double pq2x, pq2y, pq2z; + + // pseudo-dipolar component + + ra = rsq/g3[itype][jtype]/g3[itype][jtype]; + gij = 4.0*g1[itype][jtype]*ra; + gij *= (1.0-g2[itype][jtype]*ra); + gij *= exp(-ra); + + double scalar_eij_si = eij[0]*spi[0] + eij[1]*spi[1] + eij[2]*spi[2]; + double scalar_eij_sj = eij[0]*spj[0] + eij[1]*spj[1] + eij[2]*spj[2]; + double scalar_si_sj = spi[0]*spj[0] + spi[1]*spj[1] + spi[2]*spj[2]; + + double gij_eij_sj = gij*scalar_eij_sj; + double gij_3 = gij/3.0; + pdx = gij_eij_sj*eij[0] - gij_3*spj[0]; + pdy = gij_eij_sj*eij[1] - gij_3*spj[1]; + pdz = gij_eij_sj*eij[2] - gij_3*spj[2]; + + // pseudo-quadrupolar component + + ra = rsq/q3[itype][jtype]/q3[itype][jtype]; + q1ij = 4.0*q1[itype][jtype]*ra; + q1ij *= (1.0-q2[itype][jtype]*ra); + q1ij *= exp(-ra); + q2ij = (-2.0*q1ij/9.0); + + double scalar_eij_si_2 = scalar_eij_si*scalar_eij_si; + pq1x = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[0]/3.0; + pq1y = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[1]/3.0; + pq1z = -(scalar_eij_si_2*scalar_eij_si_2 - scalar_si_sj/3.0)*spj[2]/3.0; + + double pqt1 = (scalar_eij_sj*scalar_eij_sj-scalar_si_sj/3.0); + pq1x += pqt1*(2.0*scalar_eij_si*eij[0] - spj[0]/3.0); + pq1y += pqt1*(2.0*scalar_eij_si*eij[1] - spj[1]/3.0); + pq1z += pqt1*(2.0*scalar_eij_si*eij[2] - spj[2]/3.0); + + pq1x *= q1ij; + pq1y *= q1ij; + pq1z *= q1ij; + + double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + pq2x = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[0] + scalar_eij_sj_3*eij[0]; + pq2y = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[1] + scalar_eij_sj_3*eij[1]; + pq2z = 3.0*scalar_eij_si_2*scalar_eij_sj*eij[2] + scalar_eij_sj_3*eij[2]; + + pq2x *= q2ij; + pq2y *= q2ij; + pq2z *= q2ij; + + // adding three contributions + + fmi[0] += (pdx + pq1x + pq2x); + fmi[1] += (pdy + pq1y + pq2y); + fmi[2] += (pdz + pq1z + pq2z); +} + +/* ---------------------------------------------------------------------- */ + +void PairSpinNeel::compute_neel_mech(int i, int j, double rsq, double eij[3], double fi[3], double spi[3], double spj[3]) +{ + int *type = atom->type; + int itype, jtype; + itype = type[i]; + jtype = type[j]; + + double g_mech, gij, dgij; + double q_mech, q1ij, dq1ij; + double q2ij, dq2ij; + double pdx, pdy, pdz; + double pq1x, pq1y, pq1z; + double pq2x, pq2y, pq2z; + double ra, rr, drij, ig3, iq3; + + drij = sqrt(rsq); + + double scalar_si_sj = spi[0]*spj[0]+spi[1]*spj[1]+spi[2]*spj[2]; + double scalar_eij_si = eij[0]*spi[0]+eij[1]*spi[1]+eij[2]*spi[2]; + double scalar_eij_sj = eij[0]*spj[0]+eij[1]*spj[1]+eij[2]*spj[2]; + + // pseudo-dipolar component + + g_mech = g1_mech[itype][jtype]; + ig3 = 1.0/(g3[itype][jtype]*g3[itype][jtype]); + + ra = rsq*ig3; + rr = drij*ig3; + + gij = 4.0*g_mech*ra; + gij *= (1.0-g2[itype][jtype]*ra); + gij *= exp(-ra); + + dgij = 1.0-ra-g2[itype][jtype]*ra*(2.0-ra); + dgij *= 8.0*g_mech*rr*exp(-ra); + + double pdt1 = (dgij-2.0*gij/drij)*scalar_eij_si*scalar_eij_sj; + pdt1 -= scalar_si_sj*dgij/3.0; + double pdt2 = scalar_eij_sj*gij/drij; + double pdt3 = scalar_eij_si*gij/drij; + pdx = -(pdt1*eij[0] + pdt2*spi[0] + pdt3*spj[0]); + pdy = -(pdt1*eij[1] + pdt2*spi[1] + pdt3*spj[1]); + pdz = -(pdt1*eij[2] + pdt2*spi[2] + pdt3*spj[2]); + + // pseudo-quadrupolar component + + q_mech = q1_mech[itype][jtype]; + iq3 = 1.0/(q3[itype][jtype]*q3[itype][jtype]); + + ra = rsq*iq3; + rr = drij*iq3; + + q1ij = 4.0*q_mech*ra; + q1ij *= (1.0-q2[itype][jtype]*ra); + q1ij *= exp(-ra); + q2ij = -2.0*q1ij/9.0; + + dq1ij = 1.0-ra-q2[itype][jtype]*ra*(2.0-ra); + dq1ij *= 8.0*q_mech*rr*exp(-ra); + dq2ij = -2.0*dq1ij/9.0; + + double scalar_eij_si_2 = scalar_eij_si*scalar_eij_si; + double scalar_eij_sj_2 = scalar_eij_sj*scalar_eij_sj; + double pqt1 = scalar_eij_si_2 - scalar_si_sj/3.0; + double pqt2 = scalar_eij_sj_2 - scalar_si_sj/3.0; + pq1x = dq1ij * pqt1 * pqt2 * eij[0]; + pq1y = dq1ij * pqt1 * pqt2 * eij[1]; + pq1z = dq1ij * pqt1 * pqt2 * eij[2]; + + double scalar_eij_si_3 = scalar_eij_si*scalar_eij_si*scalar_eij_si; + double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + double scalar_si_sj_2 = scalar_si_sj*scalar_si_sj; +/* double pqt3 = 2.0*scalar_eij_si*scalar_eij_sj_3/drij; + double pqt4 = 2.0*scalar_eij_sj*scalar_eij_si_3/drij; + double pqt5 = -2.0*scalar_si_sj*scalar_eij_si/(3.0*drij); + double pqt6 = -2.0*scalar_si_sj*scalar_eij_sj/(3.0*drij); +// pq1x += q1ij*(spi[0]*(pqt3+pqt6) + spj[0]*(pqt4+)); + pq1x += q1ij*(pqt3*spi[0]+pqt4*spj[0]+pqt5*spi[0]+pqt6*spi[0]); + pq1y += q1ij*(pqt3*spi[1]+pqt4*spj[1]+pqt5*spi[1]+pqt6*spj[1]); + pq1z += q1ij*(pqt3*spi[2]+pqt4*spj[2]+pqt5*spi[2]+pqt6*spj[2]); +*/ + double pqt3 = 2.0*scalar_eij_si*(scalar_eij_sj_2-scalar_si_sj/3.0)/drij; + double pqt4 = 2.0*scalar_eij_sj*(scalar_eij_si_2-scalar_si_sj/3.0)/drij; + pq1x += q1ij*(pqt3*spi[0] + pqt4*spj[0]); + pq1y += q1ij*(pqt3*spi[1] + pqt4*spj[1]); + pq1z += q1ij*(pqt3*spi[2] + pqt4*spj[2]); + double pqt7 = 4.0*scalar_eij_si_2*scalar_eij_sj_2/drij; + double pqt8 = 2.0*scalar_si_sj_2*scalar_eij_sj/(3.0*drij); + double pqt9 = 2.0*scalar_si_sj_2*scalar_eij_si/(3.0*drij); + pq1x -= q1ij*(pqt7 + pqt8 + pqt9)*eij[0]; + pq1y -= q1ij*(pqt7 + pqt8 + pqt9)*eij[1]; + pq1z -= q1ij*(pqt7 + pqt8 + pqt9)*eij[2]; + +/* + double pqt3 = 2.0*scalar_eij_si*(scalar_eij_sj_2-scalar_si_sj/3.0)/drij; + double pqt4 = 2.0*scalar_eij_sj*(scalar_eij_si_2-scalar_si_sj/3.0)/drij; + pq1x += q1ij*(pqt3*spi[0] + pqt4*spj[0]); + pq1y += q1ij*(pqt3*spi[1] + pqt4*spj[1]); + pq1z += q1ij*(pqt3*spi[2] + pqt4*spj[2]); +*/ + + //double scalar_eij_si_3 = scalar_eij_si*scalar_eij_si*scalar_eij_si; + //double scalar_eij_sj_3 = scalar_eij_sj*scalar_eij_sj*scalar_eij_sj; + double pqt10 = scalar_eij_sj*scalar_eij_si_3; + double pqt11 = scalar_eij_si*scalar_eij_sj_3; + pq2x = dq2ij*(pqt10 + pqt11)*eij[0]; + pq2y = dq2ij*(pqt10 + pqt11)*eij[1]; + pq2z = dq2ij*(pqt10 + pqt11)*eij[2]; + + double pqt12 = scalar_eij_si_3/drij; + double pqt13 = scalar_eij_sj_3/drij; + double pqt14 = 3.0*scalar_eij_sj*scalar_eij_si_2/drij; + double pqt15 = 3.0*scalar_eij_si*scalar_eij_sj_2/drij; + pq2x += q2ij*((pqt12+pqt15)*spj[0]+(pqt13+pqt14)*spi[0]); + pq2y += q2ij*((pqt12+pqt15)*spj[1]+(pqt13+pqt14)*spi[1]); + pq2z += q2ij*((pqt12+pqt15)*spj[2]+(pqt13+pqt14)*spi[2]); + double pqt16 = 4.0*scalar_eij_sj*scalar_eij_si_3/drij; + double pqt17 = 4.0*scalar_eij_si*scalar_eij_sj_3/drij; + pq2x -= q2ij*(pqt16 + pqt17)*eij[0]; + pq2y -= q2ij*(pqt16 + pqt17)*eij[1]; + pq2z -= q2ij*(pqt16 + pqt17)*eij[2]; + + // adding three contributions + + fi[0] = pdx + pq1x + pq2x; + fi[1] = pdy + pq1y + pq2y; + fi[2] = pdz + pq1z + pq2z; +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairSpinNeel::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cut_spin_neel,n+1,n+1,"pair/spin/soc/neel:cut_spin_neel"); + + memory->create(g1,n+1,n+1,"pair/spin/soc/neel:g1"); + memory->create(g1_mech,n+1,n+1,"pair/spin/soc/neel:g1_mech"); + memory->create(g2,n+1,n+1,"pair/spin/soc/neel:g2"); + memory->create(g3,n+1,n+1,"pair/spin/soc/neel:g3"); + + memory->create(q1,n+1,n+1,"pair/spin/soc/neel:q1"); + memory->create(q1_mech,n+1,n+1,"pair/spin/soc/neel:q1_mech"); + memory->create(q2,n+1,n+1,"pair/spin/soc/neel:q2"); + memory->create(q3,n+1,n+1,"pair/spin/soc/neel:q3"); + + memory->create(cutsq,n+1,n+1,"pair/spin/soc/neel:cutsq"); + +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinNeel::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&g1[i][j],sizeof(double),1,fp); + fwrite(&g1_mech[i][j],sizeof(double),1,fp); + fwrite(&g2[i][j],sizeof(double),1,fp); + fwrite(&g3[i][j],sizeof(double),1,fp); + fwrite(&q1[i][j],sizeof(double),1,fp); + fwrite(&q1_mech[i][j],sizeof(double),1,fp); + fwrite(&q2[i][j],sizeof(double),1,fp); + fwrite(&q3[i][j],sizeof(double),1,fp); + fwrite(&cut_spin_neel[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinNeel::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) { + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&g1[i][j],sizeof(double),1,fp); + fread(&g1_mech[i][j],sizeof(double),1,fp); + fread(&g2[i][j],sizeof(double),1,fp); + fread(&g2[i][j],sizeof(double),1,fp); + fread(&q1[i][j],sizeof(double),1,fp); + fread(&q1_mech[i][j],sizeof(double),1,fp); + fread(&q2[i][j],sizeof(double),1,fp); + fread(&q2[i][j],sizeof(double),1,fp); + fread(&cut_spin_neel[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&g1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&g3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q1_mech[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&q3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_spin_neel[i][j],1,MPI_DOUBLE,0,world); + } + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairSpinNeel::write_restart_settings(FILE *fp) +{ + fwrite(&cut_spin_neel_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairSpinNeel::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_spin_neel_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&cut_spin_neel_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} diff --git a/src/SPIN/pair_spin_neel.h b/src/SPIN/pair_spin_neel.h new file mode 100644 index 0000000000000000000000000000000000000000..f60d7d2dca0e6ac72ea3c0111698f79d60ea2f37 --- /dev/null +++ b/src/SPIN/pair_spin_neel.h @@ -0,0 +1,90 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(spin/neel,PairSpinNeel) + +#else + +#ifndef LMP_PAIR_SPIN_NEEL_H +#define LMP_PAIR_SPIN_NEEL_H + +#include "pair_spin.h" + +namespace LAMMPS_NS { + +class PairSpinNeel : public PairSpin { + public: + PairSpinNeel(class LAMMPS *); + virtual ~PairSpinNeel(); + void settings(int, char **); + void coeff(int, char **); + void init_style(); + double init_one(int, int); + void *extract(const char *, int &); + + void compute(int, int); + void compute_single_pair(int, double *); + + void compute_neel(int, int, double, double *, double *, double *, double *); + void compute_neel_mech(int, int, double, double *, double *, double *, double *); + + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + + double cut_spin_neel_global; // global neel cutoff distance + + protected: + + // pseudo-dipolar and pseudo-quadrupolar coeff. + + double **g1, **g1_mech; // neel coeffs gij + double **g2, **g3; // g1 in eV, g2 adim, g3 in Ang + double **q1, **q1_mech; // neel coeffs qij + double **q2, **q3; // q1 in eV, q2 adim, q3 in Ang + double **cut_spin_neel; // cutoff distance exchange + + int lattice_flag; // flag for mech force computation + class FixNVESpin *lockfixnvespin; // ptr to FixNVESpin for setups + + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args in pair_spin command + +Self-explanatory. + +E: Spin simulations require metal unit style + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair spin requires atom attribute spin + +The atom style defined does not have these attributes. + +*/ diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index 37e128f55662a6e6c9152abb518d3233845604fd..7fb8a27110ba2528bf81e53f4e6e9c78de23ee54 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -846,7 +846,7 @@ void FixBocs::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) @@ -1508,7 +1508,7 @@ double FixBocs::compute_scalar() double volume; double energy; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press = 0.0; int ich; if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; else volume = domain->xprd * domain->yprd; @@ -1539,15 +1539,21 @@ double FixBocs::compute_scalar() // sum is over barostatted dimensions if (pstat_flag) { - for (i = 0; i < 3; i++) - if (p_flag[i]) + for (i = 0; i < 3; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + p_hydro*(volume-vol0) / (pdim*nktv2p); + lkt_press += kt; + } + } if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) + for (i = 3; i < 6; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + lkt_press += kt; + } + } } // extra contributions from thermostat chain for barostat @@ -1880,15 +1886,14 @@ void FixBocs::nhc_temp_integrate() void FixBocs::nhc_press_integrate() { - int ich,i; + int ich,i,pdof; double expfac,factor_etap,kecurrent; double kt = boltz * t_target; - double lkt_press = kt; // Update masses, to preserve initial freq, if flag set if (omega_mass_flag) { - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); @@ -1912,14 +1917,24 @@ void FixBocs::nhc_press_integrate() } kecurrent = 0.0; - for (i = 0; i < 3; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof = 0; + for (i = 0; i < 3; i++) { + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } + } if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + for (i = 3; i < 6; i++) { + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } + } } + double lkt_press = pdof * kt; etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; double ncfac = 1.0/nc_pchain; diff --git a/src/USER-DPD/fix_shardlow.cpp b/src/USER-DPD/fix_shardlow.cpp index 06185dee7ec702d2dfb3a4686fa88c2c7e3b16f8..7fe865c8e6a9bce50d863c5f5cb14d8b119c1fef 100644 --- a/src/USER-DPD/fix_shardlow.cpp +++ b/src/USER-DPD/fix_shardlow.cpp @@ -354,9 +354,8 @@ void FixShardlow::ssa_update_dpde( double *uMech = atom->uMech; double *dpdTheta = atom->dpdTheta; - double *cut_i, *cut2_i, *sigma_i, *kappa_i; + double *cut_i, *cut2_i, *sigma_i, *kappa_i, *alpha_i; double theta_ij_inv, theta_i_inv; - const double boltz2 = 2.0*force->boltz; const double boltz_inv = 1.0/force->boltz; const double ftm2v = force->ftm2v; @@ -389,6 +388,7 @@ while (ct-- > 0) { cut_i = pairDPDE->cut[itype]; sigma_i = pairDPDE->sigma[itype]; kappa_i = pairDPDE->kappa[itype]; + alpha_i = pairDPDE->alpha[itype]; theta_i_inv = 1.0/dpdTheta[i]; const double mass_i = (rmass) ? rmass[i] : mass[itype]; const double massinv_i = 1.0 / mass_i; @@ -448,7 +448,7 @@ while (ct-- > 0) { // Compute uCond double kappa_ij = kappa_i[jtype]; - double alpha_ij = sqrt(boltz2*kappa_ij); + double alpha_ij = alpha_i[jtype]; double del_uCond = alpha_ij*wr*dtsqrt * es_normal(RNGstate); del_uCond += kappa_ij*(theta_i_inv - theta_j_inv)*wdt; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index d1f3cceed4ca14db73014d7e252770b007d8db95..05dc52eac787b974cf628bf9fd22b984763fab57 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -65,6 +65,7 @@ PairDPDfdtEnergy::~PairDPDfdtEnergy() memory->destroy(a0); memory->destroy(sigma); memory->destroy(kappa); + memory->destroy(alpha); memory->destroy(duCond); memory->destroy(duMech); } @@ -269,7 +270,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag) // Compute uCond randnum = random->gaussian(); kappa_ij = kappa[itype][jtype]; - alpha_ij = sqrt(2.0*force->boltz*kappa_ij); + alpha_ij = alpha[itype][jtype]; randPair = alpha_ij*wr*randnum*dtinvsqrt; uTmp = kappa_ij*(1.0/dpdTheta[i] - 1.0/dpdTheta[j])*wd; @@ -322,6 +323,7 @@ void PairDPDfdtEnergy::allocate() memory->create(a0,n+1,n+1,"pair:a0"); memory->create(sigma,n+1,n+1,"pair:sigma"); memory->create(kappa,n+1,n+1,"pair:kappa"); + memory->create(alpha,n+1,n+1,"pair:alpha"); if (!splitFDT_flag) { memory->create(duCond,nlocal+nghost+1,"pair:duCond"); memory->create(duMech,nlocal+nghost+1,"pair:duMech"); @@ -374,11 +376,12 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg) double a0_one = force->numeric(FLERR,arg[2]); double sigma_one = force->numeric(FLERR,arg[3]); double cut_one = cut_global; - double kappa_one; + double kappa_one, alpha_one; a0_is_zero = (a0_one == 0.0); // Typical use with SSA is to set a0 to zero kappa_one = force->numeric(FLERR,arg[4]); + alpha_one = sqrt(2.0*force->boltz*kappa_one); if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); int count = 0; @@ -387,6 +390,7 @@ void PairDPDfdtEnergy::coeff(int narg, char **arg) a0[i][j] = a0_one; sigma[i][j] = sigma_one; kappa[i][j] = kappa_one; + alpha[i][j] = alpha_one; cut[i][j] = cut_one; setflag[i][j] = 1; count++; @@ -435,6 +439,7 @@ double PairDPDfdtEnergy::init_one(int i, int j) a0[j][i] = a0[i][j]; sigma[j][i] = sigma[i][j]; kappa[j][i] = kappa[i][j]; + alpha[j][i] = alpha[i][j]; return cut[i][j]; } @@ -488,6 +493,7 @@ void PairDPDfdtEnergy::read_restart(FILE *fp) MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&kappa[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + alpha[i][j] = sqrt(2.0*force->boltz*kappa[i][j]); a0_is_zero = a0_is_zero && (a0[i][j] == 0.0); // verify the zero assumption } } diff --git a/src/USER-DPD/pair_dpd_fdt_energy.h b/src/USER-DPD/pair_dpd_fdt_energy.h index dce39f83f071904a0e8d832095edc0f1a7d85a0a..e21b48f7bdb99a28b0735f1a25d38f47c60a8ada 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.h +++ b/src/USER-DPD/pair_dpd_fdt_energy.h @@ -43,7 +43,7 @@ class PairDPDfdtEnergy : public Pair { double **cut; double **a0; - double **sigma,**kappa; + double **sigma,**kappa,**alpha; double *duCond,*duMech; int seed; diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index d7093e79bb68c91d785a66f257338bc6ccff81bf..79fb23ab3d98cfb7cdbf62a3d1cf35fa58415b8c 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -82,7 +82,8 @@ class FixIntel : public Fix { } inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; } inline int lrt() { - if (force->kspace_match("pppm/intel", 0)) return _lrt; + if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1) + return _lrt; else return 0; } inline int pppm_table() { diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 29cc45f75561d268620dcb6a51cd2d573abfe696..2f1b02a49f48826c3cf8841b7643972ec9914354 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -134,7 +134,21 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, #define INTEL_HTHREADS 2 #endif -#define IP_PRE_get_stride(stride, n, datasize, torque) \ +#if INTEL_DATA_ALIGN > 1 + +#define IP_PRE_edge_align(n, esize) \ + { \ + const int pad_mask = ~static_cast(INTEL_DATA_ALIGN/esize-1); \ + n = (n + INTEL_DATA_ALIGN / esize - 1) & pad_mask; \ + } + +#else + +#define IP_PRE_edge_align(n, esize) \ + +#endif + +#define IP_PRE_get_stride(stride, n, datasize, torque) \ { \ int blength = n; \ if (torque) blength *= 2; \ @@ -303,7 +317,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, { \ tid = 0; \ ifrom = 0; \ - ip = 1; \ + ip = vecsize; \ ito = inum; \ } @@ -316,7 +330,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, acc_t *f_scalar = &f_start[0].x; \ flt_t *x_scalar = &pos[minlocal].x; \ int f_stride4 = f_stride * 4; \ - _alignvar(acc_t ovv[INTEL_COMPILE_WIDTH],64); \ + _alignvar(acc_t ovv[16],64); \ int vwidth; \ if (sizeof(acc_t) == sizeof(double)) \ vwidth = INTEL_COMPILE_WIDTH/2; \ @@ -516,6 +530,22 @@ inline double MIC_Wtime() { return time; } +#define IP_PRE_neighbor_pad(jnum, offload) \ +{ \ + const int opad_mask = ~static_cast(INTEL_MIC_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + const int pad_mask = ~static_cast(INTEL_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + if (offload && INTEL_MIC_NBOR_PAD > 1) \ + jnum = (jnum + INTEL_MIC_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & opad_mask; \ + else if (INTEL_NBOR_PAD > 1) \ + jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & pad_mask; \ +} + #define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \ nlocal, nall) \ { \ @@ -644,6 +674,23 @@ inline double MIC_Wtime() { #else +#if INTEL_NBOR_PAD > 1 + +#define IP_PRE_neighbor_pad(jnum, offload) \ +{ \ + const int pad_mask = ~static_cast(INTEL_NBOR_PAD * \ + sizeof(float) / \ + sizeof(flt_t) - 1); \ + jnum = (jnum + INTEL_NBOR_PAD * sizeof(float) / \ + sizeof(flt_t) - 1) & pad_mask; \ +} + +#else + +#define IP_PRE_neighbor_pad(jnum, offload) + +#endif + #define MIC_Wtime MPI_Wtime #define IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, \ nlocal, nall) diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 24d5076c34192a45e538c0435c8693e102a9f4f5..ae961e84b59f0c52038f1f14e38123ace6877d27 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -112,7 +112,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, if (pend-pstart == 0) return; const int nall = atom->nlocal + atom->nghost; - int pad = 1; int nall_t = nall; const int aend = nall; @@ -207,6 +206,17 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, const int mbinz = this->mbinz; const int * const stencilxyz = &this->stencilxyz[0][0]; + int sb = 1; + if (special_flag[1] == 0) { + sb = 2; + if (special_flag[2] == 0) { + sb = 3; + if (special_flag[3] == 0) + sb = 4; + } + } + const int special_bound = sb; + #ifdef _LMP_INTEL_OFFLOAD const int * _noalias const binhead = this->binhead; const int * _noalias const bins = this->bins; @@ -230,7 +240,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \ in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \ in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \ - in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny) \ + in(separate_buffers,aend,nlocal,molecular,ntypes,mbinx,mbiny,special_bound)\ in(mbinz,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \ in(stencilxyz:length(3*nstencil)) \ out(overflow:length(5) alloc_if(0) free_if(0)) \ @@ -287,8 +297,6 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, int e_ito = ito; const int list_size = (e_ito + tid * 2 + 2) * maxnbors; - int which; - int pack_offset = maxnbors; int ct = (ifrom + tid * 2) * maxnbors; int *neighptr = firstneigh + ct; @@ -418,41 +426,109 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, } } // for u + if (molecular && i < nlocal) { + int alln = n; + n = 0; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = 0; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n++] = j; + #else + neighptr2[n++] = j; + #endif + } + alln = n2; + n2 = maxnbors * 2; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n2; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n2++] = j; + #else + neighptr2[n2++] = j; + #endif + } + } + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { int alln = n; n = maxnbors; - for (int u = pack_offset; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n++] = j; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n++] = js; } alln = n2; n2 = maxnbors * 2; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif for (int u = n2; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n2++] = j; + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n2++] = js; } } #endif + int ns = n - maxnbors; int alln = n; atombin[i] = ns; n = 0; for (int u = maxnbors; u < alln; u++) - neighptr[n++] = neighptr[u]; + neighptr[n++] = neighptr2[u]; ns += n2 - maxnbors * 2; for (int u = maxnbors * 2; u < n2; u++) - neighptr[n++] = neighptr[u]; + neighptr[n++] = neighptr2[u]; if (ns > maxnbors) *overflow = 1; ilist[i] = i; @@ -460,9 +536,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, numneigh[i] = ns; ct += ns; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; if (ct + obound > list_size) { if (i < ito - 1) { @@ -477,84 +551,11 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, numneigh[i] = 0; #ifdef _LMP_INTEL_OFFLOAD - int ghost_offset = 0, nall_offset = e_nall; if (separate_buffers) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - #if __INTEL_COMPILER+0 > 1499 - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - if (need_ic && j < 0) j = -j - 1; - } - } - overflow[LMP_LOCAL_MIN] = 0; overflow[LMP_LOCAL_MAX] = nlocal - 1; overflow[LMP_GHOST_MIN] = nlocal; overflow[LMP_GHOST_MAX] = e_nall - 1; - - int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN]; - if (nghost < 0) nghost = 0; - if (offload) { - ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1; - nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost; - } else { - ghost_offset = overflow[LMP_GHOST_MIN] - nlocal; - nall_offset = nlocal + nghost; - } - } // if separate_buffers - #endif - - if (molecular) { - int ito_m = ito; - if (ito >= nlocal) ito_m = nlocal; - for (int i = ifrom; i < ito_m; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } // for i - } // if molecular - #ifdef _LMP_INTEL_OFFLOAD - else if (separate_buffers) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - int jj = 0; - #pragma vector aligned - #pragma simd - for (jj = 0; jj < jnum; jj++) { - if (jlist[jj] >= nlocal) { - if (jlist[jj] == e_nall) jlist[jj] = nall_offset; - else jlist[jj] -= ghost_offset; - } - } - } } #endif } // end omp diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index d3d2745aee1e6e9db2839d66e6add418400a3040..355c8db199b9bd010abb81868ce22bd2cc34d8a9 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -62,19 +62,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (aend-astart == 0) return; const int nall = atom->nlocal + atom->nghost; - int pad = 1; int nall_t = nall; #ifdef _LMP_INTEL_OFFLOAD if (offload_noghost && offload) nall_t = atom->nlocal; - if (THREE == 0 && offload) { - if (INTEL_MIC_NBOR_PAD > 1) - pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t); - } else #endif - if (THREE == 0 && INTEL_NBOR_PAD > 1) - pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t); - const int pad_width = pad; + const int pack_width = _fix->nbor_pack_width(); const ATOM_T * _noalias const x = buffers->get_x(); @@ -150,6 +143,17 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int * _noalias const ncachetag = buffers->get_ncachetag(); const int ncache_stride = buffers->ncache_stride(); + int sb = 1; + if (special_flag[1] == 0) { + sb = 2; + if (special_flag[2] == 0) { + sb = 3; + if (special_flag[3] == 0) + sb = 4; + } + } + const int special_bound = sb; + #ifdef _LMP_INTEL_OFFLOAD const int * _noalias const binhead = this->binhead; const int * _noalias const bins = this->bins; @@ -172,9 +176,9 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, in(ncachex,ncachey,ncachez,ncachej:length(0) alloc_if(0) free_if(0)) \ in(ncachejtype,ncachetag:length(0) alloc_if(0) free_if(0)) \ in(ncache_stride,maxnbors,nthreads,maxspecial,nstencil,e_nall,offload) \ - in(pad_width,offload_end,separate_buffers,astart,aend,nlocal,molecular) \ + in(offload_end,separate_buffers,astart,aend,nlocal,molecular) \ in(ntypes,xperiodic,yperiodic,zperiodic,xprd_half,yprd_half,zprd_half) \ - in(pack_width) \ + in(pack_width,special_bound) \ out(overflow:length(5) alloc_if(0) free_if(0)) \ out(timer_compute:length(1) alloc_if(0) free_if(0)) \ signal(tag) @@ -226,19 +230,25 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ifrom += astart; ito += astart; int e_ito = ito; + #ifdef LMP_INTEL_3BODY_FAST if (THREE && ito == num) { int imod = ito & (pack_width - 1); if (imod) e_ito += pack_width - imod; } + #endif const int list_size = (e_ito + tid * 2 + 2) * maxnbors; - int which; - - int pack_offset = maxnbors; - if (THREE) pack_offset *= pack_width; + #ifdef LMP_INTEL_3BODY_FAST + const int pack_offset = maxnbors * pack_width; + const int obound = pack_offset + maxnbors * 2; + #else + const int pack_offset = 0; + const int obound = maxnbors * 3; + #endif int ct = (ifrom + tid * 2) * maxnbors; int *neighptr = firstneigh + ct; - const int obound = pack_offset + maxnbors * 2; + int *neighptr2; + if (THREE) neighptr2 = neighptr; const int toffs = tid * ncache_stride; flt_t * _noalias const tx = ncachex + toffs; @@ -256,10 +266,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, // loop over all atoms in other bins in stencil, store every pair int istart, icount, ncount, oldbin = -9999999, lane, max_chunk; + #ifdef LMP_INTEL_3BODY_FAST if (THREE) { lane = 0; max_chunk = 0; } + #endif for (int i = ifrom; i < ito; i++) { const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -298,9 +310,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (FULL == 0 || TRI == 1) { icount = 0; istart = ncount; - const int alignb = INTEL_DATA_ALIGN / sizeof(int); - int nedge = istart & (alignb - 1); - if (nedge) istart + (alignb - nedge); + IP_PRE_edge_align(istart, sizeof(int)); itx = tx + istart; ity = ty + istart; itz = tz + istart; @@ -383,11 +393,12 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, // ---------------------- Loop over other bins - int n2, *neighptr2; + int n2; if (THREE) { + #ifdef LMP_INTEL_3BODY_FAST n = pack_offset; + #endif n2 = pack_offset + maxnbors; - neighptr2 = neighptr; } #if defined(LMP_SIMD_COMPILER) #pragma vector aligned @@ -461,49 +472,133 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } // for u + if (molecular) { + if (!THREE) neighptr2 = neighptr; + int alln = n; + + n = pack_offset; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n++] = j; + #else + neighptr2[n++]=j; + #endif + } + + if (THREE) { + alln = n2; + n2 = pack_offset + maxnbors; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #ifdef LMP_INTEL_NBOR_COMPAT + #pragma ivdep + #else + #pragma simd + #endif + #endif + for (int u = n2; u < alln; u++) { + int which; + int addme = 1; + int j = neighptr[u]; + if (need_ic && j < 0) { + which = 0; + j = -j - 1; + } else + ofind_special(which, special, nspecial, i, tag[j]); + if (which) { + j = j ^ (which << SBBITS); + if (which < special_bound) addme = 0; + } + #ifdef LMP_INTEL_NBOR_COMPAT + if (addme) neighptr2[n2++] = j; + #else + neighptr2[n2++]=j; + #endif + } + } + } + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { + neighptr2 = neighptr; int alln = n; - if (THREE) n = pack_offset; - else n = 0; - for (int u = pack_offset; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n++] = j; + n = pack_offset; + + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n++] = js; } if (THREE) { alln = n2; n2 = pack_offset + maxnbors; - for (int u = pack_offset + maxnbors; u < alln; u++) { - const int j = neighptr[u]; - int pj = j; - if (need_ic) - if (pj < 0) pj = -j - 1; - const int jtype = x[pj].w; - if (exclusion(i,pj,itype,jtype,mask,molecule)) continue; - neighptr[n2++] = j; + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma ivdep + #endif + for (int u = n2; u < alln; u++) { + int addme = 1; + const int js = neighptr[u]; + const int j = js & NEIGHMASK; + const int jtype = x[j].w; + if (exclusion(i,j,itype,jtype,mask,molecule)) addme = 0; + if (addme) neighptr2[n2++] = js; } } } #endif + int ns; if (THREE) { int alln = n; ns = n - pack_offset; atombin[i] = ns; + ns += n2 - pack_offset - maxnbors; + + #ifdef LMP_INTEL_3BODY_FAST n = lane; for (int u = pack_offset; u < alln; u++) { - neighptr[n] = neighptr[u]; + neighptr[n] = neighptr2[u]; n += pack_width; } - ns += n2 - pack_offset - maxnbors; + #endif + for (int u = pack_offset + maxnbors; u < n2; u++) { - neighptr[n] = neighptr[u]; + #ifdef LMP_INTEL_3BODY_FAST + neighptr[n] = neighptr2[u]; n += pack_width; + #else + neighptr[n++] = neighptr2[u]; + #endif } if (ns > maxnbors) *overflow = 1; } else @@ -512,34 +607,33 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ilist[i] = i; cnumneigh[i] = ct; if (THREE) { + #ifdef LMP_INTEL_3BODY_FAST cnumneigh[i] += lane; + #endif numneigh[i] = ns; } else { - int edge = n & (pad_width - 1); - if (edge) { - const int pad_end = n + (pad_width - edge); - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ - avg=INTEL_COMPILE_WIDTH/2 - #endif - for ( ; n < pad_end; n++) - neighptr[n] = e_nall; - } numneigh[i] = n; + int pad_end = n; + IP_PRE_neighbor_pad(pad_end, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif + for ( ; n < pad_end; n++) + neighptr[n] = e_nall; } + #ifdef LMP_INTEL_3BODY_FAST if (THREE) { if (ns > max_chunk) max_chunk = ns; lane++; if (lane == pack_width) { ct += max_chunk * pack_width; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; + neighptr2 = neighptr; max_chunk = 0; - pack_offset = maxnbors * pack_width; lane = 0; if (ct + obound > list_size) { if (i < ito - 1) { @@ -548,12 +642,13 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } } - } else { + } else + #endif + { ct += n; - const int alignb = (INTEL_DATA_ALIGN / sizeof(int)); - const int edge = ct & (alignb - 1); - if (edge) ct += alignb - edge; + //IP_PRE_edge_align(ct, sizeof(int)); neighptr = firstneigh + ct; + if (THREE) neighptr2 = neighptr; if (ct + obound > list_size) { if (i < ito - 1) { *overflow = 1; @@ -573,14 +668,14 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (separate_buffers) { for (int i = ifrom; i < ito; ++i) { int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + int jnum = numneigh[i]; + if (!THREE) IP_PRE_neighbor_pad(jnum, offload); #if __INTEL_COMPILER+0 > 1499 #pragma vector aligned #pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin) #endif for (int jj = 0; jj < jnum; jj++) { - int j = jlist[jj]; - if (need_ic && j < 0) j = -j - 1; + const int j = jlist[jj] & NEIGHMASK; if (j < nlocal) { if (j < vlmin) vlmin = j; if (j > vlmax) vlmax = j; @@ -615,72 +710,20 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, ghost_offset = overflow[LMP_GHOST_MIN] - nlocal; nall_offset = nlocal + nghost; } - } // if separate_buffers - #endif - if (molecular) { - for (int i = ifrom; i < ito; ++i) { - int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - - if (THREE) { - const int trip = jnum * pack_width; - for (int jj = 0; jj < trip; jj+=pack_width) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } else { - #if defined(LMP_SIMD_COMPILER) - #pragma vector aligned - #pragma simd - #endif - for (int jj = 0; jj < jnum; jj++) { - const int j = jlist[jj]; - if (need_ic && j < 0) { - which = 0; - jlist[jj] = -j - 1; - } else - ofind_special(which, special, nspecial, i, tag[j]); - #ifdef _LMP_INTEL_OFFLOAD - if (j >= nlocal) { - if (j == e_nall) - jlist[jj] = nall_offset; - else if (which) - jlist[jj] = (j-ghost_offset) ^ (which << SBBITS); - else jlist[jj]-=ghost_offset; - } else - #endif - if (which) jlist[jj] = j ^ (which << SBBITS); - } - } - } // for i - } // if molecular - #ifdef _LMP_INTEL_OFFLOAD - else if (separate_buffers) { for (int i = ifrom; i < ito; ++i) { int * _noalias jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + int jnum = numneigh[i]; + if (!THREE) IP_PRE_neighbor_pad(jnum, offload); int jj = 0; #pragma vector aligned #pragma simd for (jj = 0; jj < jnum; jj++) { - if (jlist[jj] >= nlocal) { - if (jlist[jj] == e_nall) jlist[jj] = nall_offset; - else jlist[jj] -= ghost_offset; + const int which = jlist[jj] >> SBBITS & 3; + const int j = jlist[jj] & NEIGHMASK; + if (j >= nlocal) { + if (j == e_nall) jlist[jj] = nall_offset; + else jlist[jj] = (j - ghost_offset) ^ (which << SBBITS); } } } diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 71aad95bc51016543352997c0ccba9e4b595ced3..39fa9014db45238da0f50c04eb171843610d2979 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -142,6 +142,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -185,6 +186,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,qqrd2e,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -221,15 +223,17 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, FORCE_T * _noalias const f = f_start + foff; if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const C_CUT_T * _noalias const c_cuti = c_cut + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index bba8a7b5e7e6a7f30133a0064bc5f102e7e5ea29..fe4d408a1333be088bb49dc200d0292ba7c1ef7d 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -142,6 +142,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -209,6 +210,7 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -255,15 +257,17 @@ void PairBuckCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; const flt_t * _noalias const rho_invi = rho_inv + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index f5dde26393d5878207df9b8775e2329cb19f272a..8ce3d121e0b6f0cfd18149bf111e27b403db4b51 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -133,6 +133,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -169,6 +170,7 @@ void PairBuckIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -205,14 +207,16 @@ void PairBuckIntel::eval(const int offload, const int vflag, FORCE_T * _noalias const f = f_start + foff; if (NEWTON_PAIR) memset(f + minlocal, 0, f_stride * sizeof(FORCE_T)); - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index cb8c06cacc258778ba944b02ccc4096600033ea1..7c33ed21d35cb130b4271e62cf9b98cfe77e2132 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -171,6 +171,7 @@ void PairDPDIntel::eval(const int offload, const int vflag, lmp_vt *v = (lmp_vt *)atom->v[0]; const flt_t dtinvsqrt = 1.0/sqrt(update->dt); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -237,7 +238,8 @@ void PairDPDIntel::eval(const int offload, const int vflag, gamma = param[3].gamma; sigma = param[3].sigma; } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, ptr_off; const FC_PACKED1_T * _noalias parami; if (!ONETYPE) { @@ -246,8 +248,9 @@ void PairDPDIntel::eval(const int offload, const int vflag, parami = param + ptr_off; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 94799cdba26b5b609aa2eb28e9966e03a23509f3..201277e68dc7dc4fbcbe4b637716c1347615888a 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -164,8 +164,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, memory->destroy(rho); memory->destroy(fp); nmax = atom->nmax; - int edge = (nmax * sizeof(acc_t)) % INTEL_DATA_ALIGN; - if (edge) nmax += (INTEL_DATA_ALIGN - edge) / sizeof(acc_t); + IP_PRE_edge_align(nmax, sizeof(acc_t)); if (NEWTON_PAIR) memory->create(rho,nmax*comm->nthreads,"pair:rho"); else @@ -192,6 +191,7 @@ void PairEAMIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -286,14 +286,16 @@ void PairEAMIntel::eval(const int offload, const int vflag, rhor_joff = rhor_ioff + _onetype * jstride; frho_ioff = fstride * _onetype; } - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype, rhor_ioff; if (!ONETYPE) { itype = x[i].w; rhor_ioff = istride * itype; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -411,7 +413,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, #pragma vector aligned #pragma simd reduction(+:tevdwl) #endif - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype; if (!ONETYPE) itype = x[i].w; flt_t p = rho[i]*frdrho + (flt_t)1.0; @@ -457,7 +460,8 @@ void PairEAMIntel::eval(const int offload, const int vflag, // compute forces on each atom // loop over neighbors of my atoms - for (int i = iifrom; i < iito; ++i) { + for (int ii = iifrom; ii < iito; ++ii) { + const int i = ilist[ii]; int itype, rhor_ioff; const flt_t * _noalias scale_fi; if (!ONETYPE) { @@ -465,8 +469,9 @@ void PairEAMIntel::eval(const int offload, const int vflag, rhor_ioff = istride * itype; scale_fi = scale_f + itype*ntypes; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; @@ -761,14 +766,12 @@ void PairEAMIntel::ForceConst::set_ntypes(const int ntypes, if (ntypes > 0) { _cop = cop; _nr = nr + 1; - int edge = (_nr * sizeof(flt_t)) % INTEL_DATA_ALIGN; - if (edge) _nr += (INTEL_DATA_ALIGN - edge) / sizeof(flt_t); + IP_PRE_edge_align(_nr, sizeof(flt_t)); memory->create(rhor_spline_f,ntypes*ntypes*_nr,"fc.rhor_spline_f"); memory->create(rhor_spline_e,ntypes*ntypes*_nr,"fc.rhor_spline_e"); memory->create(z2r_spline_t,ntypes*ntypes*_nr,"fc.z2r_spline_t"); _nrho = nrho + 1; - edge = (_nrho * sizeof(flt_t)) % INTEL_DATA_ALIGN; - if (edge) _nrho += (INTEL_DATA_ALIGN - edge) / sizeof(flt_t); + IP_PRE_edge_align(_nrho, sizeof(flt_t)); memory->create(frho_spline_f,ntypes*_nrho,"fc.frho_spline_f"); memory->create(frho_spline_e,ntypes*_nrho,"fc.frho_spline_e"); memory->create(scale_f,ntypes,ntypes,"fc.scale_f"); diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp index 1f05ad0efc82c917f847a26e4e009c90f1643a2d..30941a7594810f8bb7037ee162fc5a361a69c0fa 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/USER-INTEL/pair_gayberne_intel.cpp @@ -226,7 +226,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, } #endif - // const int * _noalias const ilist = list->ilist; + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -287,6 +287,7 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(quat:length(nall+1) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(nthreads,inum,nall,ntypes,vflag,eatom,minlocal,separate_flag) \ in(astart,nlocal,f_stride,max_nbors,mu,gamma,upsilon,offload,pad_width) \ @@ -364,15 +365,16 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, int * _noalias const jlist_form = jlist_formi + tid * max_nbors; int ierror = 0; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const FC_PACKED1_T * _noalias const ijci = ijc + ptr_off; const FC_PACKED2_T * _noalias const lj34i = lj34 + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -428,15 +430,13 @@ void PairGayBerneIntel::eval(const int offload, const int vflag, } else multiple_forms = true; } - const int edge = packed_j & (pad_width - 1); - if (edge) { - const int packed_end = packed_j + (pad_width - edge); - #if defined(LMP_SIMD_COMPILER) - #pragma loop_count min=1, max=15, avg=8 - #endif - for ( ; packed_j < packed_end; packed_j++) - jlist_form[packed_j] = nall; - } + int packed_end = packed_j; + IP_PRE_neighbor_pad(packed_end, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma loop_count min=1, max=15, avg=8 + #endif + for ( ; packed_j < packed_end; packed_j++) + jlist_form[packed_j] = nall; // ------------------------------------------------------------- diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 7485395bef089c57338097d03145a5e3f435d2e3..8e6395c3885cecf42540f303ed278996b2656ed1 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -136,6 +136,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -189,6 +190,7 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -238,16 +240,17 @@ void PairLJCharmmCoulCharmmIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index 25cca59714c9f5bdadfbf19bd5cd8b64279afb25..a01a4688a582036b6a0498b460dfbcb3691f28ba 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -140,6 +140,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -210,6 +211,7 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -258,16 +260,17 @@ void PairLJCharmmCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { - // const int i = ilist[ii]; + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const flt_t * _noalias const cutsqi = cutsq + ptr_off; const LJ_T * _noalias const lji = lj + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index cb7381270dd72d9dad1476645e901e13bc1998cb..ab0b5b3d55e65d75e0fb2acd076182931990e151 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -139,6 +139,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -204,6 +205,7 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ in(q:length(q_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ in(ccachei,ccachej:length(0) alloc_if(0) free_if(0)) \ @@ -250,15 +252,17 @@ void PairLJCutCoulLongIntel::eval(const int offload, const int vflag, int * _noalias const tj = ccachei + toffs; int * _noalias const tjtype = ccachej + toffs; - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; const int itype = x[i].w; const int ptr_off = itype * ntypes; const C_FORCE_T * _noalias const c_forcei = c_force + ptr_off; const C_ENERGY_T * _noalias const c_energyi = c_energy + ptr_off; - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp,fytmp,fztmp,fwtmp; acc_t sevdwl, secoul, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index b16f6230ccd5d30a6fc55eb239d8a5cc9f8c2cd2..c973639709e079e2f731f8eb903282ff8bcb8275 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -148,6 +148,7 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const firstneigh = buffers->firstneigh(list); @@ -207,7 +208,8 @@ void PairLJCutIntel::eval(const int offload, const int vflag, lj4 = lj34[3].lj4; offset = ljc12o[3].offset; } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, ptr_off; const FC_PACKED1_T * _noalias ljc12oi; const FC_PACKED2_T * _noalias lj34i; @@ -217,9 +219,9 @@ void PairLJCutIntel::eval(const int offload, const int vflag, ljc12oi = ljc12o + ptr_off; lj34i = lj34 + ptr_off; } - - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + int jnum = numneigh[ii]; + IP_PRE_neighbor_pad(jnum, offload); acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl, sv0, sv1, sv2, sv3, sv4, sv5; diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 421de91ee938b1137ae546b0df36422c1b9ac5cb..d1d52270be27c3f8b393fc0da5cc1f3773fca4a8 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -42,7 +42,6 @@ #include "suffix.h" #ifdef LMP_USE_AVXCD -#define OUTER_CHUNK 1 #include "intel_simd.h" using namespace ip_simd; #endif @@ -185,6 +184,7 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, nlocal, nall); ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); @@ -230,6 +230,7 @@ void PairSWIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ @@ -298,7 +299,8 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - for (int i = iifrom; i < iito; i += iip) { + for (int ii = iifrom; ii < iito; ii += iip) { + const int i = ilist[ii]; int itype, itype_offset; const flt_t xtmp = x[i].x; const flt_t ytmp = x[i].y; @@ -309,9 +311,9 @@ void PairSWIntel::eval(const int offload, const int vflag, itype_offset = itype * ntypes; } - const int * _noalias const jlist = firstneigh + cnumneigh[i]; - const int jnum = numneigh[i]; - const int jnumhalf = numneighhalf[i]; + const int * _noalias const jlist = firstneigh + cnumneigh[ii]; + const int jnum = numneigh[ii]; + const int jnumhalf = numneighhalf[ii]; acc_t fxtmp, fytmp, fztmp, fwtmp; acc_t sevdwl; @@ -346,9 +348,13 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - int ejrem = ejnum & (pad_width - 1); - if (ejrem) ejrem = pad_width - ejrem; - const int ejnum_pad = ejnum + ejrem; + int ejnum_pad = ejnum; + IP_PRE_neighbor_pad(ejnum_pad, offload); + #if defined(LMP_SIMD_COMPILER) + #pragma vector aligned + #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ + avg=INTEL_COMPILE_WIDTH/2 + #endif for (int jj = ejnum; jj < ejnum_pad; jj++) { tdelx[jj] = (flt_t)0.0; tdely[jj] = (flt_t)0.0; @@ -594,6 +600,7 @@ void PairSWIntel::eval(const int offload, const int vflag, IP_PRE_pack_separate_buffers(fix, buffers, ago, offload, nlocal, nall); ATOM_T * _noalias const x = buffers->get_x(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneighhalf = buffers->get_atombin(); const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); @@ -641,6 +648,7 @@ void PairSWIntel::eval(const int offload, const int vflag, in(cnumneigh:length(0) alloc_if(0) free_if(0)) \ in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(ccachex,ccachey,ccachez,ccachew:length(0) alloc_if(0) free_if(0)) \ @@ -714,24 +722,24 @@ void PairSWIntel::eval(const int offload, const int vflag, } } - SIMD_int ilist = SIMD_set(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15); const SIMD_int goffset = SIMD_set(0,16,32,48,64,80,96,112,128, 144,160,176,192,208,224,240); - ilist = ilist + iifrom; acc_t * const dforce = &(f[0].x); for (int i = iifrom; i < iito; i += iip) { - SIMD_mask imask = ilist < iito; + SIMD_int ilistv = SIMD_load(ilist + i); + SIMD_int goffset = ilistv * 16; + SIMD_mask imask = ilistv < iito; SIMD_flt_t xtmp, ytmp, ztmp; SIMD_int itype, itype_offset; if (ONETYPE) - SIMD_atom_gather(imask, &(x[i].x), goffset, xtmp, ytmp, ztmp); + SIMD_atom_gather(imask, &(x[0].x), goffset, xtmp, ytmp, ztmp); else { - SIMD_atom_gather(imask, &(x[i].x), goffset, xtmp, ytmp, ztmp, itype); + SIMD_atom_gather(imask, &(x[0].x), goffset, xtmp, ytmp, ztmp, itype); itype_offset = itype * ntypes; } - #ifdef OUTER_CHUNK + #ifdef LMP_INTEL_3BODY_FAST const int* ng = firstneigh + cnumneigh[i] - swidth; #else SIMD_int ng = SIMD_load(cnumneigh + i); @@ -765,7 +773,7 @@ void PairSWIntel::eval(const int offload, const int vflag, for (int jj = 0; jj < jnum_max; jj++) { SIMD_mask jmask = jj < jnum; - #ifdef OUTER_CHUNK + #ifdef LMP_INTEL_3BODY_FAST ng += swidth; SIMD_int j = SIMD_load(ng); #else @@ -1025,15 +1033,15 @@ void PairSWIntel::eval(const int offload, const int vflag, } } // for jj second loop - SIMD_iforce_update(imask, &(f[i].x), goffset, fxtmp, fytmp, fztmp, + SIMD_iforce_update(imask, &(f[0].x), goffset, fxtmp, fytmp, fztmp, EFLAG, eatom, fwtmp); if (is_same::value == 0) { imask = imask >> 8; - SIMD_iforce_update(imask, &(f[i+8].x), goffset, fxtmp2, fytmp2, + SIMD_int goffset2 = _mm512_shuffle_i32x4(goffset, goffset, 238); + SIMD_iforce_update(imask, &(f[0].x), goffset2, fxtmp2, fytmp2, fztmp2, EFLAG, eatom, fwtmp2); } if (EFLAG) oevdwl += SIMD_sum(sevdwl); - ilist = ilist + iip; } // for ii IP_PRE_fdotr_reduce_omp(1, nall, minlocal, nthreads, f_start, f_stride, diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index c772546928dff386b5272d12a428553abe50f5eb..584b3717842cfcd3b2219fd7419040a497582bb0 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -208,6 +208,7 @@ struct IntelKernelTersoff : public lmp_intel::vector_routines const int * _noalias const cnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, + const int * _noalias const ilist, const c_inner_t * _noalias const c_inner, const c_outer_t * _noalias const c_outer, typename IntelBuffers::vec3_acc_t * _noalias const f, @@ -271,6 +272,7 @@ void PairTersoffIntel::eval(const int offload, const int vflag, tagint * _noalias tag = this->atom->tag; flt_t * _noalias const q = buffers->get_q(offload); + const int * _noalias const ilist = list->ilist; const int * _noalias const numneigh = list->numneigh; const int * _noalias const cnumneigh = buffers->cnumneigh(list); const int * _noalias const numneighhalf = buffers->get_atombin(); @@ -311,6 +313,7 @@ void PairTersoffIntel::eval(const int offload, const int vflag, in(numneigh:length(0) alloc_if(0) free_if(0)) \ in(numneighhalf:length(0) alloc_if(0) free_if(0)) \ in(x:length(x_size) alloc_if(0) free_if(0)) \ + in(ilist:length(0) alloc_if(0) free_if(0)) \ in(overflow:length(0) alloc_if(0) free_if(0)) \ in(astart,nthreads,inum,nall,ntypes,vflag,eatom) \ in(f_stride,nlocal,minlocal,separate_flag,offload) \ @@ -349,8 +352,9 @@ void PairTersoffIntel::eval(const int offload, const int vflag, { acc_t sevdwl; sevdwl = 0.; - #define ARGS iito, iifrom, eatom, vflag, numneigh, numneighhalf, cnumneigh, \ - firstneigh, ntypes, x, c_inner, c_outer, f, &sevdwl + #define ARGS iito, iifrom, eatom, vflag, numneigh, numneighhalf, \ + cnumneigh, firstneigh, ntypes, x, ilist, c_inner, \ + c_outer, f, &sevdwl // Pick the variable i algorithm under specific conditions // do use scalar algorithm with very short vectors int VL = lmp_intel::vector_routines::VL; @@ -1135,6 +1139,7 @@ void IntelKernelTersoff::kernel( const int * _noalias const cnumneigh, const int * _noalias const firstneigh, int ntypes, typename IntelBuffers::atom_t * _noalias const x, + const int * _noalias const ilist, const c_inner_t * _noalias const c_inner, const c_outer_t * _noalias const c_outer, typename IntelBuffers::vec3_acc_t * _noalias const f, @@ -1155,12 +1160,12 @@ void IntelKernelTersoff::kernel( for (ii = iifrom; ii < iito; ii++) { // Right now this loop is scalar, to allow for the compiler to do // its prefetching magic. - int i = ii; + int i = ilist[ii]; int w_i = x[i].w; flt_t x_i = x[i].x; flt_t y_i = x[i].y; flt_t z_i = x[i].z; - int jlist_off_i = cnumneigh[i]; + int jlist_off_i = cnumneigh[ii]; int jnum = numneigh[ii]; for (jj = 0; jj < jnum; jj++) { int j = firstneigh[jlist_off_i + jj] & NEIGHMASK; @@ -1173,7 +1178,7 @@ void IntelKernelTersoff::kernel( if (rsq < cutsq) { is[compress_idx] = ii; js[compress_idx] = j; - if (jj < numneighhalf[i]) + if (jj < numneighhalf[ii]) repulsive_flag[compress_idx] = 1; compress_idx += 1; } diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 962202e228f74bce7e9b8486c33d50b0a04d4da3..5dd0da193911e3051ef25b4aec7265062825bc7a 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -157,7 +157,7 @@ void VerletLRTIntel::setup(int flag) pthread_create(&_kspace_thread, &_kspace_attr, &VerletLRTIntel::k_launch_loop, this); #elif defined(_LMP_INTEL_LRT_11) - std::thread kspace_thread; + std::thread _kspace_thread; if (kspace_compute_flag) _kspace_thread=std::thread([=]{ _intel_kspace->compute_first(eflag, vflag); }); diff --git a/src/USER-INTEL/verlet_lrt_intel.h b/src/USER-INTEL/verlet_lrt_intel.h index 7380cc6376b3c649351579ecbc0a563f6a85cf99..6c44ba7e5793d63fefba8482be95d58957adb5c7 100644 --- a/src/USER-INTEL/verlet_lrt_intel.h +++ b/src/USER-INTEL/verlet_lrt_intel.h @@ -24,14 +24,20 @@ IntegrateStyle(verlet/lrt/intel,VerletLRTIntel) #include "pppm_intel.h" #ifdef LMP_INTEL_USELRT -#ifdef LMP_INTEL_LRT11 -#define _LMP_INTEL_LRT_11 -#include -#else -#define _LMP_INTEL_LRT_PTHREAD -#include -#endif - + #if defined(LMP_INTEL_LRT11) || defined(__APPLE__) + #if __cplusplus > 199711L + #define _LMP_INTEL_LRT_11 + #include + #else + #undef LMP_INTEL_USELRT + #ifdef LMP_INTEL_LRT11 + #error C++11 support required for LMP_INTEL_LRT11 define + #endif + #endif + #else + #define _LMP_INTEL_LRT_PTHREAD + #include + #endif #endif namespace LAMMPS_NS { diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index ab33b5bc972627e1611bbc80bbbaa3f1e3c660b3..04172d5c92da874322344e33fcd0aa4189f184cd 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -31,12 +31,12 @@ using namespace user_manifold; // Helper functions for parameters/equal style variables in input script -inline bool was_var( const char *arg ) +static bool was_var( const char *arg ) { return strstr( arg, "v_" ) == arg; } -inline bool str_eq( const char *str1, const char *str2 ) +static bool str_eq( const char *str1, const char *str2 ) { return strcmp(str1,str2) == 0; } @@ -50,13 +50,6 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : MPI_Comm_rank(world,&me); - // Check the min-style: - int good_minner = str_eq(update->minimize_style,"hftn") | - str_eq(update->minimize_style,"quickmin"); - if( !good_minner){ - error->warning(FLERR,"Minimizing with fix manifoldforce without hftn or quickmin is fishy"); - } - // Command is given as // fix manifoldforce manifold_name manifold_args @@ -121,6 +114,18 @@ int FixManifoldForce::setmask() /* ---------------------------------------------------------------------- */ +void FixManifoldForce::init() +{ + // Check the min-style: + const bool is_good_min_style = str_eq(update->minimize_style,"hftn") + || str_eq(update->minimize_style,"quickmin"); + if (!is_good_min_style) { + error->all(FLERR,"Fix manifoldforce requires min_style hftn or quickmin"); + } +} + +/* ---------------------------------------------------------------------- */ + void FixManifoldForce::setup(int vflag) { if (strstr(update->integrate_style,"verlet")) diff --git a/src/USER-MANIFOLD/fix_manifoldforce.h b/src/USER-MANIFOLD/fix_manifoldforce.h index 89bd6bd378aeb0f4bb5e6241853812993d23a975..527bee3f86d33a976a20007b09470d318575e185 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.h +++ b/src/USER-MANIFOLD/fix_manifoldforce.h @@ -51,6 +51,7 @@ class FixManifoldForce : public Fix { public: FixManifoldForce(class LAMMPS *, int, char **); int setmask(); + void init(); void setup(int); void min_setup(int); void post_force(int); diff --git a/src/USER-MEAMC/meam_funcs.cpp b/src/USER-MEAMC/meam_funcs.cpp index 599e9019d930aedac8a7c84ba45bfb8496f7a639..29db27fc4b816f891f9ff4e3e102f5171710e278 100644 --- a/src/USER-MEAMC/meam_funcs.cpp +++ b/src/USER-MEAMC/meam_funcs.cpp @@ -277,9 +277,9 @@ MEAM::get_Zij2(const lattice_t latt, const double cmin, const double cmax, doubl break; case DIA: - Zij2 = 0; + Zij2 = 12; a = sqrt(8.0 / 3.0); - numscr = 4; + numscr = 1; if (cmin < 0.500001) { // call error('can not do 2NN MEAM for dia') } diff --git a/src/USER-MEAMC/meam_setup_done.cpp b/src/USER-MEAMC/meam_setup_done.cpp index fa71dba23636ac46a214de7d9915c770463e9ff3..e18a391378aecc384e8eda503ced210ce0985673 100644 --- a/src/USER-MEAMC/meam_setup_done.cpp +++ b/src/USER-MEAMC/meam_setup_done.cpp @@ -213,14 +213,12 @@ MEAM::compute_pair_meam(void) Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], this->Cmax_meam[a][a][b], arat, scrn); - // The B1, B2, and L12 cases with NN2 have a trick to them; we - // need to - // compute the contributions from second nearest neighbors, like - // a-a + // The B1, B2, and L12 cases with NN2 have a trick to them; we need to + // compute the contributions from second nearest neighbors, like a-a // pairs, but need to include NN2 contributions to those pairs as // well. if (this->lattce_meam[a][b] == B1 || this->lattce_meam[a][b] == B2 || - this->lattce_meam[a][b] == L12) { + this->lattce_meam[a][b] == L12 || this->lattce_meam[a][b] == DIA) { rarat = r * arat; // phi_aa @@ -247,7 +245,8 @@ MEAM::compute_pair_meam(void) } } - if (this->lattce_meam[a][b] == B1 || this->lattce_meam[a][b] == B2) { + if (this->lattce_meam[a][b] == B1 || this->lattce_meam[a][b] == B2 || + this->lattce_meam[a][b] == DIA) { // Add contributions to the B1 or B2 potential Z1 = get_Zij(this->lattce_meam[a][b]); Z2 = get_Zij2(this->lattce_meam[a][b], this->Cmin_meam[a][a][b], diff --git a/src/USER-MISC/Install.sh b/src/USER-MISC/Install.sh deleted file mode 100755 index 2d42125ec3a79cdb00cc88cb31d12b8be3959f4d..0000000000000000000000000000000000000000 --- a/src/USER-MISC/Install.sh +++ /dev/null @@ -1,40 +0,0 @@ -# Install/unInstall package files in LAMMPS -# mode = 0/1/2 for uninstall/install/update - -mode=$1 - -# enforce using portable C locale -LC_ALL=C -export LC_ALL - -# arg1 = file, arg2 = file it depends on - -action () { - if (test $mode = 0) then - rm -f ../$1 - elif (! cmp -s $1 ../$1) then - if (test -z "$2" || test -e ../$2) then - cp $1 .. - if (test $mode = 2) then - echo " updating src/$1" - fi - fi - elif (test ! -n "$2") then - if (test ! -e ../$2) then - rm -f ../$1 - fi - fi -} - -# all package files -# only a few files have dependencies - -for file in *.cpp *.h; do - if (test $file = "pair_cdeam.cpp") then - action pair_cdeam.cpp pair_eam_alloy.cpp - elif (test $file = "pair_cdeam.h") then - action pair_cdeam.h pair_eam_alloy.cpp - else - test -f ${file} && action $file - fi -done diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 222c06b4c426ff1adf271dcccf7438921eb5e5ff..0f9e7bf383bf3e005b828672ad24b360d6f9b440 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -29,6 +29,7 @@ bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 +compute entropy/atom, Pablo Piaggi (EPFL), pablo.piaggi at epfl.ch, 15 June 2018 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16 dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 @@ -64,7 +65,6 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 -pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp new file mode 100644 index 0000000000000000000000000000000000000000..922f2aaf5ee9d53b50bbadb3485142ab1bc88961 --- /dev/null +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -0,0 +1,342 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Pablo Piaggi (EPFL Lausanne) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "compute_entropy_atom.h" +#include "atom.h" +#include "update.h" +#include "modify.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "force.h" +#include "pair.h" +#include "comm.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "domain.h" + + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +ComputeEntropyAtom:: +ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) : + Compute(lmp, narg, arg), + pair_entropy(NULL), pair_entropy_avg(NULL) +{ + if (narg < 5 || narg > 10) + error->all(FLERR,"Illegal compute entropy/atom command; wrong number" + " of arguments"); + + // Arguments are: sigma cutoff avg yes/no cutoff2 local yes/no + // sigma is the gaussian width + // cutoff is the cutoff for the calculation of g(r) + // avg is optional and allows averaging the pair entropy over neighbors + // the next argument should be yes or no + // cutoff2 is the cutoff for the averaging + // local is optional and allows using the local density to normalize + // the g(r) + + sigma = force->numeric(FLERR,arg[3]); + if (sigma <= 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; sigma must be positive"); + cutoff = force->numeric(FLERR,arg[4]); + if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; cutoff must be positive"); + + avg_flag = 0; + local_flag = 0; + + // optional keywords + int iarg = 5; + while (iarg < narg) { + if (strcmp(arg[iarg],"avg") == 0) { + if (iarg+2 > narg) + error->all(FLERR,"Illegal compute entropy/atom;" + " missing arguments after avg"); + if (strcmp(arg[iarg+1],"yes") == 0) avg_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) avg_flag = 0; + else error->all(FLERR,"Illegal compute entropy/atom;" + " argument after avg should be yes or no"); + cutoff2 = force->numeric(FLERR,arg[iarg+2]); + if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute entropy/atom" + " command; negative cutoff2"); + cutsq2 = cutoff2*cutoff2; + iarg += 3; + } else if (strcmp(arg[iarg],"local") == 0) { + if (strcmp(arg[iarg+1],"yes") == 0) local_flag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) local_flag = 0; + else error->all(FLERR,"Illegal compute entropy/atom;" + " argument after local should be yes or no"); + iarg += 2; + } else error->all(FLERR,"Illegal compute entropy/atom; argument after" + " sigma and cutoff should be avg or local"); + } + + + cutsq = cutoff*cutoff; + nbin = static_cast(cutoff / sigma) + 1; + nmax = 0; + maxneigh = 0; + // Number of bins above and below the central one that will be + // considered as affected by the gaussian kernel + // 3 seems a good compromise between speed and good mollification + deltabin = 3; + deltar = sigma; + peratom_flag = 1; + size_peratom_cols = 0; +} + +/* ---------------------------------------------------------------------- */ + +ComputeEntropyAtom::~ComputeEntropyAtom() +{ + memory->destroy(pair_entropy); + if (avg_flag) memory->destroy(pair_entropy_avg); +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::init() +{ + if (force->pair == NULL) + error->all(FLERR,"Compute entropy/atom requires a pair style be" + " defined"); + + if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) ) + { + error->all(FLERR,"Compute entropy/atom cutoff is longer than the" + " pairwise cutoff. Increase the neighbor list skin" + " distance."); + } + + int count = 0; + for (int i = 0; i < modify->ncompute; i++) + if (strcmp(modify->compute[i]->style,"entropy/atom") == 0) count++; + if (count > 1 && comm->me == 0) + error->warning(FLERR,"More than one compute entropy/atom"); + + // need a full neighbor list with neighbors of the ghost atoms + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; + neighbor->requests[irequest]->occasional = 0; + neighbor->requests[irequest]->ghost = 1; + +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::init_list(int id, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void ComputeEntropyAtom::compute_peratom() +{ + int i,j,ii,jj,inum,jnum; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq; + int *ilist,*jlist,*numneigh,**firstneigh; + double *rbin = new double[nbin]; + double *rbinsq = new double[nbin]; + + invoked_peratom = update->ntimestep; + + // Initialize distance vectors + for (int i = 0; i < nbin; i++) { + rbin[i] = i*deltar; + rbinsq[i] = rbin[i]*rbin[i]; + } + + // grow pair_entropy and pair_entropy_avg array if necessary + + if (atom->nmax > nmax) { + if (!avg_flag) { + memory->destroy(pair_entropy); + nmax = atom->nmax; + memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy"); + vector_atom = pair_entropy; + } else { + memory->destroy(pair_entropy); + memory->destroy(pair_entropy_avg); + nmax = atom->nmax; + memory->create(pair_entropy,nmax,"entropy/atom:pair_entropy"); + memory->create(pair_entropy_avg,nmax, + "entropy/atom:pair_entropy_avg"); + vector_atom = pair_entropy_avg; + } + } + + inum = list->inum + list->gnum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // Compute some constants + double sigmasq2=2*sigma*sigma; + double volume = domain->xprd * domain->yprd * domain->zprd; + double density = atom->natoms / volume; + + // compute pair entropy for each atom in group + // use full neighbor list + + double **x = atom->x; + int *mask = atom->mask; + double *gofr = new double[nbin]; + double *integrand = new double[nbin]; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + if (mask[i] & groupbit) { + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // If local density is used, calculate it + if (local_flag) { + double neigh_cutoff = force->pair->cutforce + neighbor->skin; + double volume = + (4./3.)*MY_PI*neigh_cutoff*neigh_cutoff*neigh_cutoff; + density = jnum / volume; + } + + // calculate kernel normalization + // Normalization of g(r) + double normConstantBase = 4*MY_PI*density; + // Normalization of gaussian + normConstantBase *= sqrt(2.*MY_PI)*sigma; + double invNormConstantBase = 1./normConstantBase; + + // loop over list of all neighbors within force cutoff + + // initialize gofr + for(int k=0;k (nbin-1)) minbin=nbin-1; + maxbin=bin + deltabin; + if (maxbin > (nbin-1)) maxbin=nbin-1; + for(int k=minbin;kall(FLERR,"Illegal fix bond/react command 0.0"); + if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: " + "too few arguments"); MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); + newton_bond = force->newton_bond; attempted_rxn = 0; force_reneighbor = 1; @@ -92,6 +95,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : rxnID = 0; status = PROCEED; + nxspecial = NULL; + onemol_nxspecial = NULL; + twomol_nxspecial = NULL; + xspecial = NULL; + onemol_xspecial = NULL; + twomol_xspecial = NULL; + // these group names are reserved for use exclusively by bond/react master_group = (char *) "bond_react_MASTER_group"; @@ -105,24 +115,29 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[i],"react") == 0) { nreacts++; i = i + 6; // skip past mandatory arguments - if (i > narg) error->all(FLERR,"Illegal fix bond/react command 0.1"); + if (i > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'react' has too few arguments"); } } - if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: missing mandatory 'react' argument"); + if (nreacts == 0) error->all(FLERR,"Illegal fix bond/react command: " + "missing mandatory 'react' argument"); size_vector = nreacts; int iarg = 3; stabilization_flag = 0; - while (strcmp(arg[iarg],"react") != 0) { + int num_common_keywords = 1; + for (int m = 0; m < num_common_keywords; m++) { if (strcmp(arg[iarg],"stabilization") == 0) { if (strcmp(arg[iarg+1],"no") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.2"); + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'stabilization' keyword has too few arguments"); iarg += 2; } if (strcmp(arg[iarg+1],"yes") == 0) { - if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command 0.21"); + if (iarg+4 > narg) error->all(FLERR,"Illegal fix bond/react command:" + "'stabilization' keyword has too few arguments"); int n = strlen(arg[iarg+2]) + 1; exclude_group = new char[n]; strcpy(exclude_group,arg[iarg+2]); @@ -130,7 +145,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : nve_limit_xmax = arg[iarg+3]; iarg += 4; } - } + } else if (strcmp(arg[iarg],"react") == 0) { + break; + } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } // set up common variables as vectors of length 'nreacts' @@ -172,8 +189,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : char **files; files = new char*[nreacts]; - int rxn = 0; - while (iarg < narg && strcmp(arg[iarg],"react") == 0) { + for (int rxn = 0; rxn < nreacts; rxn++) { + + if (strcmp(arg[iarg],"react") != 0) error->all(FLERR,"Illegal fix bond/react command: " + "'react' or 'stabilization' has incorrect arguments"); iarg++; @@ -185,14 +204,17 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : groupbits[rxn] = group->bitmask[igroup]; nevery[rxn] = force->inumeric(FLERR,arg[iarg++]); - if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.4"); + if (nevery[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: " + "'Nevery' must be a positive integer"); double cutoff = force->numeric(FLERR,arg[iarg++]); - if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.5"); + if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command: " + "'Rmin' cannot be negative"); cutsq[rxn][0] = cutoff*cutoff; cutoff = force->numeric(FLERR,arg[iarg++]); - if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command 0.55"); + if (cutoff < 0.0) error->all(FLERR,"Illegal fix bond/react command:" + "'Rmax' cannot be negative"); cutsq[rxn][1] = cutoff*cutoff; unreacted_mol[rxn] = atom->find_molecule(arg[iarg++]); @@ -209,22 +231,26 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) { if (strcmp(arg[iarg],"prob") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command 0.6"); + if (iarg+3 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'prob' keyword has too few arguments"); fraction[rxn] = force->numeric(FLERR,arg[iarg+1]); seed[rxn] = force->inumeric(FLERR,arg[iarg+2]); if (fraction[rxn] < 0.0 || fraction[rxn] > 1.0) - error->all(FLERR,"Illegal fix bond/react command"); - if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command 0.7"); + error->all(FLERR,"Illegal fix bond/react command: " + "probability fraction must between 0 and 1, inclusive"); + if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: " + "probability seed must be positive"); iarg += 3; } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { - if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword used without stabilization keyword"); - if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command 0.8"); + if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword " + "used without stabilization keyword"); + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'stabilize_steps' has too few arguments"); limit_duration[rxn] = force->numeric(FLERR,arg[iarg+1]); stabilize_steps_flag[rxn] = 1; iarg += 2; - } else error->all(FLERR,"Illegal fix bond/react command 0.9"); + } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } - rxn++; } max_natoms = 0; // the number of atoms in largest molecule template @@ -238,11 +264,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(edge,max_natoms,nreacts,"bond/react:edge"); memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + for (int j = 0; j < nreacts; j++) + for (int i = 0; i < max_natoms; i++) edge[i][j] = 0; + // read all superimpose files afterward for (int i = 0; i < nreacts; i++) { open(files[i]); onemol = atom->molecules[unreacted_mol[i]]; twomol = atom->molecules[reacted_mol[i]]; + get_molxspecials(); read(i); fclose(fp); iatomtype[i] = onemol->type[ibonding[i]-1]; @@ -263,12 +293,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : for (int myrxn = 0; myrxn < nreacts; myrxn++) { closeneigh[myrxn] = -1; // indicates will search non-bonded neighbors onemol = atom->molecules[unreacted_mol[myrxn]]; - for (int k = 0; k < onemol->nspecial[ibonding[myrxn]-1][2]; k++) { - if (onemol->special[ibonding[myrxn]-1][k] == jbonding[myrxn]) { + get_molxspecials(); + for (int k = 0; k < onemol_nxspecial[ibonding[myrxn]-1][2]; k++) { + if (onemol_xspecial[ibonding[myrxn]-1][k] == jbonding[myrxn]) { closeneigh[myrxn] = 2; // index for 1-4 neighbor - if (k < onemol->nspecial[ibonding[myrxn]-1][1]) + if (k < onemol_nxspecial[ibonding[myrxn]-1][1]) closeneigh[myrxn] = 1; // index for 1-3 neighbor - if (k < onemol->nspecial[ibonding[myrxn]-1][0]) + if (k < onemol_nxspecial[ibonding[myrxn]-1][0]) closeneigh[myrxn] = 0; // index for 1-2 neighbor break; } @@ -289,14 +320,12 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : comm_reverse = 2; // allocate arrays local to this fix - nmax = 0; partner = finalpartner = NULL; distsq = NULL; probability = NULL; maxcreate = 0; created = NULL; - local_ncreate = NULL; ncreate = NULL; allncreate = 0; local_num_mega = 0; @@ -334,7 +363,6 @@ FixBondReact::~FixBondReact() memory->destroy(partner); memory->destroy(finalpartner); - memory->destroy(local_ncreate); memory->destroy(ncreate); memory->destroy(distsq); memory->destroy(probability); @@ -363,6 +391,15 @@ FixBondReact::~FixBondReact() memory->destroy(ghostly_rxn_count); memory->destroy(reaction_count_total); + if (newton_bond == 0) { + memory->destroy(xspecial); + memory->destroy(nxspecial); + memory->destroy(onemol_xspecial); + memory->destroy(onemol_nxspecial); + memory->destroy(twomol_xspecial); + memory->destroy(twomol_nxspecial); + } + if (attempted_rxn == 1) { memory->destroy(restore_pt); memory->destroy(restore); @@ -531,17 +568,6 @@ void FixBondReact::post_constructor() void FixBondReact::init() { - // warn if more than one bond/react fix - - int count = 0; - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"bond/react") == 0) count++; - if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix bond/react"); - - if (force->newton_bond == 0 && comm->me == 0) error->warning(FLERR,"Fewer reactions may occur in some cases " - "when 'newton off' is set for bonded interactions. " - "The reccomended setting is 'newton on'."); - if (strstr(update->integrate_style,"respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; @@ -606,21 +632,18 @@ void FixBondReact::post_integrate() memory->destroy(partner); memory->destroy(finalpartner); memory->destroy(distsq); - memory->destroy(local_ncreate); memory->destroy(ncreate); memory->destroy(probability); nmax = atom->nmax; memory->create(partner,nmax,"bond/react:partner"); memory->create(finalpartner,nmax,"bond/react:finalpartner"); memory->create(distsq,nmax,2,"bond/react:distsq"); - memory->create(local_ncreate,nreacts,"bond/react:local_ncreate"); memory->create(ncreate,nreacts,"bond/react:ncreate"); memory->create(probability,nmax,"bond/react:probability"); } // reset create counts for (int i = 0; i < nreacts; i++) { - local_ncreate[i] = 0; ncreate[i] = 0; } @@ -635,10 +658,32 @@ void FixBondReact::post_integrate() neighbor->build_one(list,1); - int j; + // here we define a full special list, independent of Newton setting + if (newton_bond == 1) { + nxspecial = atom->nspecial; + xspecial = atom->special; + } else { + int nall = atom->nlocal + atom->nghost; + memory->destroy(nxspecial); + memory->destroy(xspecial); + memory->create(nxspecial,nall,3,"bond/react:nxspecial"); + memory->create(xspecial,nall,atom->maxspecial,"bond/react:xspecial"); + for (int i = 0; i < atom->nlocal; i++) { + nxspecial[i][0] = atom->num_bond[i]; + for (int j = 0; j < nxspecial[i][0]; j++) { + xspecial[i][j] = atom->bond_atom[i][j]; + } + nxspecial[i][1] = atom->nspecial[i][1]; + nxspecial[i][2] = atom->nspecial[i][2]; + int joffset = nxspecial[i][0] - atom->nspecial[i][0]; + for (int j = nxspecial[i][0]; j < nxspecial[i][2]; j++) { + xspecial[i][j+joffset] = atom->special[i][j]; + } + } + } + int j; for (rxnID = 0; rxnID < nreacts; rxnID++) { - for (int ii = 0; ii < nall; ii++) { partner[ii] = 0; finalpartner[ii] = 0; @@ -647,14 +692,17 @@ void FixBondReact::post_integrate() } // fork between far and close_partner here - if (closeneigh[rxnID] < 0) far_partner(); - else close_partner(); - - // reverse comm of distsq and partner - // not needed if newton_pair off since I,J pair was seen by both procs - - commflag = 2; - if (force->newton_pair) comm->reverse_comm_fix(this); + if (closeneigh[rxnID] < 0) { + far_partner(); + // reverse comm of distsq and partner + // not needed if newton_pair off since I,J pair was seen by both procs + commflag = 2; + if (force->newton_pair) comm->reverse_comm_fix(this); + } else { + close_partner(); + commflag = 2; + comm->reverse_comm_fix(this); + } // each atom now knows its winning partner // for prob check, generate random value for each atom with a bond partner @@ -678,6 +726,7 @@ void FixBondReact::post_integrate() if (partner[i] == 0) { continue; } + j = atom->map(partner[i]); if (partner[j] != tag[i]) { continue; @@ -701,8 +750,7 @@ void FixBondReact::post_integrate() if (tag[i] < tag[j]) temp_ncreate++; } - local_ncreate[rxnID] = temp_ncreate; - // break loop if no even eligible bonding atoms were found (on any proc) + // cycle loop if no even eligible bonding atoms were found (on any proc) int some_chance; MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world); if (!some_chance) continue; @@ -740,7 +788,6 @@ void FixBondReact::post_integrate() ncreate[rxnID]++; } } - unlimit_bond(); //free atoms that have been relaxed } // break loop if no even eligible bonding atoms were found (on any proc) @@ -778,8 +825,6 @@ void FixBondReact::far_partner() double **x = atom->x; tagint *tag = atom->tag; - int **nspecial = atom->nspecial; - tagint **special = atom->special; int *mask = atom->mask; int *type = atom->type; @@ -809,10 +854,9 @@ void FixBondReact::far_partner() for (int jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - if (!(mask[j] & groupbits[rxnID])) { continue; -} + } if (i_limit_tags[j] != 0) { continue; @@ -820,7 +864,6 @@ void FixBondReact::far_partner() jtype = type[j]; possible = 0; - if (itype == iatomtype[rxnID] && jtype == jatomtype[rxnID]) { possible = 1; } else if (itype == jatomtype[rxnID] && jtype == iatomtype[rxnID]) { @@ -830,8 +873,8 @@ void FixBondReact::far_partner() if (possible == 0) continue; // do not allow bonding atoms within special list - for (int k = 0; k < nspecial[i][2]; k++) - if (special[i][k] == tag[j]) possible = 0; + for (int k = 0; k < nxspecial[i][2]; k++) + if (xspecial[i][k] == tag[j]) possible = 0; if (!possible) continue; delx = xtmp - x[j][0]; @@ -867,8 +910,6 @@ void FixBondReact::close_partner() tagint *tag = atom->tag; int *type = atom->type; int *mask = atom->mask; - int **nspecial = atom->nspecial; - tagint **special = atom->special; // per-atom property indicating if in bond/react master group int flag; @@ -880,10 +921,10 @@ void FixBondReact::close_partner() itype = type[ii]; n = 0; if (closeneigh[rxnID] != 0) - n = nspecial[ii][closeneigh[rxnID]-1]; - for (; n < nspecial[ii][closeneigh[rxnID]]; n++) { + n = nxspecial[ii][closeneigh[rxnID]-1]; + for (; n < nxspecial[ii][closeneigh[rxnID]]; n++) { i1 = ii; - i2 = atom->map(special[ii][n]); + i2 = atom->map(xspecial[ii][n]); jtype = type[i2]; if (!(mask[i1] & groupbits[rxnID])) continue; if (!(mask[i2] & groupbits[rxnID])) continue; @@ -894,6 +935,7 @@ void FixBondReact::close_partner() delx = x[i1][0] - x[i2][0]; dely = x[i1][1] - x[i2][1]; delz = x[i1][2] - x[i2][2]; + domain->minimum_image(delx,dely,delz); // ghost location fix rsq = delx*delx + dely*dely + delz*delz; if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue; @@ -950,12 +992,13 @@ void FixBondReact::superimpose_algorithm() } } - //let's finally begin the superimpose loop + // let's finally begin the superimpose loop for (rxnID = 0; rxnID < nreacts; rxnID++) { for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) { onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; + get_molxspecials(); status = PROCEED; @@ -985,11 +1028,11 @@ void FixBondReact::superimpose_algorithm() for (int i = 0; i < max_natoms; i++) pioneer_count[i] = 0; - for (int i = 0; i < onemol->nspecial[myibonding-1][0]; i++) - pioneer_count[onemol->special[myibonding-1][i]-1]++; + for (int i = 0; i < onemol_nxspecial[myibonding-1][0]; i++) + pioneer_count[onemol_xspecial[myibonding-1][i]-1]++; - for (int i = 0; i < onemol->nspecial[myjbonding-1][0]; i++) - pioneer_count[onemol->special[myjbonding-1][i]-1]++; + for (int i = 0; i < onemol_nxspecial[myjbonding-1][0]; i++) + pioneer_count[onemol_xspecial[myjbonding-1][i]-1]++; int hang_catch = 0; @@ -1000,7 +1043,7 @@ void FixBondReact::superimpose_algorithm() } for (int i = 0; i < onemol->natoms; i++) { - if (glove[i][0] !=0 && pioneer_count[i] < onemol->nspecial[i][0] && edge[i][rxnID] == 0) { + if (glove[i][0] !=0 && pioneer_count[i] < onemol_nxspecial[i][0] && edge[i][rxnID] == 0) { pioneers[i] = 1; } } @@ -1059,10 +1102,8 @@ void FixBondReact::superimpose_algorithm() void FixBondReact::make_a_guess() { - int **nspecial = atom->nspecial; - tagint **special = atom->special; int *type = atom->type; - int nfirst_neighs = onemol->nspecial[pion][0]; + int nfirst_neighs = onemol_nxspecial[pion][0]; // per-atom property indicating if in bond/react master group int flag; @@ -1091,7 +1132,7 @@ void FixBondReact::make_a_guess() if (status != PROCEED) return; } - nfirst_neighs = onemol->nspecial[pion][0]; + nfirst_neighs = onemol_nxspecial[pion][0]; // check if any of first neighbors are in bond_react_MASTER_group // if so, this constitutes a fail @@ -1099,18 +1140,18 @@ void FixBondReact::make_a_guess() // could technically fail unnecessarily during a wrong guess if near edge atoms // we accept this temporary and infrequent decrease in reaction occurences - for (int i = 0; i < nspecial[atom->map(glove[pion][1])][0]; i++) { - if (atom->map(special[atom->map(glove[pion][1])][i]) < 0) { + for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { + if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { error->all(FLERR,"Fix bond/react needs ghost atoms from further away1"); // parallel issues. } - if (i_limit_tags[(int)atom->map(special[atom->map(glove[pion][1])][i])] != 0) { + if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) { status = GUESSFAIL; return; } } // check for same number of neighbors between unreacted mol and simulation - if (nfirst_neighs != nspecial[atom->map(glove[pion][1])][0]) { + if (nfirst_neighs != nxspecial[atom->map(glove[pion][1])][0]) { status = GUESSFAIL; return; } @@ -1120,7 +1161,7 @@ void FixBondReact::make_a_guess() int assigned_count = 0; for (int i = 0; i < nfirst_neighs; i++) for (int j = 0; j < onemol->natoms; j++) - if (special[atom->map(glove[pion][1])][i] == glove[j][1]) { + if (xspecial[atom->map(glove[pion][1])][i] == glove[j][1]) { assigned_count++; break; } @@ -1137,8 +1178,8 @@ void FixBondReact::make_a_guess() } for (int i = 0; i < nfirst_neighs; i++) { - mol_ntypes[(int)onemol->type[(int)onemol->special[pion][i]-1]-1]++; - lcl_ntypes[(int)type[(int)atom->map(special[atom->map(glove[pion][1])][i])]-1]++; //added -1 + mol_ntypes[(int)onemol->type[(int)onemol_xspecial[pion][i]-1]-1]++; + lcl_ntypes[(int)type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])]-1]++; //added -1 } for (int i = 0; i < atom->ntypes; i++) { @@ -1164,7 +1205,7 @@ void FixBondReact::make_a_guess() void FixBondReact::neighbor_loop() { - int nfirst_neighs = onemol->nspecial[pion][0]; + int nfirst_neighs = onemol_nxspecial[pion][0]; if (status == RESTORE) { check_a_neighbor(); @@ -1172,7 +1213,7 @@ void FixBondReact::neighbor_loop() } for (neigh = 0; neigh < nfirst_neighs; neigh++) { - if (glove[(int)onemol->special[pion][neigh]-1][0] == 0) { + if (glove[(int)onemol_xspecial[pion][neigh]-1][0] == 0) { check_a_neighbor(); } } @@ -1186,39 +1227,37 @@ void FixBondReact::neighbor_loop() void FixBondReact::check_a_neighbor() { - int **nspecial = atom->nspecial; - tagint **special = atom->special; int *type = atom->type; - int nfirst_neighs = onemol->nspecial[pion][0]; + int nfirst_neighs = onemol_nxspecial[pion][0]; if (status != RESTORE) { // special consideration for hydrogen atoms (and all first neighbors bonded to no other atoms) (and aren't edge atoms) - if (onemol->nspecial[(int)onemol->special[pion][neigh]-1][0] == 1 && edge[(int)onemol->special[pion][neigh]-1][rxnID] == 0) { + if (onemol_nxspecial[(int)onemol_xspecial[pion][neigh]-1][0] == 1 && edge[(int)onemol_xspecial[pion][neigh]-1][rxnID] == 0) { for (int i = 0; i < nfirst_neighs; i++) { - if (type[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1] && - nspecial[(int)atom->map(special[(int)atom->map(glove[pion][1])][i])][0] == 1) { + if (type[(int)atom->map(xspecial[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1] && + nxspecial[(int)atom->map(xspecial[(int)atom->map(glove[pion][1])][i])][0] == 1) { int already_assigned = 0; for (int j = 0; j < onemol->natoms; j++) { - if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) { already_assigned = 1; break; } } if (already_assigned == 0) { - glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; - glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + glove[(int)onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh]; + glove[(int)onemol_xspecial[pion][neigh]-1][1] = xspecial[(int)atom->map(glove[pion][1])][i]; //another check for ghost atoms. perhaps remove the one in make_a_guess - if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { error->all(FLERR,"Fix bond/react needs ghost atoms from further away2"); } - for (int j = 0; j < onemol->nspecial[onemol->special[pion][neigh]-1][0]; j++) { - pioneer_count[onemol->special[onemol->special[pion][neigh]-1][j]-1]++; + for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) { + pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][j]-1]++; } glove_counter++; @@ -1249,28 +1288,28 @@ void FixBondReact::check_a_neighbor() for (int i = 0; i < nfirst_neighs; i++) { - if (type[atom->map((int)special[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + if (type[atom->map((int)xspecial[(int)atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) { int already_assigned = 0; //check if a first neighbor of the pioneer is already assigned to pre-reacted template for (int j = 0; j < onemol->natoms; j++) { - if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) { already_assigned = 1; break; } } if (already_assigned == 0) { - glove[(int)onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; - glove[(int)onemol->special[pion][neigh]-1][1] = special[(int)atom->map(glove[pion][1])][i]; + glove[(int)onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh]; + glove[(int)onemol_xspecial[pion][neigh]-1][1] = xspecial[(int)atom->map(glove[pion][1])][i]; //another check for ghost atoms. perhaps remove the one in make_a_guess - if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { error->all(FLERR,"Fix bond/react needs ghost atoms from further away3"); } - for (int ii = 0; ii < onemol->nspecial[onemol->special[pion][neigh]-1][0]; ii++) { - pioneer_count[onemol->special[onemol->special[pion][neigh]-1][ii]-1]++; + for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) { + pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][ii]-1]++; } glove_counter++; @@ -1296,7 +1335,7 @@ void FixBondReact::check_a_neighbor() void FixBondReact::crosscheck_the_neighbor() { - int nfirst_neighs = onemol->nspecial[pion][0]; + int nfirst_neighs = onemol_nxspecial[pion][0]; if (status == RESTORE) { inner_crosscheck_loop(); @@ -1304,8 +1343,8 @@ void FixBondReact::crosscheck_the_neighbor() } for (trace = 0; trace < nfirst_neighs; trace++) { - if (neigh!=trace && onemol->type[(int)onemol->special[pion][neigh]-1] == onemol->type[(int)onemol->special[pion][trace]-1] && - glove[onemol->special[pion][trace]-1][0] == 0) { + if (neigh!=trace && onemol->type[(int)onemol_xspecial[pion][neigh]-1] == onemol->type[(int)onemol_xspecial[pion][trace]-1] && + glove[onemol_xspecial[pion][trace]-1][0] == 0) { if (avail_guesses == MAXGUESS) { error->warning(FLERR,"Fix bond/react failed because MAXGUESS set too small. ask developer for info"); @@ -1338,30 +1377,29 @@ void FixBondReact::crosscheck_the_neighbor() void FixBondReact::inner_crosscheck_loop() { - tagint **special = atom->special; int *type = atom->type; // arbitrarily limited to 5 identical first neighbors tagint tag_choices[5]; - int nfirst_neighs = onemol->nspecial[pion][0]; + int nfirst_neighs = onemol_nxspecial[pion][0]; int num_choices = 0; for (int i = 0; i < nfirst_neighs; i++) { int already_assigned = 0; for (int j = 0; j < onemol->natoms; j++) { - if (glove[j][1] == special[atom->map(glove[pion][1])][i]) { + if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) { already_assigned = 1; break; } } if (already_assigned == 0 && - type[(int)atom->map(special[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol->special[pion][neigh]-1]) { + type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) { if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises status = GUESSFAIL; return; } - tag_choices[num_choices++] = special[atom->map(glove[pion][1])][i]; + tag_choices[num_choices++] = xspecial[atom->map(glove[pion][1])][i]; } } @@ -1372,19 +1410,19 @@ void FixBondReact::inner_crosscheck_loop() //std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]); std::sort(tag_choices, tag_choices + num_choices); //, std::greater()); - glove[onemol->special[pion][neigh]-1][0] = onemol->special[pion][neigh]; - glove[onemol->special[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1]; + glove[onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh]; + glove[onemol_xspecial[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1]; guess_branch[avail_guesses-1]--; //another check for ghost atoms. perhaps remove the one in make_a_guess - if (atom->map(glove[(int)onemol->special[pion][neigh]-1][1]) < 0) { + if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { error->all(FLERR,"Fix bond/react needs ghost atoms from further away4"); } if (guess_branch[avail_guesses-1] == 0) avail_guesses--; - for (int i = 0; i < onemol->nspecial[onemol->special[pion][neigh]-1][0]; i++) { - pioneer_count[onemol->special[onemol->special[pion][neigh]-1][i]-1]++; + for (int i = 0; i < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; i++) { + pioneer_count[onemol_xspecial[onemol_xspecial[pion][neigh]-1][i]-1]++; } glove_counter++; if (glove_counter == onemol->natoms) { @@ -1404,15 +1442,13 @@ void FixBondReact::ring_check() { // ring_check can be made more efficient by re-introducing 'frozen' atoms // 'frozen' atoms have been assigned and also are no longer pioneers - int **nspecial = atom->nspecial; - tagint **special = atom->special; for (int i = 0; i < onemol->natoms; i++) { - for (int j = 0; j < onemol->nspecial[i][0]; j++) { + for (int j = 0; j < onemol_nxspecial[i][0]; j++) { int ring_fail = 1; - int ispecial = onemol->special[i][j]; - for (int k = 0; k < nspecial[atom->map(glove[i][1])][0]; k++) { - if (special[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) { + int ispecial = onemol_xspecial[i][j]; + for (int k = 0; k < nxspecial[atom->map(glove[i][1])][0]; k++) { + if (xspecial[atom->map(glove[i][1])][k] == glove[ispecial-1][1]) { ring_fail = 0; break; } @@ -1425,6 +1461,53 @@ void FixBondReact::ring_check() } } +/* ---------------------------------------------------------------------- + Get xspecials for current molecule templates +------------------------------------------------------------------------- */ + +void FixBondReact::get_molxspecials() +{ + if (newton_bond == 1) { + onemol_nxspecial = onemol->nspecial; + onemol_xspecial = onemol->special; + twomol_nxspecial = twomol->nspecial; + twomol_xspecial = twomol->special; + } else { + memory->destroy(onemol_nxspecial); + memory->destroy(onemol_xspecial); + memory->create(onemol_nxspecial,onemol->natoms,3,"bond/react:onemol_nxspecial"); + memory->create(onemol_xspecial,onemol->natoms,atom->maxspecial,"bond/react:onemol_xspecial"); + for (int i = 0; i < onemol->natoms; i++) { + onemol_nxspecial[i][0] = onemol->num_bond[i]; + for (int j = 0; j < onemol_nxspecial[i][0]; j++) { + onemol_xspecial[i][j] = onemol->bond_atom[i][j]; + } + onemol_nxspecial[i][1] = onemol->nspecial[i][1]; + onemol_nxspecial[i][2] = onemol->nspecial[i][2]; + int joffset = onemol_nxspecial[i][0] - onemol->nspecial[i][0]; + for (int j = onemol_nxspecial[i][0]; j < onemol_nxspecial[i][2]; j++) { + onemol_xspecial[i][j+joffset] = onemol->special[i][j]; + } + } + memory->destroy(twomol_nxspecial); + memory->destroy(twomol_xspecial); + memory->create(twomol_nxspecial,twomol->natoms,3,"bond/react:twomol_nxspecial"); + memory->create(twomol_xspecial,twomol->natoms,atom->maxspecial,"bond/react:twomol_xspecial"); + for (int i = 0; i < twomol->natoms; i++) { + twomol_nxspecial[i][0] = twomol->num_bond[i]; + for (int j = 0; j < twomol_nxspecial[i][0]; j++) { + twomol_xspecial[i][j] = twomol->bond_atom[i][j]; + } + twomol_nxspecial[i][1] = twomol->nspecial[i][1]; + twomol_nxspecial[i][2] = twomol->nspecial[i][2]; + int joffset = twomol_nxspecial[i][0] - twomol->nspecial[i][0]; + for (int j = twomol_nxspecial[i][0]; j < twomol_nxspecial[i][2]; j++) { + twomol_xspecial[i][j+joffset] = twomol->special[i][j]; + } + } + } +} + /* ---------------------------------------------------------------------- Determine which pre-reacted template atoms are at least three bonds away from edge atoms. @@ -1454,9 +1537,9 @@ void FixBondReact::find_landlocked_atoms(int myrxn) if (nspecial_limit != -1) { for (int i = 0; i < twomol->natoms; i++) { - for (int j = 0; j < twomol->nspecial[i][nspecial_limit]; j++) { + for (int j = 0; j < twomol_nxspecial[i][nspecial_limit]; j++) { for (int k = 0; k < onemol->natoms; k++) { - if (equivalences[twomol->special[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) { + if (equivalences[twomol_xspecial[i][j]-1][1][myrxn] == k+1 && edge[k][myrxn] == 1) { landlocked_atoms[i][myrxn] = 0; } } @@ -1474,7 +1557,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // also, if atoms change number of bonds, but aren't landlocked, that could be bad if (me == 0) for (int i = 0; i < twomol->natoms; i++) { - if (twomol->nspecial[i][0] != onemol->nspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { + if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { char str[128]; sprintf(str,"An atom in 'react #%d' changes bond connectivity but not atom type",myrxn+1); error->warning(FLERR,str); @@ -1721,7 +1804,9 @@ void FixBondReact::unlimit_bond() int *i_react_tags = atom->ivector[index3]; for (int i = 0; i < atom->nlocal; i++) { - if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { + // unlimit atoms for next step! this resolves # of procs disparity, mostly + // first '1': indexing offset, second '1': for next step + if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { // + 1 i_limit_tags[i] = 0; i_statted_tags[i] = 1; i_react_tags[i] = 0; @@ -2363,7 +2448,6 @@ void FixBondReact::read(int myrxn) sscanf(line,"%d",&jbonding[myrxn]); } else if (strcmp(keyword,"EdgeIDs") == 0) { edgeflag = 1; - for (int i = 0; i < onemol->natoms; i++) edge[i][myrxn] = 0; EdgeIDs(line, myrxn); } else if (strcmp(keyword,"Equivalences") == 0) { equivflag = 1; @@ -2375,8 +2459,8 @@ void FixBondReact::read(int myrxn) } // error check - if (bondflag == 0 || equivflag == 0 || edgeflag == 0) - error->all(FLERR,"Superimpose file missing BondingIDs, EdgeIDs, or Equivalences section\n"); + if (bondflag == 0 || equivflag == 0) + error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n"); } void FixBondReact::EdgeIDs(char *line, int myrxn) @@ -2535,17 +2619,14 @@ int FixBondReact::pack_forward_comm(int n, int *list, double *buf, return m; } - int **nspecial = atom->nspecial; - tagint **special = atom->special; - m = 0; for (i = 0; i < n; i++) { j = list[i]; buf[m++] = ubuf(finalpartner[j]).d; - ns = nspecial[j][0]; + ns = nxspecial[j][0]; buf[m++] = ubuf(ns).d; for (k = 0; k < ns; k++) - buf[m++] = ubuf(special[j][k]).d; + buf[m++] = ubuf(xspecial[j][k]).d; } return m; } @@ -2563,25 +2644,20 @@ void FixBondReact::unpack_forward_comm(int n, int first, double *buf) for (i = first; i < last; i++) printf("hello you shouldn't be here\n"); // bondcount[i] = (int) ubuf(buf[m++]).i; - } else if (commflag == 2) { for (i = first; i < last; i++) { partner[i] = (tagint) ubuf(buf[m++]).i; probability[i] = buf[m++]; } - } else { - int **nspecial = atom->nspecial; - tagint **special = atom->special; - m = 0; last = first + n; for (i = first; i < last; i++) { finalpartner[i] = (tagint) ubuf(buf[m++]).i; ns = (int) ubuf(buf[m++]).i; - nspecial[i][0] = ns; + nxspecial[i][0] = ns; for (j = 0; j < ns; j++) - special[i][j] = (tagint) ubuf(buf[m++]).i; + xspecial[i][j] = (tagint) ubuf(buf[m++]).i; } } } diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index e60fff37fbaa93f6e4e09136a57282cd883d9fe3..8ff71141f8abf66e2ea221db207983ecc9b7eae5 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -48,6 +48,7 @@ class FixBondReact : public Fix { private: int me,nprocs; + int newton_bond; int nreacts; int *nevery; FILE *fp; @@ -71,7 +72,6 @@ class FixBondReact : public Fix { int maxcreate; int allncreate; tagint ***created; - int *local_ncreate; class Molecule *onemol; // pre-reacted molecule template class Molecule *twomol; // post-reacted molecule template @@ -112,6 +112,9 @@ class FixBondReact : public Fix { int ***reverse_equiv; // re-ordered equivalences int **landlocked_atoms; // all atoms at least three bonds away from edge atoms + int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors + tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list + int pion,neigh,trace; // important indices for various loops. required for restore points int lcl_inst; // reaction instance tagint **glove; // 1st colmn: pre-reacted template, 2nd colmn: global IDs @@ -144,6 +147,7 @@ class FixBondReact : public Fix { void far_partner(); void close_partner(); + void get_molxspecials(); void find_landlocked_atoms(int); void glove_ghostcheck(); void ghost_glovecast(); @@ -152,7 +156,7 @@ class FixBondReact : public Fix { void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove - // DEBUG (currently obsolete) + // DEBUG void print_bb(); diff --git a/src/USER-MISC/fix_smd.cpp b/src/USER-MISC/fix_smd.cpp index fb22483a073d327e188c62ac9bc782c74000ae26..a42690c280f960d55ef482f4f7d9c85a04af0d31 100644 --- a/src/USER-MISC/fix_smd.cpp +++ b/src/USER-MISC/fix_smd.cpp @@ -270,12 +270,12 @@ void FixSMD::smd_tether() ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); - v[0] = fx*massfrac*unwrap[0]; - v[1] = fy*massfrac*unwrap[1]; - v[2] = fz*massfrac*unwrap[2]; - v[3] = fx*massfrac*unwrap[1]; - v[4] = fx*massfrac*unwrap[2]; - v[5] = fy*massfrac*unwrap[2]; + v[0] = -fx*massfrac*unwrap[0]; + v[1] = -fy*massfrac*unwrap[1]; + v[2] = -fz*massfrac*unwrap[2]; + v[3] = -fx*massfrac*unwrap[1]; + v[4] = -fx*massfrac*unwrap[2]; + v[5] = -fy*massfrac*unwrap[2]; v_tally(i, v); } } @@ -291,12 +291,12 @@ void FixSMD::smd_tether() ftotal[2] -= fz*massfrac; if (evflag) { domain->unmap(x[i],image[i],unwrap); - v[0] = fx*massfrac*unwrap[0]; - v[1] = fy*massfrac*unwrap[1]; - v[2] = fz*massfrac*unwrap[2]; - v[3] = fx*massfrac*unwrap[1]; - v[4] = fx*massfrac*unwrap[2]; - v[5] = fy*massfrac*unwrap[2]; + v[0] = -fx*massfrac*unwrap[0]; + v[1] = -fy*massfrac*unwrap[1]; + v[2] = -fz*massfrac*unwrap[2]; + v[3] = -fx*massfrac*unwrap[1]; + v[4] = -fx*massfrac*unwrap[2]; + v[5] = -fy*massfrac*unwrap[2]; v_tally(i, v); } } diff --git a/src/USER-MISC/pair_cdeam.cpp b/src/USER-MISC/pair_cdeam.cpp deleted file mode 100644 index 53d9036a61d44da205f921c3272ccf41b9075cde..0000000000000000000000000000000000000000 --- a/src/USER-MISC/pair_cdeam.cpp +++ /dev/null @@ -1,644 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Alexander Stukowski - Technical University of Darmstadt, - Germany Department of Materials Science -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_cdeam.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -// This is for debugging purposes. The ASSERT() macro is used in the code to check -// if everything runs as expected. Change this to #if 0 if you don't need the checking. -#if 0 - #define ASSERT(cond) ((!(cond)) ? my_failure(error,__FILE__,__LINE__) : my_noop()) - - inline void my_noop() {} - inline void my_failure(Error* error, const char* file, int line) { - char str[1024]; - sprintf(str,"Assertion failure: File %s, line %i", file, line); - error->one(FLERR,str); - } -#else - #define ASSERT(cond) -#endif - -#define MAXLINE 1024 // This sets the maximum line length in EAM input files. - -PairCDEAM::PairCDEAM(LAMMPS *lmp, int _cdeamVersion) : PairEAM(lmp), PairEAMAlloy(lmp), cdeamVersion(_cdeamVersion) -{ - single_enable = 0; - restartinfo = 0; - - rhoB = NULL; - D_values = NULL; - hcoeff = NULL; - - // Set communication buffer sizes needed by this pair style. - if(cdeamVersion == 1) { - comm_forward = 4; - comm_reverse = 3; - } - else if(cdeamVersion == 2) { - comm_forward = 3; - comm_reverse = 2; - } - else { - error->all(FLERR,"Invalid CD-EAM potential version."); - } -} - -PairCDEAM::~PairCDEAM() -{ - memory->destroy(rhoB); - memory->destroy(D_values); - if(hcoeff) delete[] hcoeff; -} - -void PairCDEAM::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,rhoip,rhojp,recip,phi; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; - - // Grow per-atom arrays if necessary - if(atom->nmax > nmax) { - memory->destroy(rho); - memory->destroy(fp); - memory->destroy(rhoB); - memory->destroy(D_values); - nmax = atom->nmax; - memory->create(rho,nmax,"pair:rho"); - memory->create(rhoB,nmax,"pair:rhoB"); - memory->create(fp,nmax,"pair:fp"); - memory->create(D_values,nmax,"pair:D_values"); - } - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // Zero out per-atom arrays. - int m = nlocal + atom->nghost; - for(i = 0; i < m; i++) { - rho[i] = 0.0; - rhoB[i] = 0.0; - D_values[i] = 0.0; - } - - // Stage I - - // Compute rho and rhoB at each local atom site. - // Additionally calculate the D_i values here if we are using the one-site formulation. - // For the two-site formulation we have to calculate the D values in an extra loop (Stage II). - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - jtype = type[j]; - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - double localrho = RhoOfR(index, jtype, itype); - rho[i] += localrho; - if(jtype == speciesB) rhoB[i] += localrho; - if(newton_pair || j < nlocal) { - localrho = RhoOfR(index, itype, jtype); - rho[j] += localrho; - if(itype == speciesB) rhoB[j] += localrho; - } - - if(cdeamVersion == 1 && itype != jtype) { - // Note: if the i-j interaction is not concentration dependent (because either - // i or j are not species A or B) then its contribution to D_i and D_j should - // be ignored. - // This if-clause is only required for a ternary. - if((itype == speciesA && jtype == speciesB) || (jtype == speciesA && itype == speciesB)) { - double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); - D_values[i] += Phi_AB; - if(newton_pair || j < nlocal) - D_values[j] += Phi_AB; - } - } - } - } - } - - // Communicate and sum densities. - if(newton_pair) { - communicationStage = 1; - comm->reverse_comm_pair(this); - } - - // fp = derivative of embedding energy at each atom - // phi = embedding energy at each atom - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - EAMTableIndex index = rhoToTableIndex(rho[i]); - fp[i] = FPrimeOfRho(index, type[i]); - if(eflag) { - phi = FofRho(index, type[i]); - if (eflag_global) eng_vdwl += phi; - if (eflag_atom) eatom[i] += phi; - } - } - - // Communicate derivative of embedding function and densities - // and D_values (this for one-site formulation only). - communicationStage = 2; - comm->forward_comm_pair(this); - - // The electron densities may not drop to zero because then the concentration would no longer be defined. - // But the concentration is not needed anyway if there is no interaction with another atom, which is the case - // if the electron density is exactly zero. That's why the following lines have been commented out. - // - //for(i = 0; i < nlocal + atom->nghost; i++) { - // if(rho[i] == 0 && (type[i] == speciesA || type[i] == speciesB)) - // error->one(FLERR,"CD-EAM potential routine: Detected atom with zero electron density."); - //} - - // Stage II - // This is only required for the original two-site formulation of the CD-EAM potential. - - if(cdeamVersion == 2) { - // Compute intermediate value D_i for each atom. - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // This code line is required for ternary alloys. - if(itype != speciesA && itype != speciesB) continue; - - double x_i = rhoB[i] / rho[i]; // Concentration at atom i. - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - if(itype == jtype) continue; - - // This code line is required for ternary alloys. - if(jtype != speciesA && jtype != speciesB) continue; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - - // The concentration independent part of the cross pair potential. - double Phi_AB = PhiOfR(index, itype, jtype, 1.0 / r); - - // Average concentration of two sites - double x_ij = 0.5 * (x_i + rhoB[j]/rho[j]); - - // Calculate derivative of h(x_ij) polynomial function. - double h_prime = evalHprime(x_ij); - - D_values[i] += h_prime * Phi_AB / (2.0 * rho[i] * rho[i]); - if(newton_pair || j < nlocal) - D_values[j] += h_prime * Phi_AB / (2.0 * rho[j] * rho[j]); - } - } - } - - // Communicate and sum D values. - if(newton_pair) { - communicationStage = 3; - comm->reverse_comm_pair(this); - } - communicationStage = 4; - comm->forward_comm_pair(this); - } - - // Stage III - - // Compute force acting on each atom. - for(ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // Concentration at site i - double x_i = -1.0; // The value -1 indicates: no concentration dependence for all interactions of atom i. - // It will be replaced by the concentration at site i if atom i is either A or B. - - double D_i, h_prime_i; - - // This if-clause is only required for ternary alloys. - if((itype == speciesA || itype == speciesB) && rho[i] != 0.0) { - - // Compute local concentration at site i. - x_i = rhoB[i]/rho[i]; - ASSERT(x_i >= 0 && x_i<=1.0); - - if(cdeamVersion == 1) { - // Calculate derivative of h(x_i) polynomial function. - h_prime_i = evalHprime(x_i); - D_i = D_values[i] * h_prime_i / (2.0 * rho[i] * rho[i]); - } else if(cdeamVersion == 2) { - D_i = D_values[i]; - } else { - ASSERT(false); - } - } - - for(jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if(rsq < cutforcesq) { - jtype = type[j]; - double r = sqrt(rsq); - const EAMTableIndex index = radiusToTableIndex(r); - - // rhoip = derivative of (density at atom j due to atom i) - // rhojp = derivative of (density at atom i due to atom j) - // psip needs both fp[i] and fp[j] terms since r_ij appears in two - // terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji) - // hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip - rhoip = RhoPrimeOfR(index, itype, jtype); - rhojp = RhoPrimeOfR(index, jtype, itype); - fpair = fp[i]*rhojp + fp[j]*rhoip; - recip = 1.0/r; - - double x_j = -1; // The value -1 indicates: no concentration dependence for this i-j pair - // because atom j is not of species A nor B. - - // This code line is required for ternary alloy. - if(jtype == speciesA || jtype == speciesB) { - ASSERT(rho[i] != 0.0); - ASSERT(rho[j] != 0.0); - - // Compute local concentration at site j. - x_j = rhoB[j]/rho[j]; - ASSERT(x_j >= 0 && x_j<=1.0); - - double D_j=0.0; - if(cdeamVersion == 1) { - // Calculate derivative of h(x_j) polynomial function. - double h_prime_j = evalHprime(x_j); - D_j = D_values[j] * h_prime_j / (2.0 * rho[j] * rho[j]); - } else if(cdeamVersion == 2) { - D_j = D_values[j]; - } else { - ASSERT(false); - } - double t2 = -rhoB[j]; - if(itype == speciesB) t2 += rho[j]; - fpair += D_j * rhoip * t2; - } - - // This if-clause is only required for a ternary alloy. - // Actually we don't need it at all because D_i should be zero anyway if - // atom i has no concentration dependent interactions (because it is not species A or B). - if(x_i != -1.0) { - double t1 = -rhoB[i]; - if(jtype == speciesB) t1 += rho[i]; - fpair += D_i * rhojp * t1; - } - - double phip; - double phi = PhiOfR(index, itype, jtype, recip, phip); - if(itype == jtype || x_i == -1.0 || x_j == -1.0) { - // Case of no concentration dependence. - fpair += phip; - } else { - // We have a concentration dependence for the i-j interaction. - double h=0.0; - if(cdeamVersion == 1) { - // Calculate h(x_i) polynomial function. - double h_i = evalH(x_i); - // Calculate h(x_j) polynomial function. - double h_j = evalH(x_j); - h = 0.5 * (h_i + h_j); - } else if(cdeamVersion == 2) { - // Average concentration. - double x_ij = 0.5 * (x_i + x_j); - // Calculate h(x_ij) polynomial function. - h = evalH(x_ij); - } else { - ASSERT(false); - } - fpair += h * phip; - phi *= h; - } - - // Divide by r_ij and negate to get forces from gradient. - fpair /= -r; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if(newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if(eflag) evdwl = phi; - if(evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz); - } - } - } - - if(vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::coeff(int narg, char **arg) -{ - PairEAMAlloy::coeff(narg, arg); - - // Make sure the EAM file is a CD-EAM binary alloy. - if(setfl->nelements < 2) - error->all(FLERR,"The EAM file must contain at least 2 elements to be used with the eam/cd pair style."); - - // Read in the coefficients of the h polynomial from the end of the EAM file. - read_h_coeff(arg[2]); - - // Determine which atom type is the A species and which is the B species in the alloy. - // By default take the first element (index 0) in the EAM file as the A species - // and the second element (index 1) in the EAM file as the B species. - speciesA = -1; - speciesB = -1; - for(int i = 1; i <= atom->ntypes; i++) { - if(map[i] == 0) { - if(speciesA >= 0) - error->all(FLERR,"The first element from the EAM file may only be mapped to a single atom type."); - speciesA = i; - } - if(map[i] == 1) { - if(speciesB >= 0) - error->all(FLERR,"The second element from the EAM file may only be mapped to a single atom type."); - speciesB = i; - } - } - if(speciesA < 0) - error->all(FLERR,"The first element from the EAM file must be mapped to exactly one atom type."); - if(speciesB < 0) - error->all(FLERR,"The second element from the EAM file must be mapped to exactly one atom type."); -} - -/* ---------------------------------------------------------------------- - Reads in the h(x) polynomial coefficients -------------------------------------------------------------------------- */ -void PairCDEAM::read_h_coeff(char *filename) -{ - if(comm->me == 0) { - // Open potential file - FILE *fptr; - char line[MAXLINE]; - char nextline[MAXLINE]; - fptr = force->open_potential(filename); - if (fptr == NULL) { - char str[128]; - sprintf(str,"Cannot open EAM potential file %s", filename); - error->one(FLERR,str); - } - - // h coefficients are stored at the end of the file. - // Skip to last line of file. - while(fgets(nextline, MAXLINE, fptr) != NULL) { - strcpy(line, nextline); - } - char* ptr = strtok(line, " \t\n\r\f"); - int degree = atoi(ptr); - nhcoeff = degree+1; - hcoeff = new double[nhcoeff]; - int i = 0; - while((ptr = strtok(NULL," \t\n\r\f")) != NULL && i < nhcoeff) { - hcoeff[i++] = atof(ptr); - } - if(i != nhcoeff || nhcoeff < 1) - error->one(FLERR,"Failed to read h(x) function coefficients from EAM file."); - - // Close the potential file. - fclose(fptr); - } - - MPI_Bcast(&nhcoeff, 1, MPI_INT, 0, world); - if(comm->me != 0) hcoeff = new double[nhcoeff]; - MPI_Bcast(hcoeff, nhcoeff, MPI_DOUBLE, 0, world); -} - - -/* ---------------------------------------------------------------------- */ - -int PairCDEAM::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - - m = 0; - if(communicationStage == 2) { - if(cdeamVersion == 1) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = fp[j]; - buf[m++] = rho[j]; - buf[m++] = rhoB[j]; - buf[m++] = D_values[j]; - } - return m; - } - else if(cdeamVersion == 2) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = fp[j]; - buf[m++] = rho[j]; - buf[m++] = rhoB[j]; - } - return m; - } - else { ASSERT(false); return 0; } - } - else if(communicationStage == 4) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = D_values[j]; - } - return m; - } - else return 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - if(communicationStage == 2) { - if(cdeamVersion == 1) { - for(i = first; i < last; i++) { - fp[i] = buf[m++]; - rho[i] = buf[m++]; - rhoB[i] = buf[m++]; - D_values[i] = buf[m++]; - } - } - else if(cdeamVersion == 2) { - for(i = first; i < last; i++) { - fp[i] = buf[m++]; - rho[i] = buf[m++]; - rhoB[i] = buf[m++]; - } - } else { - ASSERT(false); - } - } - else if(communicationStage == 4) { - for(i = first; i < last; i++) { - D_values[i] = buf[m++]; - } - } -} - -/* ---------------------------------------------------------------------- */ -int PairCDEAM::pack_reverse_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - - if(communicationStage == 1) { - if(cdeamVersion == 1) { - for(i = first; i < last; i++) { - buf[m++] = rho[i]; - buf[m++] = rhoB[i]; - buf[m++] = D_values[i]; - } - return m; - } - else if(cdeamVersion == 2) { - for(i = first; i < last; i++) { - buf[m++] = rho[i]; - buf[m++] = rhoB[i]; - } - return m; - } - else { ASSERT(false); return 0; } - } - else if(communicationStage == 3) { - for(i = first; i < last; i++) { - buf[m++] = D_values[i]; - } - return m; - } - else return 0; -} - -/* ---------------------------------------------------------------------- */ - -void PairCDEAM::unpack_reverse_comm(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - if(communicationStage == 1) { - if(cdeamVersion == 1) { - for(i = 0; i < n; i++) { - j = list[i]; - rho[j] += buf[m++]; - rhoB[j] += buf[m++]; - D_values[j] += buf[m++]; - } - } else if(cdeamVersion == 2) { - for(i = 0; i < n; i++) { - j = list[i]; - rho[j] += buf[m++]; - rhoB[j] += buf[m++]; - } - } else { - ASSERT(false); - } - } - else if(communicationStage == 3) { - for(i = 0; i < n; i++) { - j = list[i]; - D_values[j] += buf[m++]; - } - } -} - -/* ---------------------------------------------------------------------- - memory usage of local atom-based arrays -------------------------------------------------------------------------- */ -double PairCDEAM::memory_usage() -{ - double bytes = 2 * nmax * sizeof(double); - return PairEAMAlloy::memory_usage() + bytes; -} diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 3335672ac3dd305e22e16b4631dc07039ff5ee47..79a3c2a49791346e5e22e5f3f5fbc9ca22294316 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -88,7 +88,7 @@ void PairLJExpandCoulLong::compute(int eflag, int vflag) double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; double grij,expm2,prefactor,t,erfc; int *ilist,*jlist,*numneigh,**firstneigh; - double rsq,rshift,rshiftsq; + double rsq,rshift,rshiftsq,rshift2inv; evdwl = ecoul = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); @@ -166,8 +166,8 @@ void PairLJExpandCoulLong::compute(int eflag, int vflag) r = sqrt(rsq); rshift = r - shift[itype][jtype]; rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; + rshift2inv = 1.0/rshiftsq; + r6inv = rshift2inv*rshift2inv*rshift2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); forcelj = factor_lj*forcelj/rshift/r; } else forcelj = 0.0; @@ -217,7 +217,7 @@ void PairLJExpandCoulLong::compute_inner() int i,j,ii,jj,inum,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - double rsw,r,rshift,rshiftsq; + double rsw,r,rshift,rshiftsq,rshift2inv; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; @@ -275,8 +275,8 @@ void PairLJExpandCoulLong::compute_inner() r = sqrt(rsq); rshift = r - shift[itype][jtype]; rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; + rshift2inv = 1.0/rshiftsq; + r6inv = rshift2inv*rshift2inv*rshift2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); forcelj = factor_lj*forcelj/rshift/r; } else forcelj = 0.0; @@ -306,8 +306,8 @@ void PairLJExpandCoulLong::compute_middle() { int i,j,ii,jj,inum,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,fpair; - double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; - double rsw,r,rshift,rshiftsq; + double rsq,r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; + double rsw,rshift,rshiftsq,rshift2inv; int *ilist,*jlist,*numneigh,**firstneigh; double **x = atom->x; @@ -370,8 +370,8 @@ void PairLJExpandCoulLong::compute_middle() r = sqrt(rsq); rshift = r - shift[itype][jtype]; rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; + rshift2inv = 1.0/rshiftsq; + r6inv = rshift2inv*rshift2inv*rshift2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); forcelj = factor_lj*forcelj/rshift/r; } else forcelj = 0.0; @@ -408,9 +408,8 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag) double fraction,table; double r,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj; double grij,expm2,prefactor,t,erfc; - double rsw,rshift,rshiftsq; + double rsw,rsq,rshift,rshiftsq,rshift2inv; int *ilist,*jlist,*numneigh,**firstneigh; - double rsq; evdwl = ecoul = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); @@ -507,8 +506,8 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag) r = sqrt(rsq); rshift = r - shift[itype][jtype]; rshiftsq = rshift*rshift; - r2inv = 1.0/rshiftsq; - r6inv = r2inv*r2inv*r2inv; + rshift2inv = 1.0/rshiftsq; + r6inv = rshift2inv*rshift2inv*rshift2inv; forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); forcelj = factor_lj*forcelj/rshift/r; if (rsq < cut_in_on_sq) { @@ -680,7 +679,7 @@ void PairLJExpandCoulLong::init_style() if (!atom->q_flag) error->all(FLERR,"Pair style lj/cut/coul/long requires atom attribute q"); - // request regular or rRESPA neighbor lists + // request regular or rRESPA neighbor list int irequest; int respa = 0; @@ -729,12 +728,13 @@ double PairLJExpandCoulLong::init_one(int i, int j) sigma[i][i],sigma[j][j]); sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + shift[i][j] = 0.5 * (shift[i][i] + shift[j][j]); } // include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P - double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist); - cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + double cut = MAX(cut_lj[i][j]+shift[i][j],cut_coul+2.0*qdist); + cut_ljsq[i][j] = (cut_lj[i][j]+shift[i][j]) *(cut_lj[i][j]+shift[i][j]); lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); diff --git a/src/USER-QUIP/pair_quip.cpp b/src/USER-QUIP/pair_quip.cpp index 3bf12d19d2ab3217e44bea084f53523706328425..0c00a5ef59309b824e1c534d58a6fcff9df79ceb 100644 --- a/src/USER-QUIP/pair_quip.cpp +++ b/src/USER-QUIP/pair_quip.cpp @@ -40,6 +40,7 @@ using namespace LAMMPS_NS; PairQUIP::PairQUIP(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; + restartinfo = 0; one_coeff = 1; no_virial_fdotr_compute = 1; manybody_flag = 1; diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index fcface79fd29718fb557e79ef1e1d37f18d89e3a..7932e9cbd8975596eeb9d3dbd161c153000ebb5d 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -157,6 +157,18 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, fgets( s, MAX_LINE, fp ); c = Tokenize( s, &tmp ); + /* Sanity checks */ + if (c == 2 && !lgflag) { + if (me == 0) + fprintf(stderr, "Force field file requires using 'lgvdw yes'\n"); + MPI_Abort( comm, FILE_NOT_FOUND ); + } + if (c < 9) { + if (me == 0) + fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); + MPI_Abort( comm, FILE_NOT_FOUND ); + } + for( j = 0; j < (int)(strlen(tmp[0])); ++j ) reax->sbp[i].name[j] = toupper( tmp[0][j] ); @@ -174,6 +186,13 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, fgets( s, MAX_LINE, fp ); c = Tokenize( s, &tmp ); + /* Sanity check */ + if (c < 8) { + if (me == 0) + fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); + MPI_Abort( comm, FILE_NOT_FOUND ); + } + val = atof(tmp[0]); reax->sbp[i].alpha = val; val = atof(tmp[1]); reax->sbp[i].gamma_w = val; val = atof(tmp[2]); reax->sbp[i].valency_boc= val; @@ -187,6 +206,13 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, fgets( s, MAX_LINE, fp ); c = Tokenize( s, &tmp ); + /* Sanity check */ + if (c < 8) { + if (me == 0) + fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); + MPI_Abort( comm, FILE_NOT_FOUND ); + } + val = atof(tmp[0]); reax->sbp[i].r_pi_pi = val; val = atof(tmp[1]); reax->sbp[i].p_lp2 = val; val = atof(tmp[2]); @@ -201,7 +227,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, c = Tokenize( s, &tmp ); /* Sanity check */ - if (c < 3) { + if (c < 8) { if (me == 0) fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); MPI_Abort( comm, FILE_NOT_FOUND ); @@ -222,9 +248,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, c = Tokenize( s, &tmp ); /* Sanity check */ - if (c > 3) { + if (c > 2) { if (me == 0) - fprintf(stderr, "Inconsistent ffield file (reaxc_ffield.cpp) \n"); + fprintf(stderr, "Force field file incompatible with 'lgvdw yes'\n"); MPI_Abort( comm, FILE_NOT_FOUND ); } diff --git a/src/atom.cpp b/src/atom.cpp index 56bfd04de7195afbdf1eb370ebb36f61b7aa8f52..cf4d20a71e30914a6405f9c2e84fd0e3c4fb0510 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -96,6 +96,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) rho = drho = e = de = cv = NULL; vest = NULL; + // SPIN package + + sp = fm = NULL; + // USER-DPD uCond = uMech = uChem = uCG = uCGnew = NULL; @@ -166,6 +170,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) radius_flag = rmass_flag = 0; ellipsoid_flag = line_flag = tri_flag = body_flag = 0; + // magnetic flags + + sp_flag = 0; + vfrac_flag = 0; spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0; cs_flag = csforce_flag = vforce_flag = etag_flag = 0; @@ -267,6 +275,9 @@ Atom::~Atom() memory->destroy(tri); memory->destroy(body); + memory->destroy(sp); + memory->destroy(fm); + memory->destroy(vfrac); memory->destroy(s0); memory->destroy(x0); @@ -419,6 +430,10 @@ void Atom::create_avec(const char *style, int narg, char **arg, int trysuffix) radius_flag = rmass_flag = 0; ellipsoid_flag = line_flag = tri_flag = body_flag = 0; + // magnetic flags + + sp_flag = 0; + vfrac_flag = 0; spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0; cs_flag = csforce_flag = vforce_flag = etag_flag = 0; diff --git a/src/atom.h b/src/atom.h index abfa6e5eb55ab1e3b02077492516b8ee7764d21f..7e003dff5ea15e1c9570ac425c18d5de7cef037e 100644 --- a/src/atom.h +++ b/src/atom.h @@ -61,6 +61,11 @@ class Atom : protected Pointers { double *radius,*rmass; int *ellipsoid,*line,*tri,*body; + // SPIN package + + double **sp; + double **fm; + // PERI package double *vfrac,*s0; @@ -146,6 +151,10 @@ class Atom : protected Pointers { int rho_flag,e_flag,cv_flag,vest_flag; int dpd_flag,edpd_flag,tdpd_flag; + //USER-SPIN package + + int sp_flag; + // USER-SMD package int smd_flag; diff --git a/src/balance.cpp b/src/balance.cpp index 86deb55b47ff716f6e05f1ce0d4adcc3f7d4d793..7dd13e8766ac9c16056035afe31d1e3f8e38a017 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -350,13 +350,13 @@ void Balance::command(int narg, char **arg) domain->set_local_box(); // move particles to new processors via irregular() + // set disable = 0, so weights migrate with atoms for imbfinal calculation if (domain->triclinic) domain->x2lamda(atom->nlocal); Irregular *irregular = new Irregular(lmp); if (wtflag) fixstore->disable = 0; if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc); else irregular->migrate_atoms(1); - if (wtflag) fixstore->disable = 1; delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); @@ -377,9 +377,11 @@ void Balance::command(int narg, char **arg) } // imbfinal = final imbalance + // set disable = 1, so weights no longer migrate with atoms double maxfinal; double imbfinal = imbalance_factor(maxfinal); + if (wtflag) fixstore->disable = 1; // stats output @@ -540,6 +542,8 @@ void Balance::weight_storage(char *prefix) fixstore = (FixStore *) modify->fix[modify->nfix-1]; } else fixstore = (FixStore *) modify->fix[ifix]; + // do not carry weights with atoms during normal atom migration + fixstore->disable = 1; if (prefix) delete [] fixargs[0]; diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp index 76df5a053dfc0e10b88c9369735ed597c639110f..862a66e3f947312e68a649ccbae0e196413be89b 100644 --- a/src/compute_property_atom.cpp +++ b/src/compute_property_atom.cpp @@ -141,7 +141,41 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Compute property/atom for " "atom property that isn't allocated"); pack_choice[i] = &ComputePropertyAtom::pack_mu; - + } else if (strcmp(arg[iarg],"spx") == 0) { // pack magnetic variables + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spx; + } else if (strcmp(arg[iarg],"spy") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spy; + } else if (strcmp(arg[iarg],"spz") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_spz; + } else if (strcmp(arg[iarg],"sp") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_sp; + } else if (strcmp(arg[iarg],"fmx") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmx; + } else if (strcmp(arg[iarg],"fmy") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmy; + } else if (strcmp(arg[iarg],"fmz") == 0) { + if (!atom->sp_flag) + error->all(FLERR,"Compute property/atom for " + "atom property that isn't allocated"); + pack_choice[i] = &ComputePropertyAtom::pack_fmz; } else if (strcmp(arg[iarg],"radius") == 0) { if (!atom->radius_flag) error->all(FLERR,"Compute property/atom for " @@ -1000,6 +1034,111 @@ void ComputePropertyAtom::pack_mu(int n) /* ---------------------------------------------------------------------- */ +void ComputePropertyAtom::pack_spx(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][0]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_spy(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][1]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_spz(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][2]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_sp(int n) +{ + double **sp = atom->sp; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = sp[i][3]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmx(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][0]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmy(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][1]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + +void ComputePropertyAtom::pack_fmz(int n) +{ + double **fm = atom->fm; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) buf[n] = fm[i][2]; + else buf[n] = 0.0; + n += nvalues; + } +} + +/* ---------------------------------------------------------------------- */ + void ComputePropertyAtom::pack_radius(int n) { double *radius = atom->radius; diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h index a81f39f6a9192b1ff1bfb91952f8559049689b2a..0c1ed7e305a8bd377b2a759e41cddc8ab9812d17 100644 --- a/src/compute_property_atom.h +++ b/src/compute_property_atom.h @@ -84,6 +84,14 @@ class ComputePropertyAtom : public Compute { void pack_radius(int); void pack_diameter(int); + void pack_spx(int); // pack magnetic variables + void pack_spy(int); + void pack_spz(int); + void pack_sp(int); + void pack_fmx(int); + void pack_fmy(int); + void pack_fmz(int); + void pack_omegax(int); void pack_omegay(int); void pack_omegaz(int); diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp index 40d74a1d746837209696e13f6aecfd9ea6deaf54..4c3950c0992deacc6b7741f1da30d42239b53265 100644 --- a/src/dump_custom.cpp +++ b/src/dump_custom.cpp @@ -244,15 +244,13 @@ DumpCustom::~DumpCustom() for (int i = 1; i <= ntypes; i++) delete [] typenames[i]; delete [] typenames; - if(vformat) { + if (vformat) { for (int i = 0; i < size_one; i++) delete [] vformat[i]; delete [] vformat; } - if(format_column_user) { - for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; - delete [] format_column_user; - } + for (int i = 0; i < size_one; i++) delete [] format_column_user[i]; + delete [] format_column_user; delete [] columns; } diff --git a/src/error.cpp b/src/error.cpp index 2ab816c992ac910fd0a2dd789a1c08d3f9da2576..3feaf1d1acde855d71ca3d3fd79ed5afd83934d2 100644 --- a/src/error.cpp +++ b/src/error.cpp @@ -16,6 +16,7 @@ #include #include "error.h" #include "universe.h" +#include "update.h" #include "output.h" #include "input.h" @@ -28,7 +29,7 @@ static const char *truncpath(const char *path) if (path) { int len = strlen(path); for (int i = len-4; i > 0; --i) { - if (strncmp("src/",path+i,4) == 0) + if (strncmp("src/",path+i,4) == 0) return path+i; } } @@ -69,6 +70,10 @@ void Error::universe_all(const char *file, int line, const char *str) if (universe->ulogfile) fclose(universe->ulogfile); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); throw LAMMPSException(msg); @@ -90,6 +95,10 @@ void Error::universe_one(const char *file, int line, const char *str) universe->me,str,truncpath(file),line); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); throw LAMMPSAbortException(msg, universe->uworld); @@ -137,6 +146,10 @@ void Error::all(const char *file, int line, const char *str) } #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; sprintf(msg, "ERROR: %s (%s:%d)\n", str, file, line); @@ -183,6 +196,10 @@ void Error::one(const char *file, int line, const char *str) universe->me,str,truncpath(file),line); #ifdef LAMMPS_EXCEPTIONS + + // allow commands if an exception was caught in a run + update->whichflag = 0; + char msg[100]; sprintf(msg, "ERROR on proc %d: %s (%s:%d)\n", me, str, file, line); throw LAMMPSAbortException(msg, world); diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp index 754c9ea4da41230b46836b28ca69a6e990c77b05..42cd1bd1992de2c9d474b018634bd33052e8b03f 100644 --- a/src/fix_adapt.cpp +++ b/src/fix_adapt.cpp @@ -118,7 +118,7 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL) adapt[nadapt].bparam = new char[n]; adapt[nadapt].bond = NULL; strcpy(adapt[nadapt].bparam,arg[iarg+2]); - force->bounds(FLERR,arg[iarg+3],atom->ntypes, + force->bounds(FLERR,arg[iarg+3],atom->nbondtypes, adapt[nadapt].ilo,adapt[nadapt].ihi); if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) { n = strlen(&arg[iarg+4][2]) + 1; diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index b2f545c73fbbefa4af2f2a46d244ea78be352a60..e748e0ae31c0fd0e550d35dff5b5f3898daeccac 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -114,6 +114,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : if (nevery) force_reneighbor = 1; lastbalance = -1; + next_reneighbor = -1; // compute initial outputs @@ -248,6 +249,10 @@ void FixBalance::pre_neighbor() if (!pending) return; imbfinal = balance->imbalance_factor(maxloadperproc); pending = 0; + + // set disable = 1, so weights no longer migrate with atoms + + if (wtflag) balance->fixstore->disable = 1; } /* ---------------------------------------------------------------------- @@ -275,21 +280,23 @@ void FixBalance::rebalance() // reset proc sub-domains // check and warn if any proc's subbox is smaller than neigh skin - // since may lead to lost atoms in exchange() + // since may lead to lost atoms in comm->exchange() if (domain->triclinic) domain->set_lamda_box(); domain->set_local_box(); domain->subbox_too_small_check(neighbor->skin); // move atoms to new processors via irregular() - // only needed if migrate_check() says an atom moves to far + // for non-RCB only needed if migrate_check() says an atom moves too far // else allow caller's comm->exchange() to do it + // set disable = 0, so weights migrate with atoms + // important to delay disable = 1 until after pre_neighbor imbfinal calc + // b/c atoms may migrate again in comm->exchange() if (domain->triclinic) domain->x2lamda(atom->nlocal); if (wtflag) balance->fixstore->disable = 0; if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc); else if (irregular->migrate_check()) irregular->migrate_atoms(); - if (wtflag) balance->fixstore->disable = 1; if (domain->triclinic) domain->lamda2x(atom->nlocal); // invoke KSpace setup_grid() to adjust to new proc sub-domains diff --git a/src/fix_dt_reset.cpp b/src/fix_dt_reset.cpp index 006bf27e77729c1f45078642f80bec2014631f65..f2a50fd6d1c416ee9b8c1f551a1ef56305a3b945 100644 --- a/src/fix_dt_reset.cpp +++ b/src/fix_dt_reset.cpp @@ -69,6 +69,7 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) : int scaleflag = 1; + emax = -1.0; int iarg = 7; while (iarg < narg) { if (strcmp(arg[iarg],"units") == 0) { @@ -77,6 +78,11 @@ FixDtReset::FixDtReset(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; else error->all(FLERR,"Illegal fix dt/reset command"); iarg += 2; + } else if (strcmp(arg[iarg],"emax") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix dt/reset command"); + emax = force->numeric(FLERR,arg[iarg+1]); + if (emax <= 0.0) error->all(FLERR,"Illegal fix dt/reset command"); + iarg += 2; } else error->all(FLERR,"Illegal fix dt/reset command"); } @@ -117,6 +123,7 @@ void FixDtReset::init() "Dump dcd/xtc timestamp may be wrong with fix dt/reset"); ftm2v = force->ftm2v; + mvv2e = force->mvv2e; dt = update->dt; } @@ -131,12 +138,10 @@ void FixDtReset::setup(int vflag) void FixDtReset::end_of_step() { - double dtv,dtf,dtsq; + double dtv,dtf,dte,dtsq; double vsq,fsq,massinv; double delx,dely,delz,delr; - // compute vmax and amax of any atom in group - double **v = atom->v; double **f = atom->f; double *mass = atom->mass; @@ -153,10 +158,14 @@ void FixDtReset::end_of_step() else massinv = 1.0/mass[type[i]]; vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]; fsq = f[i][0]*f[i][0] + f[i][1]*f[i][1] + f[i][2]*f[i][2]; - dtv = dtf = BIG; + dtv = dtf = dte = BIG; if (vsq > 0.0) dtv = xmax/sqrt(vsq); if (fsq > 0.0) dtf = sqrt(2.0*xmax/(ftm2v*sqrt(fsq)*massinv)); dt = MIN(dtv,dtf); + if (emax > 0.0 && vsq > 0.0 && fsq > 0.0) { + dte = emax/sqrt(fsq*vsq)/sqrt(ftm2v*mvv2e); + dt = MIN(dt, dte); + } dtsq = dt*dt; delx = dt*v[i][0] + 0.5*dtsq*massinv*f[i][0] * ftm2v; dely = dt*v[i][1] + 0.5*dtsq*massinv*f[i][1] * ftm2v; diff --git a/src/fix_dt_reset.h b/src/fix_dt_reset.h index 6e08b14f634d638e42fb8212445be342bf002a28..6df69138952b79eef80a2b762c06435a24627564 100644 --- a/src/fix_dt_reset.h +++ b/src/fix_dt_reset.h @@ -37,8 +37,8 @@ class FixDtReset : public Fix { private: bigint laststep; int minbound,maxbound; - double tmin,tmax,xmax; - double ftm2v; + double tmin,tmax,xmax,emax; + double ftm2v,mvv2e; double dt,t_laststep; int respaflag; }; diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 186376d95230bc8d2bbbf977c95fba8c5c16243f..73c70420c5bc84e001d448a5d580b1fe10ce9ece 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -798,7 +798,7 @@ void FixNH::setup(int vflag) if (pstat_flag) { double kt = boltz * t_target; - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) @@ -1446,7 +1446,7 @@ double FixNH::compute_scalar() double volume; double energy; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press = 0.0; int ich; if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd; else volume = domain->xprd * domain->yprd; @@ -1477,15 +1477,21 @@ double FixNH::compute_scalar() // sum is over barostatted dimensions if (pstat_flag) { - for (i = 0; i < 3; i++) - if (p_flag[i]) + for (i = 0; i < 3; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] + p_hydro*(volume-vol0) / (pdim*nktv2p); + lkt_press += kt; + } + } if (pstyle == TRICLINIC) { - for (i = 3; i < 6; i++) - if (p_flag[i]) + for (i = 3; i < 6; i++) { + if (p_flag[i]) { energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i]; + lkt_press += kt; + } + } } // extra contributions from thermostat chain for barostat @@ -1818,15 +1824,15 @@ void FixNH::nhc_temp_integrate() void FixNH::nhc_press_integrate() { - int ich,i; + int ich,i,pdof; double expfac,factor_etap,kecurrent; double kt = boltz * t_target; - double lkt_press = kt; + double lkt_press; // Update masses, to preserve initial freq, if flag set if (omega_mass_flag) { - double nkt = atom->natoms * kt; + double nkt = (atom->natoms + 1) * kt; for (int i = 0; i < 3; i++) if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]); @@ -1850,14 +1856,22 @@ void FixNH::nhc_press_integrate() } kecurrent = 0.0; + pdof = 0; for (i = 0; i < 3; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } if (pstyle == TRICLINIC) { for (i = 3; i < 6; i++) - if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + if (p_flag[i]) { + kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i]; + pdof++; + } } + lkt_press = pdof * kt; etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; double ncfac = 1.0/nc_pchain; diff --git a/src/fix_store.cpp b/src/fix_store.cpp index 3b1f3dca77dde1d15d645938e000a012c202ee9c..350e12097270c1e64f80313af5665ca60e719963 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -154,8 +154,6 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller) if (vecflag) memory->create(vstore,nrow,"fix/store:vstore"); else memory->create(astore,nrow,ncol,"fix/store:astore"); memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf"); - - // printf("AAA HOW GET HERE\n"); } /* ---------------------------------------------------------------------- diff --git a/src/info.cpp b/src/info.cpp index 65c0cd9b53dcb4f480b54d4095752b9179546a6b..748354e8784aeda7a28d347e896ab3b53d8c56e1 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -259,14 +259,35 @@ void Info::command(int narg, char **arg) fprintf(out,"Printed on %s\n",ctime(&now)); if (flags & CONFIG) { - - fprintf(out,"\nLAMMPS version: %s / %s\n", + fprintf(out,"\nLAMMPS version: %s / %s\n\n", universe->version, universe->num_ver); fprintf(out,"sizeof(smallint): %3d-bit\n",(int)sizeof(smallint)*8); fprintf(out,"sizeof(imageint): %3d-bit\n",(int)sizeof(imageint)*8); fprintf(out,"sizeof(tagint): %3d-bit\n",(int)sizeof(tagint)*8); fprintf(out,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8); + fputs("\nActive compile time flags:\n\n",out); + if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out); + if (has_png_support()) fputs("-DLAMMPS_PNG\n",out); + if (has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",out); + if (has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",out); + if (has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",out); + + const char *pkg; + int ncword, ncline = 0; + + fputs("\nInstalled packages:\n\n",out); + for (int i = 0; NULL != (pkg = lmp->installed_packages[i]); ++i) { + ncword = strlen(pkg); + if (ncline + ncword > 78) { + ncline = 0; + fputs("\n",out); + } + fprintf(out,"%s ",pkg); + ncline += ncword + 1; + } + fputs("\n",out); + #if defined(_WIN32) DWORD fullversion,majorv,minorv,buildv=0; @@ -1129,7 +1150,7 @@ static void print_columns(FILE* fp, vector & styles) } } -bool Info::has_gzip_support() const { +bool Info::has_gzip_support() { #ifdef LAMMPS_GZIP return true; #else @@ -1137,7 +1158,7 @@ bool Info::has_gzip_support() const { #endif } -bool Info::has_png_support() const { +bool Info::has_png_support() { #ifdef LAMMPS_PNG return true; #else @@ -1145,7 +1166,7 @@ bool Info::has_png_support() const { #endif } -bool Info::has_jpeg_support() const { +bool Info::has_jpeg_support() { #ifdef LAMMPS_JPEG return true; #else @@ -1153,7 +1174,7 @@ bool Info::has_jpeg_support() const { #endif } -bool Info::has_ffmpeg_support() const { +bool Info::has_ffmpeg_support() { #ifdef LAMMPS_FFMPEG return true; #else @@ -1161,7 +1182,7 @@ bool Info::has_ffmpeg_support() const { #endif } -bool Info::has_exceptions() const { +bool Info::has_exceptions() { #ifdef LAMMPS_EXCEPTIONS return true; #else @@ -1169,6 +1190,15 @@ bool Info::has_exceptions() const { #endif } +bool Info::has_package(const char * package_name) { + for(int i = 0; LAMMPS::installed_packages[i] != NULL; ++i) { + if(strcmp(package_name, LAMMPS::installed_packages[i]) == 0) { + return true; + } + } + return false; +} + /* ---------------------------------------------------------------------- */ char **Info::get_variable_names(int &num) { diff --git a/src/info.h b/src/info.h index fb7ca58c4711dede0b0475114b59419762dbe880..058400df781935fcc6dd7b6165d8de6808a25752 100644 --- a/src/info.h +++ b/src/info.h @@ -33,11 +33,12 @@ class Info : protected Pointers { bool is_defined(const char *, const char *); bool is_available(const char *, const char *); - bool has_gzip_support() const; - bool has_png_support() const; - bool has_jpeg_support() const; - bool has_ffmpeg_support() const; - bool has_exceptions() const; + static bool has_gzip_support(); + static bool has_png_support(); + static bool has_jpeg_support(); + static bool has_ffmpeg_support(); + static bool has_exceptions(); + static bool has_package(const char * package_name); char **get_variable_names(int &num); diff --git a/src/input.cpp b/src/input.cpp index b83a3683e4a3eae3984e842f55f33e672471fd85..f41c8458eae18e2b3200decaa69b0ff5c8b4fe22 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -497,7 +497,7 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) beyond = ptr + strlen(var) + 3; value = variable->retrieve(var); - // immediate variable between parenthesis, e.g. $(1/2) + // immediate variable between parenthesis, e.g. $(1/3) or $(1/3:%.6g) } else if (*(ptr+1) == '(') { var = ptr+2; @@ -516,10 +516,20 @@ void Input::substitute(char *&str, char *&str2, int &max, int &max2, int flag) if (var[i] == '\0') error->one(FLERR,"Invalid immediate variable"); var[i] = '\0'; beyond = ptr + strlen(var) + 3; - sprintf(immediate,"%.20g",variable->compute_equal(var)); + + // check if an inline format specifier was appended with a colon + + char fmtstr[64] = "%.20g"; + char *fmtflag; + if ((fmtflag=strrchr(var, ':')) && (fmtflag[1]=='%')) { + strncpy(fmtstr,&fmtflag[1],sizeof(fmtstr)-1); + *fmtflag='\0'; + } + + sprintf(immediate,fmtstr,variable->compute_equal(var)); value = immediate; - // single character variable name, e.g. $a + // single character variable name, e.g. $a } else { var = ptr; diff --git a/src/lammps.cpp b/src/lammps.cpp index d25d5473e80ecfccdfce8b8aa7f9748da9f34494..b73b62537f02a3bfbd8d205b997d3f19eb9f445d 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -31,6 +31,7 @@ #include "style_region.h" #include "universe.h" #include "input.h" +#include "info.h" #include "atom.h" #include "update.h" #include "neighbor.h" @@ -50,6 +51,8 @@ #include "version.h" #include "error.h" +#include "lmpinstalledpkgs.h" + using namespace LAMMPS_NS; static void print_style(FILE *fp, const char *str, int &pos); @@ -827,7 +830,9 @@ void LAMMPS::help() "-var varname value : set index style variable (-v)\n\n", exename); - fprintf(fp,"List of style options included in this LAMMPS executable\n\n"); + + print_config(fp); + fprintf(fp,"List of individual style options included in this LAMMPS executable\n\n"); int pos = 80; fprintf(fp,"* Atom styles:\n"); @@ -978,3 +983,28 @@ void print_style(FILE *fp, const char *str, int &pos) pos += 80; } } + +void LAMMPS::print_config(FILE *fp) +{ + const char *pkg; + int ncword, ncline = 0; + + fputs("Active compile time flags:\n\n",fp); + if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp); + if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp); + if (Info::has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",fp); + if (Info::has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",fp); + if (Info::has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",fp); + + fputs("\nInstalled packages:\n\n",fp); + for (int i = 0; NULL != (pkg = installed_packages[i]); ++i) { + ncword = strlen(pkg); + if (ncline + ncword > 78) { + ncline = 0; + fputs("\n",fp); + } + fprintf(fp,"%s ",pkg); + ncline += ncword + 1; + } + fputs("\n\n",fp); +} diff --git a/src/lammps.h b/src/lammps.h index 1323dcccc810a29634d7d6348844925daf34004a..b2c867347108edee9814906e42185db56a9a21f9 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -59,12 +59,15 @@ class LAMMPS { class CiteMe *citeme; // citation info + static const char * installed_packages[]; + LAMMPS(int, char **, MPI_Comm); ~LAMMPS(); void create(); void post_create(); void init(); void destroy(); + void print_config(FILE *); // print compile time settings private: void help(); diff --git a/src/library.cpp b/src/library.cpp index 0162c560cea7e21b66cc759a481aae6420c86d51..13e07568667d6319bd52b2c9fe6166decf292953 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -38,6 +38,7 @@ #include "memory.h" #include "error.h" #include "force.h" +#include "info.h" using namespace LAMMPS_NS; @@ -1522,6 +1523,56 @@ void lammps_create_atoms(void *ptr, int n, tagint *id, int *type, END_CAPTURE } +// ---------------------------------------------------------------------- +// library API functions for accessing LAMMPS configuration +// ---------------------------------------------------------------------- + +int lammps_config_has_package(char * package_name) { + return Info::has_package(package_name); +} + +int lammps_config_package_count() { + int i = 0; + while(LAMMPS::installed_packages[i] != NULL) { + ++i; + } + return i; +} + +int lammps_config_package_name(int index, char * buffer, int max_size) { + int i = 0; + while(LAMMPS::installed_packages[i] != NULL && i < index) { + ++i; + } + + if(LAMMPS::installed_packages[i] != NULL) { + strncpy(buffer, LAMMPS::installed_packages[i], max_size); + return true; + } + + return false; +} + +int lammps_config_has_gzip_support() { + return Info::has_gzip_support(); +} + +int lammps_config_has_png_support() { + return Info::has_png_support(); +} + +int lammps_config_has_jpeg_support() { + return Info::has_jpeg_support(); +} + +int lammps_config_has_ffmpeg_support() { + return Info::has_ffmpeg_support(); +} + +int lammps_config_has_exceptions() { + return Info::has_exceptions(); +} + // ---------------------------------------------------------------------- // library API functions for error handling // ---------------------------------------------------------------------- diff --git a/src/library.h b/src/library.h index 7c21b98daee2894ee4191788eefd94ee80f146dc..82071f673b6755191f5a5e58a99cd6acb24ff4b5 100644 --- a/src/library.h +++ b/src/library.h @@ -55,6 +55,15 @@ void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *); void lammps_scatter_atoms(void *, char *, int, int, void *); void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *); +int lammps_config_has_package(char * package_name); +int lammps_config_package_count(); +int lammps_config_package_name(int index, char * buffer, int max_size); +int lammps_config_has_gzip_support(); +int lammps_config_has_png_support(); +int lammps_config_has_jpeg_support(); +int lammps_config_has_ffmpeg_support(); +int lammps_config_has_exceptions(); + // lammps_create_atoms() takes tagint and imageint as args // ifdef insures they are compatible with rest of LAMMPS // caller must match to how LAMMPS library is built diff --git a/src/molecule.cpp b/src/molecule.cpp index 56e56dab2cd16ef45c9c6068161c29a4815d51ca..dfbe3e1e08e07527096f6db6d4de80557c370415 100644 --- a/src/molecule.cpp +++ b/src/molecule.cpp @@ -52,6 +52,9 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) : if (index >= narg) error->all(FLERR,"Illegal molecule command"); + if (domain->box_exist == 0) + error->all(FLERR,"Molecule command before simulation box is defined"); + int n = strlen(arg[0]) + 1; id = new char[n]; strcpy(id,arg[0]); @@ -684,7 +687,7 @@ void Molecule::types(char *line) } for (int i = 0; i < natoms; i++) - if (type[i] <= 0) + if (type[i] <= 0 || type[i] > atom->ntypes) error->all(FLERR,"Invalid atom type in molecule file"); for (int i = 0; i < natoms; i++) @@ -771,10 +774,10 @@ void Molecule::bonds(int flag, char *line) error->all(FLERR,"Invalid Bonds section in molecule file"); itype += boffset; - if (atom1 <= 0 || atom1 > natoms || - atom2 <= 0 || atom2 > natoms) + if ((atom1 <= 0) || (atom1 > natoms) || + (atom2 <= 0) || (atom2 > natoms) || (atom1 == atom2)) error->one(FLERR,"Invalid atom ID in Bonds section of molecule file"); - if (itype <= 0) + if (itype <= 0 || itype > atom->nbondtypes) error->one(FLERR,"Invalid bond type in Bonds section of molecule file"); if (flag) { @@ -829,11 +832,12 @@ void Molecule::angles(int flag, char *line) error->all(FLERR,"Invalid Angles section in molecule file"); itype += aoffset; - if (atom1 <= 0 || atom1 > natoms || - atom2 <= 0 || atom2 > natoms || - atom3 <= 0 || atom3 > natoms) + if ((atom1 <= 0) || (atom1 > natoms) || + (atom2 <= 0) || (atom2 > natoms) || + (atom3 <= 0) || (atom3 > natoms) || + (atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3)) error->one(FLERR,"Invalid atom ID in Angles section of molecule file"); - if (itype <= 0) + if (itype <= 0 || itype > atom->nangletypes) error->one(FLERR,"Invalid angle type in Angles section of molecule file"); if (flag) { @@ -902,13 +906,15 @@ void Molecule::dihedrals(int flag, char *line) error->all(FLERR,"Invalid Dihedrals section in molecule file"); itype += doffset; - if (atom1 <= 0 || atom1 > natoms || - atom2 <= 0 || atom2 > natoms || - atom3 <= 0 || atom3 > natoms || - atom4 <= 0 || atom4 > natoms) + if ((atom1 <= 0) || (atom1 > natoms) || + (atom2 <= 0) || (atom2 > natoms) || + (atom3 <= 0) || (atom3 > natoms) || + (atom4 <= 0) || (atom4 > natoms) || + (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || + (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) error->one(FLERR, "Invalid atom ID in dihedrals section of molecule file"); - if (itype <= 0) + if (itype <= 0 || itype > atom->ndihedraltypes) error->one(FLERR, "Invalid dihedral type in dihedrals section of molecule file"); @@ -989,13 +995,15 @@ void Molecule::impropers(int flag, char *line) error->all(FLERR,"Invalid Impropers section in molecule file"); itype += ioffset; - if (atom1 <= 0 || atom1 > natoms || - atom2 <= 0 || atom2 > natoms || - atom3 <= 0 || atom3 > natoms || - atom4 <= 0 || atom4 > natoms) + if ((atom1 <= 0) || (atom1 > natoms) || + (atom2 <= 0) || (atom2 > natoms) || + (atom3 <= 0) || (atom3 > natoms) || + (atom4 <= 0) || (atom4 > natoms) || + (atom1 == atom2) || (atom1 == atom3) || (atom1 == atom4) || + (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) error->one(FLERR, "Invalid atom ID in impropers section of molecule file"); - if (itype <= 0) + if (itype <= 0 || itype > atom->nimpropertypes) error->one(FLERR, "Invalid improper type in impropers section of molecule file"); diff --git a/src/pair.cpp b/src/pair.cpp index 73dbb9428e37939a7a407ad70d8b9ea516a8a133..5c308cc7ce51e840713abfaeacdcbd8190ce95e9 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -693,9 +693,19 @@ void Pair::compute_dummy(int eflag, int vflag) } /* ---------------------------------------------------------------------- */ + void Pair::read_restart(FILE *) { - error->all(FLERR,"BUG: restartinfo=1 but no restart support in pair style"); + if (comm->me == 0) + error->warning(FLERR,"Pair style restartinfo set but has no restart support"); +} + +/* ---------------------------------------------------------------------- */ + +void Pair::write_restart(FILE *) +{ + if (comm->me == 0) + error->warning(FLERR,"Pair style restartinfo set but has no restart support"); } /* ------------------------------------------------------------------- diff --git a/src/pair.h b/src/pair.h index 26488103a05e2044d537f31dcf8a4b8b2fa0073b..844bc0cdc75c12983d98da16273b70c1257044a8 100644 --- a/src/pair.h +++ b/src/pair.h @@ -157,7 +157,7 @@ class Pair : protected Pointers { virtual void free_tables(); virtual void free_disp_tables(); - virtual void write_restart(FILE *) {} + virtual void write_restart(FILE *); virtual void read_restart(FILE *); virtual void write_restart_settings(FILE *) {} virtual void read_restart_settings(FILE *) {} @@ -303,7 +303,9 @@ No kspace style is defined. E: BUG: restartinfo=1 but no restart support in pair style -UNDOCUMENTED +The pair style has a bug, where it does not support reading +and writing information to a restart file, but does not set +the member variable restartinfo to 0 as required in that case. E: Cannot yet use compute tally with Kokkos diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 1164de6faa91acea7ebc08b985d317618c723e9f..7d8e6ca3955c0d547e354cde414ba3838864cf18 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -62,7 +62,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, IMAGEINT,BOUNDMIN,TIMESTEP, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, - COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR}; + COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, + EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; #define LB_FACTOR 1.1 @@ -914,6 +916,17 @@ void ReadRestart::header(int incompatible) } else if (flag == COMM_VEL) { comm->ghost_velocity = read_int(); + } else if (flag == EXTRA_BOND_PER_ATOM) { + atom->extra_bond_per_atom = read_int(); + } else if (flag == EXTRA_ANGLE_PER_ATOM) { + atom->extra_angle_per_atom = read_int(); + } else if (flag == EXTRA_DIHEDRAL_PER_ATOM) { + atom->extra_dihedral_per_atom = read_int(); + } else if (flag == EXTRA_IMPROPER_PER_ATOM) { + atom->extra_improper_per_atom = read_int(); + } else if (flag == EXTRA_SPECIAL_PER_ATOM) { + force->special_extra = read_int(); + } else error->all(FLERR,"Invalid flag in header section of restart file"); flag = read_int(); diff --git a/src/reset_ids.cpp b/src/reset_ids.cpp index 8a33cd535bf9d60746b90910e370145dd1f31113..fd898bd3ab63db79f7b45e659ae346e6d19bdab9 100644 --- a/src/reset_ids.cpp +++ b/src/reset_ids.cpp @@ -16,6 +16,7 @@ #include "atom_vec.h" #include "domain.h" #include "comm.h" +#include "special.h" #include "memory.h" #include "error.h" @@ -44,7 +45,7 @@ void ResetIDs::command(int narg, char **arg) } // create an atom map if one doesn't exist already - + int mapflag = 0; if (atom->map_style == 0) { mapflag = 1; @@ -93,7 +94,7 @@ void ResetIDs::command(int narg, char **arg) // forward_comm_array acquires new IDs for ghost atoms double **newIDs; - memory->create(newIDs,nall,1,"reset_ids:newIDs"); + memory->create(newIDs,nall,1,"reset_ids:newIDs"); for (int i = 0; i < nlocal; i++) { newIDs[i][0] = tag[i]; @@ -105,7 +106,7 @@ void ResetIDs::command(int narg, char **arg) // loop over bonds, angles, etc and reset IDs in stored topology arrays // only necessary for molecular = 1, not molecular = 2 // badcount = atom IDs that could not be found - + int badcount = 0; if (atom->molecular == 1) { @@ -232,8 +233,15 @@ void ResetIDs::command(int narg, char **arg) atom->map_init(); atom->map_set(); + // need to update exclusions with new atom IDs + + if (atom->molecular == 1) { + Special special(lmp); + special.build(); + } + // delete temporary atom map - + if (mapflag) { atom->map_delete(); atom->map_style = 0; diff --git a/src/set.cpp b/src/set.cpp index f741760ed56c56ab85bb42c29015a4db87a07228..7eca4e9a9c64c0db21618933d8747d903441cea6 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -44,10 +44,11 @@ using namespace MathConst; enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT}; enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI, - DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,THETA,THETA_RANDOM,ANGMOM,OMEGA, + DIPOLE,DIPOLE_RANDOM,SPIN,SPIN_RANDOM,QUAT,QUAT_RANDOM, + THETA,THETA_RANDOM,ANGMOM,OMEGA, DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER, MESO_E,MESO_CV,MESO_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY, - SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME}; + SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME,VX,VY,VZ}; #define BIG INT_MAX @@ -140,6 +141,27 @@ void Set::command(int narg, char **arg) set(Z); iarg += 2; + } else if (strcmp(arg[iarg],"vx") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VX); + iarg += 2; + + } else if (strcmp(arg[iarg],"vy") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VY); + iarg += 2; + + } else if (strcmp(arg[iarg],"vz") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + set(VZ); + iarg += 2; + } else if (strcmp(arg[iarg],"charge") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -215,6 +237,34 @@ void Set::command(int narg, char **arg) setrandom(DIPOLE_RANDOM); iarg += 3; + } else if (strcmp(arg[iarg],"spin") == 0) { + if (iarg+4 > narg) error->all(FLERR,"Illegal set command"); + if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); + else dvalue = force->numeric(FLERR,arg[iarg+1]); + if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) varparse(arg[iarg+2],2); + else xvalue = force->numeric(FLERR,arg[iarg+2]); + if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) varparse(arg[iarg+3],3); + else yvalue = force->numeric(FLERR,arg[iarg+3]); + if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) varparse(arg[iarg+4],4); + else zvalue = force->numeric(FLERR,arg[iarg+4]); + if (!atom->sp_flag) + error->all(FLERR,"Cannot set this attribute for this atom style"); + set(SPIN); + iarg += 5; + + } else if (strcmp(arg[iarg],"spin/random") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal set command"); + ivalue = force->inumeric(FLERR,arg[iarg+1]); + dvalue = force->numeric(FLERR,arg[iarg+2]); + if (!atom->sp_flag) + error->all(FLERR,"Cannot set this attribute for this atom style"); + if (ivalue <= 0) + error->all(FLERR,"Invalid random number seed in set command"); + if (dvalue <= 0.0) + error->all(FLERR,"Invalid dipole length in set command"); + setrandom(SPIN_RANDOM); + iarg += 3; + } else if (strcmp(arg[iarg],"quat") == 0) { if (iarg+5 > narg) error->all(FLERR,"Illegal set command"); if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1); @@ -703,6 +753,9 @@ void Set::set(int keyword) else if (keyword == X) atom->x[i][0] = dvalue; else if (keyword == Y) atom->x[i][1] = dvalue; else if (keyword == Z) atom->x[i][2] = dvalue; + else if (keyword == VX) atom->v[i][0] = dvalue; + else if (keyword == VY) atom->v[i][1] = dvalue; + else if (keyword == VZ) atom->v[i][2] = dvalue; else if (keyword == CHARGE) atom->q[i] = dvalue; else if (keyword == MASS) { if (dvalue <= 0.0) error->one(FLERR,"Invalid mass in set command"); @@ -821,6 +874,18 @@ void Set::set(int keyword) mu[i][2]*mu[i][2]); } + // set magnetic moments + + else if (keyword == SPIN) { + double **sp = atom->sp; + double inorm = 1.0/sqrt(xvalue*xvalue+yvalue*yvalue+zvalue*zvalue); + sp[i][0] = inorm*xvalue; + sp[i][1] = inorm*yvalue; + sp[i][2] = inorm*zvalue; + sp[i][3] = dvalue; + } + + // set quaternion orientation of ellipsoid or tri or body particle // set quaternion orientation of ellipsoid or tri or body particle // enforce quat rotation vector in z dir for 2d systems @@ -981,6 +1046,48 @@ void Set::setrandom(int keyword) } } + + // set spin moments to random orientations in 3d or 2d + // spin length is fixed to unity + + } else if (keyword == SPIN_RANDOM) { + double **sp = atom->sp; + int nlocal = atom->nlocal; + + double sp_sq,scale; + + if (domain->dimension == 3) { + for (i = 0; i < nlocal; i++) + if (select[i]) { + random->reset(seed,x[i]); + sp[i][0] = random->uniform() - 0.5; + sp[i][1] = random->uniform() - 0.5; + sp[i][2] = random->uniform() - 0.5; + sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1] + sp[i][2]*sp[i][2]; + scale = 1.0/sqrt(sp_sq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][2] *= scale; + sp[i][3] = dvalue; + count++; + } + + } else { + for (i = 0; i < nlocal; i++) + if (select[i]) { + random->reset(seed,x[i]); + sp[i][0] = random->uniform() - 0.5; + sp[i][1] = random->uniform() - 0.5; + sp[i][2] = 0.0; + sp_sq = sp[i][0]*sp[i][0] + sp[i][1]*sp[i][1]; + scale = 1.0/sqrt(sp_sq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][3] = dvalue; + count++; + } + } + // set quaternions to random orientations in 3d and 2d } else if (keyword == QUAT_RANDOM) { diff --git a/src/variable.cpp b/src/variable.cpp index b5c19a48439cd2342273e7af4b7d21936ffe9bd2..f005221400509f76fd5887f0323fa11cc8f30a32 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -284,12 +284,21 @@ void Variable::set(int narg, char **arg) } else if (strcmp(arg[1],"string") == 0) { if (narg != 3) error->all(FLERR,"Illegal variable command"); + + int maxcopy = strlen(arg[2]) + 1; + int maxwork = maxcopy; + char *scopy = new char[maxcopy]; + char *work = new char[maxwork]; + strcpy(scopy,arg[2]); + input->substitute(scopy,work,maxcopy,maxwork,1); + delete [] work; + int ivar = find(arg[0]); if (ivar >= 0) { if (style[ivar] != STRING) error->all(FLERR,"Cannot redefine variable as a different style"); delete [] data[ivar][0]; - copy(1,&arg[2],data[ivar]); + copy(1,&scopy,data[ivar]); replaceflag = 1; } else { if (nvar == maxvar) grow(); @@ -298,8 +307,9 @@ void Variable::set(int narg, char **arg) which[nvar] = 0; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; - copy(1,&arg[2],data[nvar]); + copy(1,&scopy,data[nvar]); } + delete [] scopy; // GETENV // remove pre-existing var if also style GETENV (allows it to be reset) @@ -1566,7 +1576,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) newtree->nextra = 0; treestack[ntreestack++] = newtree; - } else print_var_error(FLERR,"Mismatched compute in variable formula",ivar); + } else print_var_error(FLERR, + "Mismatched compute in variable formula",ivar); // ---------------- // fix @@ -1574,7 +1585,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (strncmp(word,"f_",2) == 0 || strncmp(word,"F_",2) == 0) { if (domain->box_exist == 0) - print_var_error(FLERR,"Variable evaluation before simulation box is defined",ivar); + print_var_error(FLERR,"Variable evaluation before " + "simulation box is defined",ivar); // uppercase used to force access of // global vector vs global scalar, and global array vs global vector @@ -1657,11 +1669,14 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > fix->size_array_rows && fix->size_array_rows_variable == 0) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "accessed out-of-range",ivar); if (index2 > fix->size_array_cols) - print_var_error(FLERR,"Variable formula fix array is accessed out-of-range",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at a compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at a " + "compatible time",ivar); value1 = fix->compute_array(index1-1,index2-1); if (tree) { @@ -1678,13 +1693,17 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) } else if (nbracket == 0 && fix->vector_flag) { if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); if (tree == NULL) - print_var_error(FLERR,"Fix global vector in ""equal-style variable formula",ivar); + print_var_error(FLERR,"Fix global vector in " + "equal-style variable formula",ivar); if (treetype == ATOM) - print_var_error(FLERR,"Fix global vector in ""atom-style variable formula",ivar); + print_var_error(FLERR,"Fix global vector in " + "atom-style variable formula",ivar); if (fix->size_vector == 0) - print_var_error(FLERR,"Variable formula fix vector is zero length",ivar); + print_var_error(FLERR,"Variable formula " + "fix vector is zero length",ivar); int nvec = fix->size_vector; double *vec; @@ -1716,7 +1735,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) print_var_error(FLERR,"Fix global vector in " "atom-style variable formula",ivar); if (fix->size_array_rows == 0) - print_var_error(FLERR,"Variable formula fix array is zero length",ivar); + print_var_error(FLERR,"Variable formula fix array is " + "zero length",ivar); int nvec = fix->size_array_rows; double *vec; @@ -1775,10 +1795,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) fix->size_peratom_cols == 0) { if (tree == NULL) - print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar); + print_var_error(FLERR,"Per-atom fix in " + "equal-style variable formula",ivar); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); Tree *newtree = new Tree(); newtree->type = ATOMARRAY; @@ -1795,13 +1817,15 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) fix->size_peratom_cols > 0) { if (tree == NULL) - print_var_error(FLERR,"Per-atom fix in equal-style variable formula",ivar); + print_var_error(FLERR,"Per-atom fix in " + "equal-style variable formula",ivar); if (index1 > fix->size_peratom_cols) print_var_error(FLERR,"Variable formula fix array " "is accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); Tree *newtree = new Tree(); newtree->type = ATOMARRAY; @@ -1868,7 +1892,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) char *var = retrieve(word+2); if (var == NULL) - print_var_error(FLERR,"Invalid variable evaluation in variable formula",ivar); + print_var_error(FLERR,"Invalid variable evaluation in " + "variable formula",ivar); if (tree) { Tree *newtree = new Tree(); newtree->type = VALUE; @@ -1967,7 +1992,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) double *vec; int nvec = compute_vector(ivar,&vec); if (index <= 0 || index > nvec) - print_var_error(FLERR,"Invalid index into vector-style variable",ivar); + print_var_error(FLERR,"Invalid index into " + "vector-style variable",ivar); int m = index; // convert from tagint to int if (tree) { @@ -1979,7 +2005,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) treestack[ntreestack++] = newtree; } else argstack[nargstack++] = vec[m-1]; - } else print_var_error(FLERR,"Mismatched variable in variable formula",ivar); + } else print_var_error(FLERR,"Mismatched variable in " + "variable formula",ivar); // ---------------- // math/group/special function or atom value/vector or @@ -2184,7 +2211,8 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (value2 == 0.0) argstack[nargstack++] = 1.0; else if ((value1 == 0.0) && (value2 < 0.0)) - print_var_error(FLERR,"Invalid power expression in variable formula",ivar); + print_var_error(FLERR,"Invalid power expression in " + "variable formula",ivar); else argstack[nargstack++] = pow(value1,value2); } else if (opprevious == UNARY) { argstack[nargstack++] = -value2; @@ -3358,7 +3386,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = LN; else { if (value1 <= 0.0) - print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar); + print_var_error(FLERR,"Log of zero/negative value in " + "variable formula",ivar); argstack[nargstack++] = log(value1); } } else if (strcmp(word,"log") == 0) { @@ -3367,7 +3396,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = LOG; else { if (value1 <= 0.0) - print_var_error(FLERR,"Log of zero/negative value in variable formula",ivar); + print_var_error(FLERR,"Log of zero/negative value in " + "variable formula",ivar); argstack[nargstack++] = log10(value1); } } else if (strcmp(word,"abs") == 0) { @@ -3472,7 +3502,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 2) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use ramp in " + "variable formula between runs",ivar); if (tree) newtree->type = RAMP; else { double delta = update->ntimestep - update->beginstep; @@ -3607,7 +3638,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 2) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use vdisplace in " + "variable formula between runs",ivar); if (tree) newtree->type = VDISPLACE; else { double delta = update->ntimestep - update->beginstep; @@ -3619,7 +3651,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 3) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use swiggle in " + "variable formula between runs",ivar); if (tree) newtree->type = CWIGGLE; else { if (values[0] == 0.0) @@ -3634,7 +3667,8 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (narg != 3) print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Cannot use cwiggle in " + "variable formula between runs",ivar); if (tree) newtree->type = CWIGGLE; else { if (values[0] == 0.0) @@ -3699,7 +3733,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, if (strcmp(word,"count") == 0) { if (narg == 1) value = group->count(igroup); - else if (narg == 2) value = group->count(igroup,region_function(args[1],ivar)); + else if (narg == 2) + value = group->count(igroup,region_function(args[1],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); } else if (strcmp(word,"mass") == 0) { @@ -3709,7 +3744,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"charge") == 0) { if (narg == 1) value = group->charge(igroup); - else if (narg == 2) value = group->charge(igroup,region_function(args[1],ivar)); + else if (narg == 2) + value = group->charge(igroup,region_function(args[1],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); } else if (strcmp(word,"xcm") == 0) { @@ -3722,7 +3758,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, int iregion = region_function(args[2],ivar); double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = xcm[0]; else if (strcmp(args[1],"y") == 0) value = xcm[1]; else if (strcmp(args[1],"z") == 0) value = xcm[2]; @@ -3738,7 +3775,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, int iregion = region_function(args[2],ivar); double masstotal = group->mass(igroup,iregion); group->vcm(igroup,masstotal,vcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = vcm[0]; else if (strcmp(args[1],"y") == 0) value = vcm[1]; else if (strcmp(args[1],"z") == 0) value = vcm[2]; @@ -3757,7 +3795,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"bound") == 0) { double minmax[6]; if (narg == 2) group->bounds(igroup,minmax); - else if (narg == 3) group->bounds(igroup,minmax,region_function(args[2],ivar)); + else if (narg == 3) + group->bounds(igroup,minmax,region_function(args[2],ivar)); else print_var_error(FLERR,"Invalid group function in variable formula",ivar); if (strcmp(args[1],"xmin") == 0) value = minmax[0]; else if (strcmp(args[1],"xmax") == 0) value = minmax[1]; @@ -3779,7 +3818,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); value = group->gyration(igroup,masstotal,xcm,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); } else if (strcmp(word,"ke") == 0) { if (narg == 1) value = group->ke(igroup); @@ -3798,7 +3838,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->angmom(igroup,xcm,lmom,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = lmom[0]; else if (strcmp(args[1],"y") == 0) value = lmom[1]; else if (strcmp(args[1],"z") == 0) value = lmom[2]; @@ -3816,7 +3857,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->torque(igroup,xcm,tq,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = tq[0]; else if (strcmp(args[1],"y") == 0) value = tq[1]; else if (strcmp(args[1],"z") == 0) value = tq[2]; @@ -3834,7 +3876,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, double masstotal = group->mass(igroup,iregion); group->xcm(igroup,masstotal,xcm,iregion); group->inertia(igroup,xcm,inertia,iregion); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"xx") == 0) value = inertia[0][0]; else if (strcmp(args[1],"yy") == 0) value = inertia[1][1]; else if (strcmp(args[1],"zz") == 0) value = inertia[2][2]; @@ -3859,7 +3902,8 @@ int Variable::group_function(char *word, char *contents, Tree **tree, group->angmom(igroup,xcm,angmom,iregion); group->inertia(igroup,xcm,inertia,iregion); group->omega(angmom,inertia,omega); - } else print_var_error(FLERR,"Invalid group function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid group function in " + "variable formula",ivar); if (strcmp(args[1],"x") == 0) value = omega[0]; else if (strcmp(args[1],"y") == 0) value = omega[1]; else if (strcmp(args[1],"z") == 0) value = omega[2]; @@ -3914,7 +3958,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, Tree **treestack, int &ntreestack, double *argstack, int &nargstack, int ivar) { - double value,xvalue,sx,sy,sxx,sxy; + bigint sx,sxx; + double value,xvalue,sy,sxy; // word not a match to any special function @@ -4010,11 +4055,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else index = 0; int ifix = modify->find_fix(&args[0][2]); - if (ifix < 0) print_var_error(FLERR,"Invalid fix ID in variable formula",ivar); + if (ifix < 0) + print_var_error(FLERR,"Invalid fix ID in variable formula",ivar); fix = modify->fix[ifix]; if (index == 0 && fix->vector_flag) { if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); nvec = fix->size_vector; nstride = 1; } else if (index && fix->array_flag) { @@ -4022,7 +4069,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, print_var_error(FLERR,"Variable formula fix array " "is accessed out-of-range",ivar); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) - print_var_error(FLERR,"Fix in variable not computed at compatible time",ivar); + print_var_error(FLERR,"Fix in variable not computed at " + "compatible time",ivar); nvec = fix->size_array_rows; nstride = fix->size_array_cols; } else print_var_error(FLERR,"Mismatched fix in variable formula",ivar); @@ -4038,10 +4086,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else index = 0; if (index) - print_var_error(FLERR,"Invalid special function in variable formula",ivar); + print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); ivar = find(&args[0][2]); if (ivar < 0) - print_var_error(FLERR,"Invalid special function in variable formula",ivar); + print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); if (style[ivar] != VECTOR) print_var_error(FLERR,"Mis-matched special function variable " "in variable formula",ivar); @@ -4052,12 +4102,16 @@ int Variable::special_function(char *word, char *contents, Tree **tree, nvec = compute_vector(ivar,&vec); nstride = 1; - } else print_var_error(FLERR,"Invalid special function in variable formula",ivar); + } else print_var_error(FLERR,"Invalid special function in " + "variable formula",ivar); value = 0.0; - if (method == SLOPE) sx = sy = sxx = sxy = 0.0; - if (method == XMIN) value = BIG; - if (method == XMAX) value = -BIG; + if (method == SLOPE) { + sx = sxx = 0; + sy = sxy = 0.0; + } + else if (method == XMIN) value = BIG; + else if (method == XMAX) value = -BIG; if (compute) { double *vec; @@ -4074,12 +4128,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += vec[j]; else if (method == TRAP) value += vec[j]; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += vec[j]; - sxx += xvalue*xvalue; - sxy += xvalue*vec[j]; + sxx += i*i; + sxy += i*vec[j]; } j += nstride; } @@ -4097,12 +4149,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += one; else if (method == TRAP) value += one; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += one; - sxx += xvalue*xvalue; - sxy += xvalue*one; + sxx += i*i; + sxy += i*one; } } if (method == TRAP) { @@ -4124,12 +4174,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree, else if (method == AVE) value += one; else if (method == TRAP) value += one; else if (method == SLOPE) { - if (nvec > 1) xvalue = (double) i / (nvec-1); - else xvalue = 0.0; - sx += xvalue; + sx += i; sy += one; - sxx += xvalue*xvalue; - sxy += xvalue*one; + sxx += i*i; + sxy += i*one; } } if (method == TRAP) value -= 0.5*vec[0] + 0.5*vec[nvec-1]; @@ -4138,9 +4186,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree, if (method == AVE) value /= nvec; if (method == SLOPE) { - double numerator = sxy - sx*sy; - double denominator = sxx - sx*sx; - if (denominator != 0.0) value = numerator/denominator / nvec; + double numerator = nvec*sxy - sx*sy; + double denominator = nvec*sxx - sx*sx; + if (denominator != 0.0) value = numerator/denominator; else value = BIG; } @@ -4159,7 +4207,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"gmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Gmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Gmask function in equal-style " + "variable formula",ivar); if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4176,7 +4225,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"rmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Rmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Rmask function in equal-style " + "variable formula",ivar); if (narg != 1) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4192,7 +4242,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"grmask") == 0) { if (tree == NULL) - print_var_error(FLERR,"Grmask function in equal-style variable formula",ivar); + print_var_error(FLERR,"Grmask function in equal-style " + "variable formula",ivar); if (narg != 2) print_var_error(FLERR,"Invalid special function in variable formula",ivar); @@ -4218,7 +4269,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, int ivar = find(args[0]); if (ivar < 0) - print_var_error(FLERR,"Variable ID in variable formula does not exist",ivar); + print_var_error(FLERR,"Variable ID in " + "variable formula does not exist",ivar); // SCALARFILE has single current value, read next one // save value in tree or on argstack @@ -4243,7 +4295,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (style[ivar] == ATOMFILE) { if (tree == NULL) - print_var_error(FLERR,"Atomfile variable in equal-style variable formula",ivar); + print_var_error(FLERR,"Atomfile variable in " + "equal-style variable formula",ivar); double *result; memory->create(result,atom->nlocal,"variable:result"); @@ -4261,11 +4314,13 @@ int Variable::special_function(char *word, char *contents, Tree **tree, newtree->nextra = 0; treestack[ntreestack++] = newtree; - } else print_var_error(FLERR,"Invalid variable style in special function next",ivar); + } else print_var_error(FLERR,"Invalid variable style in " + "special function next",ivar); } else if (strcmp(word,"is_active") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_active() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_active() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_active(args[0],args[1])) ? 1.0 : 0.0; @@ -4283,7 +4338,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"is_available") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_available() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_available() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_available(args[0],args[1])) ? 1.0 : 0.0; @@ -4301,7 +4357,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (strcmp(word,"is_defined") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid is_defined() function in variable formula",ivar); + print_var_error(FLERR,"Invalid is_defined() function in " + "variable formula",ivar); Info info(lmp); value = (info.is_defined(args[0],args[1])) ? 1.0 : 0.0; diff --git a/src/variable.h b/src/variable.h index a74cdba980f4cee3c75486a08706e3c3ba4f96ca..b20eb7e6b93e566f77d5421e820e59eb1a9b79b1 100644 --- a/src/variable.h +++ b/src/variable.h @@ -16,6 +16,7 @@ #include #include "pointers.h" +#include "input.h" namespace LAMMPS_NS { diff --git a/src/version.h b/src/version.h index 981ec8eeb8c8e47627ab4d756be509e7b7fe2872..b95c259dd68c7322ff261a38a925d32eec0aa984 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "11 May 2018" +#define LAMMPS_VERSION "2 Aug 2018" diff --git a/src/write_restart.cpp b/src/write_restart.cpp index 69b731870d0c28fe6f389da0183f1905664a0400..1bfbb382a8c6b835bb315652a91c93c90fd7123d 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -61,7 +61,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT, MULTIPROC,MPIIO,PROCSPERFILE,PERPROC, IMAGEINT,BOUNDMIN,TIMESTEP, ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN, - COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR}; + COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, + EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, + EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM}; /* ---------------------------------------------------------------------- */ @@ -527,6 +529,12 @@ void WriteRestart::header() write_double(COMM_CUTOFF,comm->cutghostuser); write_int(COMM_VEL,comm->ghost_velocity); + write_int(EXTRA_BOND_PER_ATOM,atom->extra_bond_per_atom); + write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom); + write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom); + write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom); + write_int(EXTRA_SPECIAL_PER_ATOM,force->special_extra); + // -1 flag signals end of header int flag = -1; diff --git a/tools/emacs/README.md b/tools/emacs/README.md new file mode 100644 index 0000000000000000000000000000000000000000..75504a7000a0dcb9b5876985fe9ae4fafb63a912 --- /dev/null +++ b/tools/emacs/README.md @@ -0,0 +1,82 @@ +# GNU Emacs Syntax Highlighting + +> Copyright (C) 2010-2018 Aidan Thompson +> Copyright (C) 2018 Rohit Goswami + +The `lammps-mode.el` file provided in this directory will enable syntax +highlighting for the lammps script syntax in GNU Emacs. The groupings of +commands were originally copied from `tools/vim`. + +## Installation +**Requirements: GNU Emacs 24.\*** + +### Obtaining the Package + +#### MELPA + +The easiest installation method is via MELPA and it is advisable to use one of +the many [MELPA installation methods](https://melpa.org/#/getting-started). + +For example, with [use-package](https://github.com/jwiegley/use-package) one can +simply use the following: + +``` emacs-lisp +(use-package lammps-mode) +``` + +#### Manually + +Assuming for some reason you have downloaded the file to `~/.emacs.d/lisp` you +would do the following (kanged [from here](http://ergoemacs.org/emacs/emacs_installing_packages.html)): + +``` emacs-lisp +;; Tell emacs where is your personal elisp lib dir +(add-to-list 'load-path "~/.emacs.d/lisp/") + +;; load the package. +(load "lammps-mode") +``` + +### Autoloading \& Auto-recognition + +To automatically turn on the LAMMPS mode for editing your input scripts, +use the following line as the **first** line of your script: +``` +# -*- lammps -*- +``` + +For automatically switching on the LAMMPS mode based on filename patterns, +e.g. for `in.*` and `*.lmp` files, add the following code to your `.emacs`: + +``` emacs-lisp +(autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t) +(setq auto-mode-alist (append auto-mode-alist + '(("in\\." . lammps-mode)) + '(("\\.lmp\\'" . lammps-mode)) + )) +``` + +## Status + +By far not all commands are included in the syntax file (lammps-mode.el). You +can easily add new ones to the existing classes. + +## Implementation Details + +`lammps-mode` is derived from `shell-script-mode` which provides some basic +syntax highlighting of strings, comments, etc. + +The MELPA recipe used for this package is simply: + +``` emacs-lisp +(lammps-mode :fetcher github :repo "HaoZeke/lammps-mode") +``` + +## Caveats + +* Does not work with Xemacs [See [this comment](https://github.com/lammps/lammps/pull/1022#issuecomment-408871233)] + +## License + +[GNU GPL v2](https://github.com/HaoZeke/lammps-mode/blob/master/LICENSE). +Check the file for more details. diff --git a/tools/emacs/README.txt b/tools/emacs/README.txt deleted file mode 100644 index 8dfc37cb851d3100ec052a7550d9b839f856c146..0000000000000000000000000000000000000000 --- a/tools/emacs/README.txt +++ /dev/null @@ -1,23 +0,0 @@ -=== Emacs Syntax Highlighting === -Created by Aidan Thompson 12/2010 -=============================== - -The lammps.el file provided in this directory will enable syntax -highlighting for the lammps script syntax in emacs. The groupings -of commands were copied from tools/vim. The simulation scripts have to -end on *.lmp or start with in.* (see lammps.el). By far not all -commands are included in the syntax file (lammps.el). -You can easily add new ones to the existing classes. -'lammps-mode' is derived from 'shell-script-mode' which provides -some basic syntax highlighting of strings, comments, etc. - -=To enable the highlighting: -============================ -(0) Create/edit the emacs init file ~/.emacs to contain: - -(load "~/.emacs.d/lammps") - -This file may also be called ~/.emacs.el, or ~/.emacs.d/init.el - -(1) Copy lammps.el to the directory ~/.emacs.d - diff --git a/tools/emacs/lammps.el b/tools/emacs/lammps-mode.el similarity index 73% rename from tools/emacs/lammps.el rename to tools/emacs/lammps-mode.el index d1ebebbbbfe9e9e75ca9c8403f0e9e54719ed515..37e8a32116755ff967380b772c442ef436b88341 100644 --- a/tools/emacs/lammps.el +++ b/tools/emacs/lammps-mode.el @@ -1,7 +1,48 @@ -;; LAMMPS auto-mode +;;; lammps-mode.el --- basic syntax highlighting for LAMMPS files + +;; Copyright (C) 2010-18 Aidan Thompson +;; Copyright (C) 2018 Rohit Goswami + +;; Author: Aidan Thompson +;; Maintainer: Rohit Goswami +;; Created: December 4, 2010 +;; Modified: July 30, 2018 +;; Version: 1.5.0 +;; Keywords: languages, faces +;; Homepage: https://github.com/lammps/lammps/tree/master/tools/emacs +;; Package-Requires: ((emacs "24.4")) + +;; This file is not part of GNU Emacs. + +;; This program is free software; you can redistribute it and/or modify +;; it under the terms of the GNU General Public License as published by +;; the Free Software Foundation; either version 2 of the License, or +;; (at your option) any later version. + +;; This program is distributed in the hope that it will be useful, +;; but WITHOUT ANY WARRANTY; without even the implied warranty of +;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;; GNU General Public License for more details. + +;; You should have received a copy of the GNU General Public License along +;; with this program; if not, write to the Free Software Foundation, Inc., +;; 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +;;; Commentary: ;; translation of keyword classes from tools/vim ;; see http://xahlee.org/emacs/elisp_syntax_coloring.html +;; Put this in your .emacs file to enable autoloading of lammps-mode +;; and auto-recognition of "in.*" and "*.lmp" files: +;; +;; (autoload 'lammps-mode "lammps-mode.el" "LAMMPS mode." t) +;; (setq auto-mode-alist (append auto-mode-alist +;; '(("in\\." . lammps-mode)) +;; '(("\\.lmp\\'" . lammps-mode)) +;; )) +;; + +;;; Code: ;; define several keyword classes (defvar lammps-output '("log" @@ -136,6 +177,8 @@ (defvar lammps-variable-regexp "\\$\\({[a-zA-Z0-9_]+}\\)\\|\\$[A-Za-z]") +(defvar lammps-font-lock-keywords) + ;; clear memory (setq lammps-output nil) (setq lammps-read nil) @@ -151,8 +194,7 @@ ;; create the list for font-lock. ;; each class of keyword is given a particular face -(setq - lammps-font-lock-keywords +(setq lammps-font-lock-keywords `((,lammps-output-regexp . font-lock-function-name-face) (,lammps-read-regexp . font-lock-preprocessor-face) (,lammps-lattice-regexp . font-lock-type-face) @@ -199,12 +241,5 @@ (setq lammps-comment-regexp nil) (setq lammps-variable-regexp nil)) -;; apply it to specified filename patterns -(setq - auto-mode-alist - (append - auto-mode-alist - '(("in\\." . lammps-mode)) - '(("\\.lmp\\'" . lammps-mode)) - )) - +(provide 'lammps-mode) +;;; lammps-mode.el ends here diff --git a/tools/moltemplate/.gitignore b/tools/moltemplate/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..d2053ce4dcd16d884194150462c18d4acf24ab43 --- /dev/null +++ b/tools/moltemplate/.gitignore @@ -0,0 +1,180 @@ +# from https://github.com/github/gitignore/blob/master/Python.gitignore + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*,cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# dotenv +.env + +# virtualenv +.venv/ +venv/ +ENV/ + +# Spyder project settings +.spyderproject + +# Rope project settings +.ropeproject + +# text-editor temporary files: +*~ + +# misc rubbish +deleteme* +DELETEME* + +######## files specific to moltemplate and lammps ######## + +# latex/bibtex temporary files for the moltemplate manual: +moltemplate_manual*.aux +moltemplate_manual*.bbl +moltemplate_manual*.blg +moltemplate_manual*.log +moltemplate_manual*.out +moltemplate_manual*.toc + +######## files created by running LAMMPS: ######## + +log.lammps +log.cite +traj*.lammpstrj + +######## files generated by running moltemplate: ######## + +system.data +system.in +system.in.init +system.in.settings +system.in.charges +system.psf +ttree_assignments.txt +output_ttree/ + +# Sections from the LAMMPS data file generated by moltemplate.sh +"Data Header"* +"Data Atoms"* +"Data Masses"* +"Data Velocities"* +"Data Bonds"* +"Data Bond List"* +"Data Bonds AtomId AtomId"* +"Data Angles"* +"Data Dihedrals"* +"Data Impropers"* +"Data Bond Coeffs"* +"Data Angle Coeffs"* +"Data Dihedral Coeffs"* +"Data Improper Coeffs"* +"Data Pair Coeffs"* +"Data PairIJ Coeffs"* + +# interactions-by-type (not id. This is not part of the LAMMPS standard.) +"Data Charge By Bond"* +"Data Bonds By Type"* +"Data Angles By Type"* +"Data Dihedrals By Type"* +"Data Impropers By Type"* + +# class2 data sections +"Data BondBond Coeffs"* +"Data BondAngle Coeffs"* +"Data MiddleBondTorsion Coeffs"* +"Data EndBondTorsion Coeffs"* +"Data AngleTorsion Coeffs"* +"Data AngleAngleTorsion Coeffs"* +"Data BondBond13 Coeffs"* +"Data AngleAngle Coeffs"* + +# sections for non-point-like particles: +"Data Ellipsoids"* +"Data Lines"* +"Data Triangles"* + +# periodic boundary conditions +"Data Boundary"* + +# Sections from the LAMMPS input script(s) generated by moltemplate.sh + +"In Init"* +"In Settings"* +"In Coords"* +"In Charges"* +#temporary file created by moltemplate.sh for storing coordinates +tmp_atom_coords.dat + diff --git a/tools/moltemplate/README.md b/tools/moltemplate/README.md index dc63a6bf4a5342c54630923f4d91659c0ff8ea1b..c0bcb28296ec993f16630b689fdb3e48191e286c 100644 --- a/tools/moltemplate/README.md +++ b/tools/moltemplate/README.md @@ -1,9 +1,11 @@ +[![Build Status](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master) + Moltemplate =========== ## Description -Moltemplate is a cross-platform text-based molecule builder for LAMMPS. +Moltemplate is a *general* cross-platform text-based molecule builder for **LAMMPS** and **ESPResSo**. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It currently supports the **OPLS**, **COMPASS**, **AMBER**(GAFF,GAFF2), **MARTINI**, **SDK**, **LOPLS**(2015), and **TraPPE**(1998) force fields, and includes approximately 40 examples. (New force fields and examples are added continually by users.) ## Typical usage @@ -45,7 +47,7 @@ Make sure that your default pip install bin directory is in your PATH. (This is pip uninstall moltemplate -If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "virtualenv", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands: +If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "*virtualenv*", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands: cd ~/moltemplate virtualenv venv @@ -53,7 +55,9 @@ If you continue to run into difficulty, try installing moltemplate into a tempor pip install . #(now do something useful with moltemplate...) -(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.) If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. +(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate. +The *virtualenv* tool is +[explained in detail here](http://docs.python-guide.org/en/latest/dev/virtualenvs/)) If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. ## Manual installation: diff --git a/tools/moltemplate/doc/moltemplate_manual.pdf b/tools/moltemplate/doc/moltemplate_manual.pdf index b0122a3fd875a12c698a128a9646c50eae7a4351..54d8b132bfd5ad1e7f205f673f4754e2a9bdc283 100644 Binary files a/tools/moltemplate/doc/moltemplate_manual.pdf and b/tools/moltemplate/doc/moltemplate_manual.pdf differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_residue.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_residue.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptide.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptide.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_nopbc_t=0_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_nopbc_t=0_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_t=100ps_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/2bead_peptides_t=100ps_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/dimer+dimer0_transparent_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/dimer+dimer0_transparent_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/dimer_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg similarity index 100% rename from tools/moltemplate/doc/moltemplate_manual_src/dimer_LR.jpg rename to tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg diff --git a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex b/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex index 10a3d4fd38e096b174b1258c22e14d72c2a8fe83..f8ce810fd5feec2021893a9f003e6cb817e8b0ae 100644 --- a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex +++ b/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex @@ -36,7 +36,7 @@ \author{ Andrew Jewett, \\ - Jensen Lab (Caltech), Shea Lab (UCSB) \\ + MGL Lab (Scripps), Jensen Lab (Caltech), Shea Lab (UCSB) \\ \includegraphics[height=0.3cm]{author_email.png} } \date \today @@ -57,8 +57,16 @@ %(which is distributed with moltemplate). %These were created to supplement the moltemplate documentation. +\subsubsection*{Warning: This manual does not explain how to run ``active-matter'' simulations or use all-atom force fields.} +However numerous examples and README files are available to +demonstrate how to run these kinds of simulations. +Downloading these examples is \textit{highly recommended}. +(See section \ref{sec:installation}.) + \section{Introduction} + + Moltemplate is a general molecule builder and force-field database system for LAMMPS. A simple file format has been created to store molecule definitions and force-fields (the LAMMPS-template format, “LT”). LT files are templates containing \textit{all} of the text relevant to a particular molecule (including coordinates, bond-topology, angles, force-field parameters, constraints, groups and fixes). Moltemplate can then duplicate the molecule, customize it, and use it as a building-block for constructing larger, more complex molecules. (These molecules can be used to build even larger molecules.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be inserted, moved, deleted and/or replaced). @@ -320,57 +328,82 @@ under the terms of the open-source 3-clause BSD license. \section{Installation} - -\subsection*{Obtaining Moltemplate} -\textit{If you don't already have moltemplate}, -the most up-to-date version can be downloaded at -\url{http://www.moltemplate.org} -If you obtained moltemplate as a .tar.gz file, -(as opposed to github or pip), you can unpack it using: -\begin{verbatim} -tar -xzvf moltemplate_2017-8-22.tar.gz -\end{verbatim} -(The date will vary from version to version.) -Alternately, if you obtained moltemplate bundled with LAMMPS, -then the \textit{``moltemplate''} directory will probably be located -in the \textit{``tools''} subdirectory of your lammps installation. +\label{sec:installation} There are two ways to install moltemplate: \subsubsection*{Installation Method 1 (pip)} -\textit{If you are familiar with pip}, then run the following command from within outermost directory: +\textit{If you are familiar with pip}, you can install +moltemplate by typing following command in the terminal/shell: + %from within outermost directory: \begin{verbatim} -pip install . +pip install moltemplate \end{verbatim} -\textit{In order for this to work, this directory should contain a file named ``\textbf{setup.py}''.} (If no such file exists, then either proceed to ``Installation Method 2'' below, or download a newer version of moltemplate.) If you receive an error regarding permissions, then run pip this way instead: +%\textit{In order for this to work, this directory should contain a file named ``\textbf{setup.py}''.} (If no such file exists, then either proceed to ``Installation Method 2'' below, or download a newer version of moltemplate.) +If you receive an error regarding permissions, then run pip this way instead: \begin{verbatim} -pip install . --user +pip install moltemplate --user \end{verbatim} Make sure that your default pip install bin directory is in your PATH. (This is usually something like \textapprox/.local/bin/ or \textapprox/anaconda3/bin/. If you have installed anaconda, your PATH should have been updated for you automatically.) Later, you can uninstall moltemplate using: \begin{verbatim} pip uninstall moltemplate \end{verbatim} -\textit{If you continue to run into difficulty}, try installing moltemplate into a temporary virtual environment by installing ``virtualenv'', downloading moltemplate (to ``\textapprox/moltemplate'' in the example below), and running these commands: +\textit{Note: There are is a large variety of detailed moltemplate examples +which will be omitted if you install moltemplate this way. +\textbf{Downloading the examples is strongly recommended.}} +You can do this either by using git: \begin{verbatim} -cd ~/moltemplate +git clone https://github.com/jewettaij/moltemplate ~/moltemplate +\end{verbatim} +or by visiting the \url{http://www.moltemplate.org} web site. +They will be in the ``examples'' subdirectory.) + +\textit{If you run into difficulty with pip}, then try installing +moltemplate into a temporary virtual environment +by installing ``virtualenv'', +%downloading moltemplate (to ``\textapprox/moltemplate'' in the example below), +and running these commands: +\begin{verbatim} +mkdir ~/moltemplate_v +cd ~/moltemplate_v virtualenv venv source venv/bin/activate -pip install . +pip install moltemplate #(now do something useful with moltemplate...) \end{verbatim} -You will have to ``run source \textapprox/moltemplate/venv/bin/activate'' beforehand whenver you want to run moltemplate. If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. +You will have to ``run source \textapprox/moltemplate\_v/venv/bin/activate'' beforehand whenver you want to run moltemplate again. If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. \subsubsection*{Installation Method 2} -Alternatively, you can edit your PATH variable manually to include +Alternatively, you can download the moltemplate files and edit your +PATH variable manually to include the subdirectory where the moltemplate.sh script is located (typically ``\textapprox/moltemplate/moltemplate/scripts/''), as well as -the directory containing the most of the python scripts (``\textapprox/moltemplate/moltemplate/''). -Suppose the directory where with the README file is named ``moltemplate'' -and it is located in your home directory: +the directory containing the most of the python scripts +(``\textapprox/moltemplate/moltemplate/''). + +\subsection*{Obtaining Moltemplate} +The most up-to-date version of moltemplate can be downloaded using git. +\begin{verbatim} +git clone https://github.com/jewettaij/moltemplate ~/moltemplate +\end{verbatim} +Later, you can update to the latest version of moltemplate using: +\begin{verbatim} +git pull +\end{verbatim} +Alternatively, you can also download moltemplate as a .tar.gz archive from +\url{http://www.moltemplate.org} +and can unpack it using: +\begin{verbatim} +tar -xzvf moltemplate_2017-8-22.tar.gz +\end{verbatim} +(The date will vary from version to version.) +Somewhat older versions of moltemplate are also bundled with the LAMMPS +source code and are located in the \textit{``tools''} subdirectory. + If you use the \textbf{bash} shell, typically you would edit your \mbox{$\sim$/.bash\_profile}, @@ -409,7 +442,7 @@ If you are using an older version of windows, try following the tutorial written To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: nano, ne, emacs, vim, and jove. (Unfortunately, as of 2017-5-17, graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now. (\url{https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/}) -%\pagebreak +\pagebreak \section{Quick reference \textit{(skip on first reading)}} \section*{ @@ -674,7 +707,7 @@ create\_var \{ \textit{variable} \} & Create a variable specific to this molecule object. (Typically this is used to create molecule-ID numbers, for a molecule built from smaller components. -See section \ref{sec:2beadPeptide}.) +See section \ref{sec:2beadPolymer}.) \\ \hline replace \{ \textit{oldvariable} \textit{newvariable} \} & @@ -761,7 +794,7 @@ Note: \mbox{\textit{``\$mol''}} is shorthand for \mbox{\textit{``\$mol:.''}}) \$\textit{mol:}... & The ID number assigned to the molecule to which this object belongs (if applicable). -See sections \ref{sec:2beadPeptide}, +See sections \ref{sec:2beadPolymer}, \ref{sec:ellipsis_mol}, %\ref{sec:paths}, and appendix \ref{sec:adv_variable_syntax}. @@ -897,6 +930,21 @@ you want the scaling to occur. Of omitted, the origin is used.) \\ \hline +\begin{tabular}[t]{l} + \textit{.quat($a,b,c,d$)} \\ + \textit{.quat($a,b,c,d,x_0,y_0,z_0$)} \\ + \textit{.quatT($a,b,c,d$)} \\ + \textit{.quatT($a,b,c,d,x_0,y_0,z_0$)} \\ +\end{tabular} + & + Rotate atom coordinates by the rotation corresponding + to quaternion $a+b\mathbf{i}+c\mathbf{j}+b\mathbf{k}$ + (around \mbox{$(x_0,y_0,z_0)$}, if specified) + The \textit{.quatT(a,b,c,d)} variant performs the inverse rotation. + (Equivalent to \textit{.quat(a,-b,-c,-d)}.) + % Otherwise around $(0,0,0)$) +\\ +\hline \multicolumn{2}{c} { \textbf{ \textit{Note:} @@ -940,7 +988,6 @@ In this example, the first transformation, ``rot()'', is applied to both ``monom - \subsection{moltemplate.sh command line arguments:} \label{sec:args_table} %\begin{table} @@ -1055,7 +1102,7 @@ Do \textit{not} check for common LAMMPS/moltemplate syntax errors. This forces moltemplate.sh to check that there are valid angle and dihedral interactions defined for every 3 or 4 consecutively bonded atoms in the system -(defined in "Data Angles By Type'' and ``Data Dihedrals By Type" sections). +(defined in ``Data Angles By Type'' and ``Data Dihedrals By Type'' sections). \\ \hline -vmd & @@ -1094,10 +1141,16 @@ Invoke VMD after running moltemplate to view the system you have just created. Normally moltemplate.sh reorders the atoms in each bond, angle, dihedral, and improper interaction before writing them to the DATA file in order to help avoid duplicate interactions between the same atoms if listed in different but equivalent orders. Sometimes this is undesirable. \textit{\textbf{To disable this behavior, set ``file.py'' to ``None''.}} You can also manually choose alternate symmetry rules for unusual force fields. (Such as class2 force fields, dihedral\_style spherical, etc... For an example of the file format for ``file.py'', see the ``nbody\_Impropers.py'' file.) \\ \hline +-allow-wildcards & +Allow the use of ``*'' and ``?'' characters within +``pair\_coeff'', ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', +and ``improper\_coeff'' commands. (Default) +\\ +\hline \end{tabular} -%\pagebreak +\pagebreak @@ -2061,30 +2114,30 @@ within moltemplate is discouraged. See section \ref{sec:wildcard_bug}.) Objects can be connected together to form larger molecule objects. These objects can be used to form still larger objects. As an example, we define a small 2-atom molecule named ``Monomer'', -and use it to construct a short polymer (``Peptide''). +and use it to construct a short polymer (``Polymer''). \begin{figure}[htbp] \centering \textbf{a)} -\includegraphics[height=3cm]{2bead_residue.jpg} +\includegraphics[height=3cm]{2bead_monomer.jpg} \quad \quad \quad \quad \quad \textbf{b)} -\includegraphics[height=3cm]{2bead_peptide.jpg} +\includegraphics[height=3cm]{2bead_polymer.jpg} \newline \vspace{10 mm} \newline \textbf{c)} -\includegraphics[width=4cm]{2bead_peptides_nopbc_t=0_LR.jpg} +\includegraphics[width=4cm]{2bead_polymers_nopbc_t=0_LR.jpg} \textbf{d)} -\includegraphics[width=4cm]{2bead_peptides_t=100ps_LR.jpg} +\includegraphics[width=4cm]{2bead_polymers_t=100ps_LR.jpg} \caption{ -\label{fig:2bead_peptide} +\label{fig:2bead_polymer} \textbf{a)-b)} \textit{Building a complex system from small pieces:} Construction of a polymer (\textbf{b}) out of smaller (2-atom) subunits (\textbf{a}) using composition and rigid-body transformations. -Bonds connecting different residues together (blue) +Bonds connecting different monomer together (blue) must be declared explicitly, but angle and dihedral interactions will be generated automatically. See section \ref{sec:2bead} for details. @@ -2130,20 +2183,123 @@ Monomer inherits ForceField { \end{verbatim} -Soon will use it to construct a polymer (``Peptide'') +Soon will use it to construct a polymer (``Polymer'') \textit{Note: The ellipsis notation used here ``\$mol:...''. warns moltemplate that the ``Monomer'' molecule may be part of a larger molecule. (This is explained in more detail in section \ref{sec:ellipsis_mol}.) +(Note: The meaning of ``inherits ForceField'' + will be explained below in section \ref{sec:nbody_by_type_intro}) } - + In this example we will define two kinds of molecule objects: -``Monomer'', and ``Peptide'' (\textit{defined later}). -It is often convenient to store atom types, masses, and force-field -parameters in a separate file so that they -can be shared between these different molecules. -We do that in the ``forcefield.lt'' file below: +``Monomer'', and ``Polymer'' (\textit{defined later}). +\subsubsection*{Building a simple polymer} +We construct a short polymer by making 7 copies of ``Monomer'', +rotating and moving each copy: +\label{sec:2beadPolymer} +\begin{verbatim} +# -- file "polymer.lt" -- + +import "monomer.lt" #(defines "Monomer" and "ForceField") + +Polymer inherits ForceField { + + # The next line is optional: + create_var {$mol} #(force all monomers to share the same molecule-ID) + + # Now create some monomers + + mon1 = new Monomer #(no need to move the first monomer) + mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) + mon3 = new Monomer.rot(360.0, 1,0,0).move(6.4,0,0) + mon4 = new Monomer.rot(540.0, 1,0,0).move(9.6,0,0) + mon5 = new Monomer.rot(720.0, 1,0,0).move(12.8,0,0) + mon6 = new Monomer.rot(900.0, 1,0,0).move(16.0,0,0) + mon7 = new Monomer.rot(1080.0, 1,0,0).move(19.2,0,0) + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca + $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca + $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca + $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca + $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca + $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca + } +} +\end{verbatim} +The position and orientation of each copy of ``Monomer'' +is specified after the ``new'' statement. +Each ``new'' statement is typically followed by a chain of +move/rotate/scale functions separated by dots, evaluated left-to-right +(optionally followed by square brackets and then more dots). +For example, ``mon2'' is a copy of ``Monomer'' which is first rotated +180 degrees around the X axis (denoted by ``1,0,0''), +and \textbf{then} moved in the (3.2,0,0) direction. +(The last three arguments to the ``rot()'' command + denote the axis of rotation, which does not have to be normalized.) +(A list of available coordinate transformations +is provided in section \ref{sec:xforms_table}.) + +\textit{(Note: Although we did not do this here, +it is sometimes convenient to represent polymers as 1-dimensional arrays. +See sections \ref{sec:arrays} and \ref{sec:random_arrays} for examples.)} + +To bond atoms in different molecules or molecular subunits together, we used +the write(``Data Bonds'') command to append additional bonds to the system. + +%\subsubsection{Sharing atom, bond and angle types} +%Normally you must separately define the parameters for all of the atoms types, +%and bond types, angle types etc... in every type of molecule. +%However different kinds of monomers in a heteropolymer typically will +%share some common backbone atom types and other properties. +%You must be careful to indicate which atom and bond types are shared between +%different monomers by referring them using a ``../'' prefix. +%(See sections \ref{sec:variable_scope}, +%\ref{sec:paths}, and +%\ref{sec:butane} for details and examples.) +%\textit{Note: There is a heteropolymer example in the the +%``2bead\_heteropolymer/'' directory in the online examples. +%This example demonstrates how to share backbone atoms, bonds, and angles. +%You can also define specific angle or dihedral interactions which are +%specific to the atom types in different monomers.} + + +\subsection{Bonded interactions \textit{by type}} +\label{sec:nbody_by_type_intro} + +In this example we did \textit{not} provide a list of all 3-body +and 4-body angle forces between bonded atoms in the polymer. +Moltemplate allows you to manually list all of these interactions +(using the ``write\_once("Data Angles")'' command +from section \ref{sec:spce_example}, +\textit{or} +the ``write\_once("Data Dihedrals")'', +or ``write\_once("Data Impropers")'' commands). +However there are usually many of them. +For this reason, it is often more convenient to provide +moltemplate with instructions to help it automatically figure out +which atoms participate in 3-body and 4-body angle interactions, +and what force field parameters to assign to them. +We will do that below using the following commands: +``write\_once("Data Angles By Type")'', +``write\_once("Data Dihedrals By Type")'', and +``write\_once("Data Impropers By Type")'' + + %Moltemplate can detect consecutively bonded atoms and + %determine the forces between them based on atom type (and bond type). + +Furthermoree, since many different kinds molecules often share +the same rules for creating 3-body and 4-body angle interactions, +it is convenient to organize all of this information +together into one place (eg an object named ``ForceField''). +A ``ForceField'' object will typically include many +``write\_once("Data Angles By Type")'' +commands, as well as force field parameters and related atom type properties. +We also typically store that information in a separate file +(eg ``forcefield.lt'', ``oplsaa.lt'', ``gaff2.lt'', ``compass.lt'', etc...). \begin{verbatim} # -- file "forcefield.lt" -- @@ -2199,14 +2355,14 @@ ForceField { angle_coeff @angle:Sidechain 30.00 132 } + # 4-body interactions in this example are listed by atomType # Rules for determining 4-body (dihedral) interactions by atom & bond type: write_once("Data Dihedrals By Type") { - # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bnd2 bnd3 + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* } - # 4-body interactions in this example are listed by atomType # The forumula used is: # # Udihedral(phi) = K * (1 + cos(n*phi - d)) @@ -2229,111 +2385,22 @@ ForceField { bond_style harmonic angle_style harmonic dihedral_style charmm - pair_style lj/cut/coul/debye 0.1 11.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 - } -} -\end{verbatim} - - - -\subsubsection{Building a simple polymer} -We construct a short polymer by making 7 copies of ``Monomer'', -rotating and moving each copy: -\label{sec:2beadPeptide} -\begin{verbatim} -# -- file "peptide.lt" -- - -import "monomer.lt" - -Peptide inherits ForceField { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - # (The "Data Atoms" in Monomer must use the "$mol:..." notation.) - - res1 = new Monomer - res2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) - res3 = new Monomer.rot(360.0, 1,0,0).move(6.4,0,0) - res4 = new Monomer.rot(540.0, 1,0,0).move(9.6,0,0) - res5 = new Monomer.rot(720.0, 1,0,0).move(12.8,0,0) - res6 = new Monomer.rot(900.0, 1,0,0).move(16.0,0,0) - res7 = new Monomer.rot(1080.0, 1,0,0).move(19.2,0,0) - - # Now, link the residues together this way: - write("Data Bonds") { - $bond:backbone1 @bond:Backbone $atom:res1/ca $atom:res2/ca - $bond:backbone2 @bond:Backbone $atom:res2/ca $atom:res3/ca - $bond:backbone3 @bond:Backbone $atom:res3/ca $atom:res4/ca - $bond:backbone4 @bond:Backbone $atom:res4/ca $atom:res5/ca - $bond:backbone5 @bond:Backbone $atom:res5/ca $atom:res6/ca - $bond:backbone6 @bond:Backbone $atom:res6/ca $atom:res7/ca + pair_style lj/cut 11.0 } } \end{verbatim} -The position and orientation of each copy of ``Monomer'' -is specified after the ``new'' statement. -Each ``new'' statement is typically followed by a chain of -move/rotate/scale functions separated by dots, evaluated left-to-right -(optionally followed by square brackets and then more dots). -For example, ``res2'' is a copy of ``Monomer'' which is first rotated -180 degrees around the X axis (denoted by ``1,0,0''), -and \textbf{then} moved in the (3.2,0,0) direction. -(The last three arguments to the ``rot()'' command - denote the axis of rotation, which does not have to be normalized.) -(A list of available coordinate transformations -is provided in section \ref{sec:xforms_table}.) - -\textit{(Note: Although we did not do this here, -it is sometimes convenient to represent polymers as 1-dimensional arrays. -See sections \ref{sec:arrays} and \ref{sec:random_arrays} for examples.)} - -To bond atoms in different molecules or molecular subunits together, we used -the write(``Data Bonds'') command to append additional bonds to the system. - -%\subsubsection{Sharing atom, bond and angle types} -%Normally you must separately define the parameters for all of the atoms types, -%and bond types, angle types etc... in every type of molecule. -%However different kinds of monomers in a heteropolymer typically will -%share some common backbone atom types and other properties. -%You must be careful to indicate which atom and bond types are shared between -%different monomers by referring them using a ``../'' prefix. -%(See sections \ref{sec:variable_scope}, -%\ref{sec:paths}, and -%\ref{sec:butane} for details and examples.) -%\textit{Note: There is a heteropolymer example in the the -%``2bead\_heteropolymer/'' directory in the online examples. -%This example demonstrates how to share backbone atoms, bonds, and angles. -%You can also define specific angle or dihedral interactions which are -%specific to the atom types in different residues.} - - -\subsection{Bonded interactions \textit{by type}} -\label{sec:nbody_by_type_intro} - -In this example we did \textit{not} provide a list of all 3-body -and 4-body forces between bonded atoms in the polymer. -(for example using the ``write\_once("Data Angles")'' command -from section \ref{sec:spce_example}, -\textit{or} -the ``write\_once("Data Dihedrals")'', -or ``write\_once("Data Impropers")'' commands.) -Instead we provided moltemplate.sh with instructions to help it figure out -which atoms participate in 3-body and 4-body bonded interactions. -Moltemplate can detect consecutively bonded atoms and -determine the forces between them based on atom type. -(Bond type can also be used as a criteria.) -We did this in ``forcefield.lt'' using the -\mbox{``write\_once("Data Angles By Type")''} and -\mbox{``write\_once("Data Dihedrals By Type")''} -commands. -You can also generate improper interactions -between any 4-atoms bonded together in a T-shaped topology -using the ``write\_once("Impropers By Type")'' command. -See appendix \ref{sec:nbody_by_type} for more details. -\textit{(More general interactions are possible. - See appendix \ref{sec:nbody_by_type_custom}.)} +Any molecule that wants to access this information can use the +``inherits ForceField'' keyword. +\textit{(...as we did in the ``monomer.lt'' and ``polymer.lt'' files in theexample above. + Note: the ``import forcefield'' statement was also necessary because the + information is located in a separate file: ``forcefield.lt''.} +%\textit{(Note: You can also generate \textbf{improper} interactions +% %between any 4-atoms bonded together in a T-shaped topology +% the same way, using the ``write\_once("Impropers By Type")'' command. +% See appendix \ref{sec:nbody_by_type} for more details. +\textit{You can customize these ``By Type'' rules further + by altering the bond topology search rules and atom type symmetry. + See appendix \ref{sec:nbody_by_type_custom} for details.)} %\subsubsection*{\textit{(Advanced)} Order matters when sets overlap} %Bonded-interactions are generated in the order they appear in the LT file. @@ -2379,17 +2446,17 @@ with molecules or atoms. (See sections \ref{sec:coords_intro} and \ref{sec:multidimensional_arrays}.) Here we show an easier way to create the short polymer -shown in section \ref{sec:2beadPeptide}. +shown in section \ref{sec:2beadPolymer}. You can make 7 copies of the \textit{Monomer} molecule this way: \begin{verbatim} - res = new Monomer[7] + monomers = new Monomer[7] \end{verbatim} This creates 7 new \textit{Monomer} molecules (named -\mbox{\textit{res[0]}}, -\mbox{\textit{res[1]}}, -\mbox{\textit{res[2]}}, -\mbox{\textit{res[3]}}, ... -\mbox{\textit{res[6]}}). +\mbox{\textit{monomers[0]}}, +\mbox{\textit{monomers[1]}}, +\mbox{\textit{monomers[2]}}, +\mbox{\textit{monomers[3]}}, ... +\mbox{\textit{monomers[6]}}). Unfortunately, by default, the coordinates of each molecule are identical. To prevent the atom coordinates from overlapping, you have several choices: @@ -2398,13 +2465,13 @@ To prevent the atom coordinates from overlapping, you have several choices: After every square-bracket [] in a new command, you can specify a list of transformations to apply. For example, we could have generated atomic coordinates for the -the short polymer in section \ref{sec:2beadPeptide} +the short polymer in section \ref{sec:2beadPolymer} using this command: \begin{verbatim} - res = new Monomer [7].rot(180, 1,0,0).move(3.2,0,0) + monomers = new Monomer [7].rot(180, 1,0,0).move(3.2,0,0) \end{verbatim} This will create 7 molecules. -The coordinates of the first molecule \textit{res[0]} are will be unmodified. +The coordinates of the first molecule \textit{monomers[0]} are will be unmodified. However each successive molecule will have its coordinates cumulatively modified by the commands ``rot(180, 1,0,0)'' followed by ``move(3.2,0,0)''. \subsubsection*{optional: initial customizations (preceding [] brackets)} @@ -2413,7 +2480,7 @@ You can also make adjustments to the initial coordinates of the molecule before it is copied, and before any of the array transformations are applied. For example: \begin{verbatim} - res = new Monomer.scale(1.5) [7].rot(180, 1,0,0).move(3.2,0,0) + monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).move(3.2,0,0) \end{verbatim} In this example, the ``scale(1.5)'' transformation is applied once to enlarge every \textit{Monomer} object initially. @@ -2426,17 +2493,17 @@ are applied to build the polymer Alternately you apply transformations to a molecule after they have been created (even if they are part of an array). \begin{verbatim} - res = new Monomer [7] + monomers = new Monomer [7] # Again, the first line creates the molecules named - # "res[0]", "res[1]", "res[2]", "res[3]", ... "res[6]". + # "monomers[0]", "monomers[1]", "monomers[2]", ... "monomers[6]". # The following lines move them into position. - res[1].rot(180.0, 1,0,0).move(3.2,0,0) - res[2].rot(360.0, 1,0,0).move(6.4,0,0) - res[3].rot(540.0, 1,0,0).move(9.6,0,0) - res[4].rot(720.0, 1,0,0).move(12.8,0,0) - res[5].rot(900.0, 1,0,0).move(16.0,0,0) - res[6].rot(1080.0, 1,0,0).move(19.2,0,0) + monomers[1].rot(180.0, 1,0,0).move(3.2,0,0) + monomers[2].rot(360.0, 1,0,0).move(6.4,0,0) + monomers[3].rot(540.0, 1,0,0).move(9.6,0,0) + monomers[4].rot(720.0, 1,0,0).move(12.8,0,0) + monomers[5].rot(900.0, 1,0,0).move(16.0,0,0) + monomers[6].rot(1080.0, 1,0,0).move(19.2,0,0) \end{verbatim} \subsection{Transformation order (general case)} @@ -2454,13 +2521,13 @@ copy of the molecule multiple times. XFORMS2 will be applied $i$ times.) Finally after all the molecules have been created, the list of transformations in XFORMS3 will be applied. -For example, to create a ring of 10 peptides of radius 30.0, +For example, to create a ring of 10 polymers of radius 30.0, centered at position (0,25,0), use this notation: \begin{verbatim} -peptide_ring = new Peptide.move(0,30,0) [10].rot(36,1,0,0) +polymer_ring = new Polymer.move(0,30,0) [10].rot(36,1,0,0) # After creating it, we can move the entire ring # (These commands are applied last.) -peptide_ring[*].move(0,25,0) +polymer_ring[*].move(0,25,0) \end{verbatim} @@ -2618,19 +2685,19 @@ commands appearing later (following ``[50]'') are carried out. \label{sec:array_wildcards_intro} You can move the entire array of molecules using ``[*]'' notation: \begin{verbatim} - res[*].move(0,0,40) + monomers[*].move(0,0,40) \end{verbatim} -(Note that ``res.move(0,0,40)'' does not work. +(Note that ``monomers.move(0,0,40)'' does not work. You must include the ``[*]''.) -You can also use range limits to move only some of the residues: +You can also use range limits to move only some of the monomers: \begin{verbatim} - res[2-4].move(0,0,40) + monomers[2-4].move(0,0,40) \end{verbatim} -This will move only the third, fourth, and fifth residues. +This will move only the third, fourth, and fifth monomers. If you are more familiar with python's slice notation, you can accomplish the same thing using: \begin{verbatim} - res[2:5].move(0,0,40) + monomers[2:5].move(0,0,40) \end{verbatim} (In this case, the second integer (eg ``5'') is interpreted as a strict upper bound.) @@ -2678,10 +2745,10 @@ You can build multidimensional arrays using slice notation as well, for example The same techniques work with multidimensional arrays. Coordinate transformations can be applied to each layer in a multi-dimensional array. -For example, to create a cubic lattice of 3x3x3 peptides: +For example, to create a cubic lattice of 3x3x3 polymers: you would use this syntax: \begin{verbatim} -molecules = new Peptide [3].move(30.0, 0, 0) +molecules = new Polymer [3].move(30.0, 0, 0) [3].move(0, 30.0, 0) [3].move(0, 0, 30.0) \end{verbatim} @@ -2689,14 +2756,14 @@ molecules = new Peptide [3].move(30.0, 0, 0) with cylindrical, helical, conical, or toroidal symmetry.) \subsection{Customizing individual rows, columns, or layers} -Similarly, you can customize the position of individual peptides, +Similarly, you can customize the position of individual polymers, or layers or columns using the methods above: \begin{verbatim} molecules[1][*][*].move(0,20,0) molecules[*][1][*].move(0,0,20) molecules[*][*][1].move(20,0,0) \end{verbatim} -See figure \ref{fig:2bead_peptide}c) +See figure \ref{fig:2bead_polymer}c) \textit{(You can also use slice notation, eg ``molecules[1][0-2][0-1].move(20,0,0)'')} @@ -2858,48 +2925,57 @@ And all of this can be done from anywhere else in the LT file. %\textit{(The notation in section \ref{sec:paths} explains % how to navigate the object hierarchy.)} -For example, suppose we used the ``Peptide'' molecule we defined above -to create a larger, more complex ``Dimer'' molecule. +For example, suppose we used the ``Polymer'' molecule we defined above +to create a larger, more complicated ``MolecularComplex'' molecule. \begin{verbatim} -Dimer { - peptides[0] = new Peptide - peptides[1] = new Peptide.rot(180,1,0,0).move(0, 12.4, 0) +MolecularComplex { + polymers[0] = new Polymer + polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) } -dimer = new Dimer +mol_complex = new MolecularComplex \end{verbatim} -The \textit{Dimer} molecule is shown in figure \ref{fig:dimers}a). -\textit{Optional: If you want all the atoms in a ``Dimer'' to share the same molecule-ID, -then define ``Dimer'' this way:} +The \textit{MolecularComplex} molecule is shown in figure \ref{fig:mol_complex}a). +\textit{Optional: If you want all the atoms in a ``MolecularComplex'' to share the same molecule-ID, +then define ``MolecularComplex'' this way:} \begin{verbatim} -Dimer inherits ForceField { +MolecularComplex inherits ForceField { create_var { $mol } - peptides[0] = new Peptide - peptides[1] = new Peptide.rot(180,1,0,0).move(0, 12.4, 0) + polymers[0] = new Polymer + polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) } \end{verbatim} \textit{For this to work, you must also delete the \mbox{\textit{``create\_var \{\$mol:.\}''}} line from - the definition of the Peptide molecule. See section \ref{sec:2bead}.} + the definition of the Polymer molecule. See section \ref{sec:2bead}.} -We can subsquently customize the position of the 3rd residue -of the second peptide this way: +We can subsquently customize the position of the 3rd monomer (``monomers[2]'') +of the second polymer (``polymers[1]''), this way: \begin{verbatim} -dimer/peptides[1]/res[2].move(0,0.2,0.6) +mol_complex/polymers[1]/monomers[2].move(0,0.2,0.6) \end{verbatim} -This does not effect the position of \textit{res[2]} in \textit{peptides[0]}. -(or in any other \textit{``Peptide''} or \textit{``Dimer''} molecule.) -If you want to move both residues, you could use a wildcard character ``*'' +This does not effect the position of +\textit{monomers[2]} in \textit{polymers[0]}. +(or in any other \textit{``Polymer''} or +\textit{``MolecularComplex''} molecule.) +If you want to do the same thing for both polymers, +you could use a wildcard character ``*'' +\begin{verbatim} +mol_complex/polymers[*]/res[2].move(0,0.2,0.6) +\end{verbatim} +If you want to move both polymers, you can use: \begin{verbatim} -dimer/peptides[*]/res[2].move(0,0.2,0.6) +mol_complex/polymers[*].move(0,0.2,0.6) \end{verbatim} -(You can also use ranged (slice) notation, such as ``peptides[0-1]'', - as an alternative to ``peptides[*]''. +you could use a wildcard character ``*'' +(You can also use ranged (slice) notation, such as ``polymers[0-1]'', + as an alternative to ``polymers[*]''. See section \ref{sec:array_wildcards_intro}. -To make changes that apply to every subsequently created \textit{``Peptide''} or -\textit{``Dimer''} molecule, see section \ref{sec:molecule_customization}.) +To make changes that apply to every subsequently created \textit{``Polymer''} +or \textit{``MolecularComplex''} molecule, +see section \ref{sec:molecule_customization}.) \subsection{Customizing individual atom locations} @@ -2907,10 +2983,10 @@ To make changes that apply to every subsequently created \textit{``Peptide''} or The ``move'' or ``rot'' commands can not be used to control the positions of \textit{individual atoms}. Instead simply overwrite their coordinates this way: -%$atom:dimer/peptides[0]/res[2]/CA $mol:dimer/peptides[1] @atom:R 0 6.4 8.0 0 +%$atom:mol_complex/polymers[0]/res[2]/CA $mol:mol_complex/polymers[1] @atom:R 0 6.4 8.0 0 \begin{verbatim} write("Data Atoms") { - $atom:dimer/peptides[0]/res[2]/ca $mol:... @atom:R 0 6.4 8.2 0.6 + $atom:mol_complex/polymers[0]/res[2]/ca $mol:... @atom:R 0 6.4 8.2 0.6 } \end{verbatim} @@ -2918,8 +2994,8 @@ write("Data Atoms") { \label{sec:adding_atoms_bonds} Adding additional bonds within a molecule can be accomplished by writing additional lines of text to the ``Data Bonds'' section. -(This is what we did when we added bonds between residues to create a polymer - in section \ref{sec:2beadPeptide}.) +(This is what we did when we added bonds between monomers to create a polymer + in section \ref{sec:2beadPolymer}.) Again, bonds and atom names must be referred to by their \textit{full} names. Bonds and bonded interactions can be deleted using the ``delete'' command. (See section \ref{sec:delete}.) @@ -2931,18 +3007,18 @@ Bonds and bonded interactions can be deleted using the ``delete'' command. \subsubsection{Deleting molecules or molecular subunits} Molecules can be further customized by deleting individual atoms, bonds, bonded-interactions, and entire subunits. -We can \textbf{delete} the 3rd residue of the second peptide, +We can \textbf{delete} the 3rd monomer of the second polymer, use the ``delete'' command: \begin{verbatim} -delete dimer/peptides[1]/res[2] +delete mol_complex/polymers[1]/res[2] \end{verbatim} \subsubsection{Deleting atoms, bonds, angles, dihedrals, and impropers} \label{sec:delete_atoms_bonds} Individual atoms or bonds can be deleted in a similar way: \begin{verbatim} -delete dimer/peptides[1]/res[3]/ca #<-- deletes the "ca" atom -delete dimer/peptides[1]/res[4]/cr #<-- deletes the "cr" bond +delete mol_complex/polymers[1]/res[3]/ca #<-- deletes the "ca" atom +delete mol_complex/polymers[1]/res[4]/cr #<-- deletes the "cr" bond \end{verbatim} Whenever an atom or a molecule is deleted, the bonds, angles, dihedrals, and improper interactions involving those atoms are deleted as well. @@ -2961,10 +3037,10 @@ generated by moltemplate are removed as well. are not removed. These need to be deleted manually.) Multiple molecules can moved or deleted in a single command. For example, -the following command deletes the third, fourth, and fifth residues from -both peptides[0] and peptides[1]: +the following command deletes the third, fourth, and fifth monomers from +both polymers[0] and polymers[1]: \begin{verbatim} -delete dimer/peptides[*]/res[2-4] +delete mol_complex/polymers[*]/res[2-4] \end{verbatim} See section \ref{sec:array_wildcards_intro} for an explanation of ranged (``[2-4]'') array notation, @@ -3001,13 +3077,13 @@ to make sure they look reasonable. %By default, this transformations is applied relative %to the coordinate system in which the command was given. %In other words, this command will move the third - %residue of peptides[1] in the +Y direction + %monomer of polymers[1] in the +Y direction %regardless of the direction that the molecule ``res[2]'' is facing. %Alternately, if we want to apply this transformation - %in peptides[1]'s local coordinate system, - %we would use the context(peptides[1]) command: + %in polymers[1]'s local coordinate system, + %we would use the context(polymers[1]) command: %\begin{verbatim} - %dimer2/peptides[1]/res[2].context(peptides[1]).move(0,1,0) + %mol_complex/polymers[1]/res[2].context(polymers[1]).move(0,1,0) %\end{verbatim} @@ -3032,14 +3108,14 @@ to make sure they look reasonable. You can create modified versions of existing molecule \textit{types}, without having to redefine the entire molecule. For example: \begin{verbatim} -Dimer0 = Dimer.move(-9.6,-6.2, 0).scale(0.3125) +MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} or equivalently: \begin{verbatim} -Dimer0 = Dimer -Dimer0.move(-9.6,-6.2, 0).scale(0.3125) +MolecularComplex0 = MolecularComplex +MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} -This creates a new type of molecule named ``Dimer0'' whose +This creates a new type of molecule named ``MolecularComplex0'' whose coordinates have been centered and rescaled. (Note that the ``scale()'' command only effects the atomic coordinates. (You will have to override earlier force field settings, @@ -3047,11 +3123,11 @@ such as atomic radii and bond-lengths in order for this to work properly.) If we want to make additional customizations (such as adding atoms, bonds, or molecular subunits), we could use this syntax: \begin{verbatim} -Dimer0 = Dimer +MolecularComplex0 = MolecularComplex -# Add some new atoms connecting the two peptides in the dimer +# Add some new atoms connecting the two polymers in the mol_complex -Dimer0 inherits ForceField { +MolecularComplex0 inherits ForceField { write("Data Atoms") { $atom:t1 $mol:. @atom:CA 0.0 23.0 0.0 0.0 $atom:t2 $mol:. @atom:CA 0.0 24.7 4.0 0.0 @@ -3059,36 +3135,36 @@ Dimer0 inherits ForceField { $atom:t4 $mol:. @atom:CA 0.0 23.0 12.4 0.0 } write("Data Bonds") { - $bond:b1 @bond:Backbone $atom:peptides[0]/res7/CA $atom:t1 + $bond:b1 @bond:Backbone $atom:polymers[0]/res7/CA $atom:t1 $bond:b2 @bond:Backbone $atom:t1 $atom:t2 $bond:b3 @bond:Backbone $atom:t2 $atom:t3 $bond:b4 @bond:Backbone $atom:t3 $atom:t4 - $bond:b5 @bond:Backbone $atom:t4 $atom:peptides[1]/res7/ca + $bond:b5 @bond:Backbone $atom:t4 $atom:polymers[1]/res7/ca } } -# Center and rescale the atoms in all "Dimer0" -Dimer0.move(-9.6,-6.2, 0).scale(0.3125) +# Center and rescale the atoms in all "MolecularComplex0" +MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) \end{verbatim} -The result of these modifications is shown in figure \ref{fig:dimers}b). +The result of these modifications is shown in figure \ref{fig:mol_complex}b). \begin{figure}[htbp] \centering \textbf{a)} -\includegraphics[height=3cm]{dimer_LR.jpg} +\includegraphics[height=3cm]{mol_complex_LR.jpg} \hspace{1cm} \textbf{b)} -\includegraphics[height=3cm]{dimer+dimer0_transparent_LR.jpg} +\includegraphics[height=3cm]{mol_complex+mol_complex0_transparent_LR.jpg} %\newline %\vspace{10 mm} %\newline \caption{ -\label{fig:dimers} +\label{fig:mol_complex} \textbf{a)} -The ``Dimer'' molecule. This is a contrived example consisting of -two ``Peptides''. See section \ref{sec:2beadPeptide} +The ``MolecularComplex'' molecule. This is a contrived example consisting of +two ``Polymers''. See section \ref{sec:2beadPolymer} \textbf{b)} -A customized version of the ``Dimer'' molecule. -(The original ``Dimer'' is shown faded in the background for comparison.) +A customized version of the ``MolecularComplex'' molecule. +(The original ``MolecularComplex'' is shown faded in the background for comparison.) } \end{figure} @@ -3109,18 +3185,18 @@ an entire molecule type \textbf{after} all of its internal details \subsubsection*{\textit{(Advanced)} Inheritance} \label{sec:inheritance_intro} -The \textit{Dimer0} molecule is a type of \textit{Dimer} molecule. +The \textit{MolecularComplex0} molecule is a type of \textit{MolecularComplex} molecule. For those who are familiar with programming, relationships like this are analogous to the relationship between parent and child objects in an object-oriented programming language. %What we have done is equivalent to saying that - %\textit{Dimer0} inherits from \textit{Dimer}. + %\textit{MolecularComplex0} inherits from \textit{MolecularComplex}. More general kinds of inheritance are supported by moltemplate and are discussed in section \ref{sec:inheritance}. \subsubsection*{\textit{(Advanced)} Multiple Inheritance} If we wanted, we could have created a new molecule type -(like \textit{``Dimer0''}) +(like \textit{``MolecularComplex0''}) which includes atom types and features from \textit{multiple} different types of molecules. Section \ref{sec:inheritance} mentions one way to do this @@ -3984,10 +4060,8 @@ starting moltemplate and kill the process if it's memory usage exceeds 80\%. \textbf{3)} Limited support for non-point-like atoms: -As of 2014-12-09, only the ``full'', ``angle'', ``atomic'', ``charge'', -and ``molecular'' styles have been tested. -The ``dipole'' atom style \textit{is} fully supported -but it has not been tested. +As of 2017-8-31, only the ``full'', ``angle'', ``atomic'', ``charge'', +``sphere'', ``dipole'', and ``molecular'' styles have been tested. Non-point-like atoms like ``ellipsoid'', ``tri'', ``line'' \textit{should} also work with moltemplate. However these objects @@ -4027,28 +4101,36 @@ Please let me know if it is not working. \textbf{6)} Inconsistent support for wildcard characters (``*'' and ``?'') \label{sec:wildcard_bug} - As of 2014-1-28, - the wildcard character ``*'' + The wildcard character ``*'' is interpreted differently in different parts of an LT file. Wildcard characters work reliably and are used for \textit{string} - pattern matching when inside any of the \textit{``By Type''} sections + pattern matching when inside + ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', ``improper\_coeff'', + and most ``pair\_coeff'' commands, + as well as any of the \textit{``By Type''} sections in an LT file (such as \textit{``Data Angles By Type''}, \textit{``Data Dihedrals By Type''}, and \textit{``Data Impropers By Type''}). - However these characters are interpreted differently when they appear - in \textit{pair\_coeff}, \textit{bond\_coeff}, \textit{angle\_coeff} - \textit{dihedral\_coeff}, and \textit{improper\_coeff} commands - (and their corresponding \textit{``Coeff''} sections of a data file). - LAMMPS interprets ``*'' characters appearing in any of the - \textit{coeff} commands as \textit{numeric} wildcard characters. + However these wildcard characters \textit{do not} + within pair\_coeff commands that require \textit{more} + than 2 atom types as arguments. + (such as ``pair\_style hbond/dreiding/lj''. + However manybody pair\_styles which use ``pair\_coeff * *'' + notation work fine.) + As of 2017-8-31, wildcard characters (``*'', ``?'') also fail to work inside + \textit{``bond\_modify''} commands, and other commands used for running + active matter simulations. (Such commands are typically located within the + \textit{``write\_once("In Transitions")''} section of an .LT file.) + LAMMPS interprets ``*'' characters appearing here as + \textit{numeric ranges}, and their behavior depends on the + integers which moltemplate assigns to these variables, + \textit{not} the \textit{names} of the variables. + (See the official documentation for bond\_modify, and bond\_coeff + commands to see how ``*'' characters are interpreted. This can lead to unintended side-effects and is discouraged. - So please avoid ``*'' characters in any of the - \textit{``coeff''} commands - (eg \textit{pair\_coeff, bond\_coeff, angle\_coeff, - dihedral\_coeff, improper\_coeff}). - The ``*'' character can be safely used in array brackets, \textit{[*]}, - or in the \textit{``By Type''} sections. + The ``*'' character can be safely used in array brackets, \textit{[*]}, or in + the varios \textit{``\_coeff''} commands and \textit{``By Type''} sections. (See section \ref{sec:array_wildcards_intro} and appendix \ref{sec:nbody_by_type}.) @@ -4452,7 +4534,7 @@ To specify the atoms in each \textit{representation}, click on the \mbox{\textbf{Selections}} tab. By default ``all'' atoms are selected, however you can select atoms according to atom -\textbf{type}, \textbf{index}, \textbf{resid}, +\textbf{type}, \textbf{index}, \textbf{molid}, \textbf{charge}, \textbf{mass}, \textbf{x}, \textbf{y}, \textbf{z}. This will limit the current display settings to a subset of the atoms/bonds present in your system. @@ -4470,7 +4552,7 @@ and \textit{\textbf{Note:}} In VMD/topotools, -the \textbf{type}, \textbf{index}, and \textbf{resid} +the \textbf{type}, \textbf{index}, and \textbf{molid} properties of each atom correspond to the \textit{@atom}, \textit{\$atom}, and \textit{\$mol} variables for each atom in moltemplate. @@ -4745,7 +4827,7 @@ Keep in mind, that in this example, this could cause other atom-types (for example ``@atom:SPCE/H'') to be assigned to overlapping numbers. %For this reason, the ``-b'' flag is usually used only for %custom user-defined variable categories - %(such as the ``\$resid'' counter example described + %(such as the ``\$monomerid'' counter example described %in section \ref{sec:custom_categories}). @@ -4839,35 +4921,35 @@ By default variables in a given category are always assigned to unique integers. This can be overridden using the ``category'' command. For example, you might have a variable that keeps track of -the position index of each residue in each protein chain. -The first residue in a protein (N-terminus) is assigned ``1'', -the second residue, ``2'', etc, -\textit{regardless} of the number of protein chains in your system. +the monomer in every polymer. +The first monomer in a polymer is assigned ``1'', +the second monomer, ``2'', etc, +\textit{regardless} of the number of polymer in your system. -To do this, we can create a new variable category named ``resid'' which -is defined within the scope of each instance of the ``Protein'' molecule: +To do this, we can create a new variable category named ``monomerid'' which +is defined within the scope of each instance of the ``Polymer'' molecule: \begin{verbatim} -Residue { +Monomer { write("Data Atoms") { - $atom:ca @atom:CA $resid:. 0.0 0.0 0.0 0.0 - $atom:cb @atom:CB $resid:. 0.0 1.53 0.0 0.0 + $atom:ca @atom:CA $monomerid:. 0.0 0.0 0.0 0.0 + $atom:cb @atom:CB $monomerid:. 0.0 1.53 0.0 0.0 } } -Protein { - category $resid(1,1) - residues = Residue[100] +Polymer { + category $monomerid(1,1) + monomers = Monomer[100] } -proteins = Protein[10] +polymers = Polymer[10] \end{verbatim} -In this example, there are 10 proteins containing 100 residues each. -The ``\$resid'' counters will be replaced with integers in the range +In this example, there are 10 polymers containing 100 monomers each. +The ``\$monomerid'' counters will be replaced with integers in the range $1\ldots 100$, (not $1\ldots 1000$, as you might expect). -Because the ``\$resid'' counter is local to the +Because the ``\$monomerid'' counter is local to the protein it is defined within, -``\$resid'' variables in other proteins do not share the same counter, +``\$monomerid'' variables in other proteins do not share the same counter, and can overlap. \subsection{Counting order} @@ -5446,10 +5528,10 @@ However the \textit{\textbf{cpath}} can be specified explicitly, as in this example: ``\$/atom:'' (``/'' denotes explicitly that the counter has global scope). Another example with an explicit \textit{\textbf{cpath}} is -the custom local counter variable named ``\$/proteins[5]/resid:.'' +the custom local counter variable named ``\$/proteins[5]/monomerid:.'' (See section \ref{sec:cpath_simple}.) In this example, the \textit{\textbf{cpath}} is ``\$/proteins[5]'', the -\textit{\textbf{catname}} is ``resid'', +\textit{\textbf{catname}} is ``monomerid'', and the \textit{\textbf{lpath}} is ``.''. (In section \ref{sec:cpath_simple}, @@ -5488,7 +5570,7 @@ then it is equivalent to: \$\textit{\textbf{catname}}:\textit{\textbf{lpath}}. Again, in these cases, \textit{\textbf{lpath}} is a path which is relative to the object in which the variable was referenced. -If \$\textit{\textbf{lpath}} is omitted, then this is equivalent to \$\textit{\textbf{catname}}:. In other words, the the leaf node is the current node, ``.''. (This syntax is often used to count keep track of molecule ID numbers. You can use the counter variable ``\$mol'' to keep track of the current molecule id number, because it counts the molecular objects in which this variable was defined. In this case the name of the category is ``mol''. As in most examples, the category object, \textit{\textbf{cpath}}, is not specified. This means the category object is automatically global. A global category object means that every molecule object is given a unique ID number which is unique for the entire system, not just unique within some local molecule. As a counter-example, consider amino acid residue counters. Each amino acid in a protein can be assigned a residue ID number which identifies it within a single protein chain. However because their category was defined locally at the protein level, these residue ID numbers are not global, and are not uniquely defined if there are multiple protein chains present.) +If \$\textit{\textbf{lpath}} is omitted, then this is equivalent to \$\textit{\textbf{catname}}:. In other words, the the leaf node is the current node, ``.''. (This syntax is often used to count keep track of molecule ID numbers. You can use the counter variable ``\$mol'' to keep track of the current molecule id number, because it counts the molecular objects in which this variable was defined. In this case the name of the category is ``mol''. As in most examples, the category object, \textit{\textbf{cpath}}, is not specified. This means the category object is automatically global. A global category object means that every molecule object is given a unique ID number which is unique for the entire system, not just unique within some local molecule. As a counter-example, consider amino acid residue counters. Each amino acid in a protein can be assigned a residue ID number which identifies it within a single protein chain. However because their category was defined locally at the protein level, these residue ID numbers are not global, and are not uniquely defined if there are multiple protein chains present.) (See section \ref{sec:cpath_simple} for details.) diff --git a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt b/tools/moltemplate/doc/utils/docs_genpoly_lt.txt index dbc751176da0a1eb5b3c82f713d0c7b169d03766..31a0359b6d4275da89a4bbff6189b8076d95fd36 100644 --- a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt +++ b/tools/moltemplate/doc/utils/docs_genpoly_lt.txt @@ -13,22 +13,22 @@ Explanation: Usage: - genpoly_lt.py \\ - [-bond btype a1 a2] \\ - [-helix deltaphi] \\ - [-axis x,y,z] \\ - [-circular yes/no/connected] \\ + genpoly_lt.py \ + [-bond btype a1 a2] \ + [-helix deltaphi] \ + [-axis x,y,z] \ + [-circular yes/no/connected] \ [-dir-indices ia ib] \ - [-angle atype a1 a2 a3 i1 i2 i3] \\ - [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-monomer-name mname] \\ - [-sequence sequence.txt] \\ - [-polymer-name pname] \\ - [-inherits ForceFieldObject] \\ - [-header "import \"monomer.lt\""] \\ - [-cuts cuts.txt] \\ - [-box paddingX,paddingY,paddingZ] \\ + [-angle atype a1 a2 a3 i1 i2 i3] \ + [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \ + [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \ + [-monomer-name mname] \ + [-sequence sequence.txt] \ + [-polymer-name pname] \ + [-inherits ForceFieldObject] \ + [-header "import monomer.lt"] \ + [-cuts cuts.txt] \ + [-box paddingX,paddingY,paddingZ] \ < coords.raw > polymer.lt Arguments (optional): diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt index 05c55482d3b39477ee65e0b531e5e4c3a20e8c99..8d736e72b344a5c0500bd01b9dd95b5a43e61dfc 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt @@ -20,18 +20,18 @@ Benzene inherits GAFF { # atomID molID atomType charge X Y Z write('Data Atoms') { - $atom:C1 $mol @atom:ca -0.115 5.274 1.999 -8.568 - $atom:C2 $mol @atom:ca -0.115 6.627 2.018 -8.209 - $atom:C3 $mol @atom:ca -0.115 7.366 0.829 -8.202 - $atom:C4 $mol @atom:ca -0.115 6.752 -0.379 -8.554 - $atom:C5 $mol @atom:ca -0.115 5.399 -0.398 -8.912 - $atom:C6 $mol @atom:ca -0.115 4.660 0.791 -8.919 - $atom:H11 $mol @atom:ha 0.115 4.704 2.916 -8.573 - $atom:H21 $mol @atom:ha 0.115 7.101 2.950 -7.938 - $atom:H31 $mol @atom:ha 0.115 8.410 0.844 -7.926 - $atom:H41 $mol @atom:ha 0.115 7.322 -1.296 -8.548 - $atom:H51 $mol @atom:ha 0.115 4.925 -1.330 -9.183 - $atom:H61 $mol @atom:ha 0.115 3.616 0.776 -9.196 + $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 + $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 + $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 + $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 + $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 + $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 + $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 + $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 + $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 + $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 + $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 + $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 } write('Data Bond List') { diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt index a3e3ed620ec8b32fb6da484368dc3fc299bad6de..b39d8901ad7317dc16a3afbd97ce23b0156c3593 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b9ff053fcb48e18052a81039fb4a3a8ab65cb1a2 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg deleted file mode 100644 index 00c82d3d9f5f13a5dd36eaee35d982557be2b1b1..0000000000000000000000000000000000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..65949a4684b3102a625d628e8760884493029781 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt index 008391688eb5b9f4f588140423e2849aa153c289..25f58dfde8d4f81b6c94f8b567b0f29a2d4662f1 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt @@ -15,19 +15,20 @@ import "gaff.lt" Benzene inherits GAFF { + # atomID molID atomType charge X Y Z write('Data Atoms') { - $atom:C1 $mol @atom:ca 0.115 5.274 1.999 -8.568 - $atom:C2 $mol @atom:ca 0.115 6.627 2.018 -8.209 - $atom:C3 $mol @atom:ca 0.115 7.366 0.829 -8.202 - $atom:C4 $mol @atom:ca 0.115 6.752 -0.379 -8.554 - $atom:C5 $mol @atom:ca 0.115 5.399 -0.398 -8.912 - $atom:C6 $mol @atom:ca 0.115 4.660 0.791 -8.919 - $atom:H11 $mol @atom:ha -0.115 4.704 2.916 -8.573 - $atom:H21 $mol @atom:ha -0.115 7.101 2.950 -7.938 - $atom:H31 $mol @atom:ha -0.115 8.410 0.844 -7.926 - $atom:H41 $mol @atom:ha -0.115 7.322 -1.296 -8.548 - $atom:H51 $mol @atom:ha -0.115 4.925 -1.330 -9.183 - $atom:H61 $mol @atom:ha -0.115 3.616 0.776 -9.196 + $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 + $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 + $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 + $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 + $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 + $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 + $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 + $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 + $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 + $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 + $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 + $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 } write('Data Bond List') { diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt index f9984a1bb8d4bea7595a2d4f939f9b9f6eeef72e..994b66b2cd21fa5dbcd4bd9df9b5f1ae3eae80c9 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt @@ -4,26 +4,25 @@ import "benzene.lt" # <- defines the "Benzene" molecule type. # Periodic boundary conditions: write_once("Data Boundary") { - 0.0 80.00 xlo xhi - 0.0 80.00 ylo yhi - 0.0 80.00 zlo zhi + 0.0 48.00 xlo xhi + 0.0 48.00 ylo yhi + 0.0 48.00 zlo zhi } -# Create 1000 ethylenes and 500 benzenes +# Create 216 ethylenes and 108 benzenes -ethylenes = new Ethylene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [10].move(0, 0, 8.0) +ethylenes = new Ethylene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [6].move(0, 0, 8.0) -benzenes = new Benzene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [5].move(0, 0, 16.0) +benzenes = new Benzene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [3].move(0, 0, 16.0) # Now shift the positions of all of the benzene molecules, # to reduce the chance that they overlap with the ethylene molecules. benzenes[*][*][*].move(4.0, 4.0, 4.0) -# Note: There is also an example in the OPLSAA directory which shows how to -# generate the coordinates using PACKMOL. That allows us to omit all of -# the coordinates and .move() commands. (This works with AMBER/GAFF too.) +# Note: There is also an example which shows how to generate the coordinates +# using PACKMOL. (That allows us to omit the coordinates and .move() commands.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt index 15283ff82ba9afe695177d33c9f51464a2bf1e05..e06cd825b3984f1dc5d0c81f638dd33adb54f871 100644 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt @@ -35,7 +35,7 @@ include system.in.settings # -- simulation protocol -- -timestep 1.0 +timestep 2.0 dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 thermo 500 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt new file mode 100644 index 0000000000000000000000000000000000000000..5b2fcfb4b26130a1b3258f0be4d6a0bf0446446f --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt @@ -0,0 +1,38 @@ +# -------- WARNING: -------- + +This directory contains some examples of all-atom simulations using the COMPASS +force field. + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that simulations +prepared using moltemplate will reproduce the behavior of other MD codes. + +The moltemplate implementation of COMPASS currently relies on the same +incomplete force-field file that "msi2lmp" uses ("compass_published.frc"). +Unfortunately this means that many force field parameters and some atom types +(such as sp2-carbons) have not (yet) been publicly released and are not +available. + +Currently I recommend that users should run the "cleanup_moltemplate.sh" +script after running "moltemplate.sh system.lt". Then manually check that +the "system.in.settings" and "system.in.charges" files which remain +make sense. Specifically, you must check that the angle_coeff, +dihedral_coeff, bond_coeff commands are not full of zeros (in places +where they should not be zero. This is another consequence of the +fact that the .FRC files I mentioned above are incomplete.) It's a +good idea to also check that the charges in the "system.in.charges" +file seem reasonable (ie. not all zeros). (There is a list of +warnings at the end of the "compass_published.lt" file. You can check +to see if any of the bonds in your system are covered by these +warnings.) Later on hopefully I'll add some automated way to warn +users when these problems arise, but now you should check for them +manually. + +# -------- REQUEST FOR HELP: -------- + +If you notice a problem with these examples, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2017-10-03) + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..7bf9a484d7412991d2f03e945c70c3f849fb4382 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of a long alkane chain, +in a vacuum at room temperature using the COMPASS force field. + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "alkane50.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Alkane50 inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000000000000000000000000000000000..5957289da9592f8a25e6796ea16ceb5e7abde043 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..94d6de972c4b228f570c2f203a03b08ef46cc024 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..5cd2142a4128c41eb75945198e3fcdb8cf9e52b3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3e3ed620ec8b32fb6da484368dc3fc299bad6de --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg new file mode 100644 index 0000000000000000000000000000000000000000..39a88795579f33345539451daac4815f999961a6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg new file mode 100644 index 0000000000000000000000000000000000000000..ab140a8f9ec82a71118681ba46b7b3ba8365ea7b Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg new file mode 100644 index 0000000000000000000000000000000000000000..39633edd5e6987b9b6f72e09ce493a1e3f3ff018 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg new file mode 100644 index 0000000000000000000000000000000000000000..da2fe1185e571b35f1199805a1f37645b2f5c787 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt new file mode 100644 index 0000000000000000000000000000000000000000..da75694c4536abc41819853c7ef4d0be9f2bd4fa --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt @@ -0,0 +1,137 @@ +# This is a simple example showing how to build a long polymer +# (in this case, an alkane chain). I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + + +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + + +Alkane50 inherits COMPASS { + + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps. + # Rather than create them one-by-one, I decided to create them all + # using a single "new" command. Later, I can modify this array. + + # Create an array of 50 "CH2" objects distributed along the X axis + + monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0) + + # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each + # successive monomer is rotated 180 degrees (with respect to the previous + # monomer), and then moved 1.2533223 Angstroms down the X axis. + # Alternately, if you are reading the coordinates from a file, you don't have + # to indicate the position & orientation of each monomer. In that case, use: + # monomers = new CH2 [50] + + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + + delete monomers[0] + delete monomers[49] + + monomers[0] = new CH3 + monomers[49] = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place) + monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223 + + + ## NOTE: Alternately, you can define the polymer without deleting the ends: + # monomers[0] = new CH3 + # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0) + ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room: + # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers + ## Now add the final monomer at the end: + # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0) + # + ## NOTE: Alternately, you can read the coordinates from a file. + ## In that case, you can use simpler commands: + # monomers[0] = new CH3 + # monomers[1-48] = new CH2[48] + # monomers[49] = new CH3 + + + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C + $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C + $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C + $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C + $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C + $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C + $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C + $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C + $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C + $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C + $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C + $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C + $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C + $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C + $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C + $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C + $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C + $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C + $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C + $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C + $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C + $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C + $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C + $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C + $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C + $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C + $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C + $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C + $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C + $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C + $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C + $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C + $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C + $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C + $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C + } + +} # Alkane50 + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000000000000000000000000000000000..9bf2c82d7d37e4a696ef52546786f5dc0cb2822e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt @@ -0,0 +1,76 @@ +# This file contains a definition for the "CH2" molecular subunit. + +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) + + +# Then define "CH2": + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + + # COMMENTS: + # 1) Atom type names are defined in "compass_published.lt". + # 2) In this example, the atomic charge of an atom is calculated by summing + # partial charge contributions from neighboring atoms bonded to this atom. + # (according to the rules in "compass_published.lt"). For this reason, + # we can ignore the "charge" column in the "Data Atoms" section. Just + # leave theses charges as "0.0" for now. Moltemplate will recalculate them. + # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part + # of a larger molecule, and (if so) to use the larger parent object's + # molecule id number as it's own. + +} # CH2 + + + + + + + + + + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000000000000000000000000000000000..e66579bf0b62decb82cd733ac0e514f4937c6251 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt @@ -0,0 +1,78 @@ +# This file contains a definition for the "CH3" molecular subunit. + +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) + + +# Then define "CH3": + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + + # COMMENTS: + # 1) Atom type names are defined in "compass_published.lt". + # 2) In this example, the atomic charge of an atom is calculated by summing + # partial charge contributions from neighboring atoms bonded to this atom. + # (according to the rules in "compass_published.lt"). For this reason, + # we can ignore the "charge" column in the "Data Atoms" section. Just + # leave theses charges as "0.0" for now. Moltemplate will recalculate them. + # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part + # of a larger molecule, and (if so) to use the larger parent object's + # molecule id number as it's own. + +} # CH3 + + + + + + + + + + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..39c8e4f78d1ae87fd29959d9cc691d8fd2579bcd --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt @@ -0,0 +1,30 @@ +import "alkane50.lt" # Defines the "Alkane50" molecule + + +polymer = new Alkane50 + + +# Specify the size of the world the polymer lives in: +write_once("Data Boundary") { + 0.0 72.0 xlo xhi + 0.0 72.0 ylo yhi + 0.0 72.0 zlo zhi +} + + + + + +############################################################################### +# Note: If you want to create multiple polymers, and/or mix them with other +# molecules, just add more "new" commands, for example: +# polymer1 = new Alkane50.move(0,0,10) +# polymer2 = new Alkane50.move(0,0,20) +# : +# ...or use array notation, for example: +# polymers = new Alkane50[20].move(0,0,10) +# +# Note: Multidimensional arrays can be used to fill a planar region or a volume +# polymers = new Alkane50 [4].move(0, 0, 30.0) +# [4].move(0, 30.0, 0) +# [2].move(70.0, 0, 0) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min new file mode 100644 index 0000000000000000000000000000000000000000..5d0bcffd8eccb8f9854b7d39a612f466e63b2871 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min @@ -0,0 +1,37 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" +include "system.in.charges" + +# ------------------------------- Run Section ------------------------------- + + +# -- minimization protocol -- + +# Note: The minimization step is not necessary in this example. However +# in general, it's always a good idea to minimize the system beforehand. + +thermo 50 +dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz +minimize 1.0e-4 1.0e-6 100000 400000 + + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + +write_data system_after_min.data + + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt new file mode 100644 index 0000000000000000000000000000000000000000..d5b77423a280b957773ed657fd13706416a7fbe9 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt @@ -0,0 +1,38 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must minimize the system beforehand by using "run.in.min". +# This will create the file "system_after_min.data" which this file reads. + +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +# Read the coordinates generated by an earlier simulation + +read_data "system_after_min.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" +include "system.in.charges" + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo 500 +#thermo_modify flush yes + +run 1000000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..7a16faaed75d4bdedfd275e52af0d1a9df6be2df --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of many short alkane chains (butane) in +a box near the boiling point at atmospheric pressure.(Please read "WARNING.TXT") + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Butane" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "butane.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Butane inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000000000000000000000000000000000..5957289da9592f8a25e6796ea16ceb5e7abde043 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..94d6de972c4b228f570c2f203a03b08ef46cc024 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..5cd2142a4128c41eb75945198e3fcdb8cf9e52b3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt new file mode 100644 index 0000000000000000000000000000000000000000..3ddb8e60655d7626119779d278da0e497c1fe76e --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.9 -style tubes + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..093f557dd9011f11456a082bcfbe1340b94c5df6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg new file mode 100644 index 0000000000000000000000000000000000000000..d1a6e5060ba85d475a2160190a211eb3a3a1dee0 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg new file mode 100644 index 0000000000000000000000000000000000000000..39a88795579f33345539451daac4815f999961a6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg new file mode 100644 index 0000000000000000000000000000000000000000..3fa79ce3600f449e256120e6b65681140f35122b Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9fa7d195f3db76d596c4d37116daabbba0c40e39 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt new file mode 100644 index 0000000000000000000000000000000000000000..ed2c65640e58cde7731a6d49975bd2eb1eccee5c --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt @@ -0,0 +1,39 @@ +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + +Butane inherits COMPASS { + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # Create an array of 4 objects distributed along the X axis + + monomer1 = new CH3 + monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) + monomer3 = new CH2.move(2.5066446,0,0) + monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomer1/C $atom:monomer2/C + $bond:b2 $atom:monomer2/C $atom:monomer3/C + $bond:b3 $atom:monomer3/C $atom:monomer4/C + } + +} # Butane + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000000000000000000000000000000000..c281e4d6ff2025c47c8a82c58dfc5676730dad5a --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt @@ -0,0 +1,71 @@ +# This file contains a definition for the "CH2" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH2": + + + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000000000000000000000000000000000..394080230a69111042d62d8aab289d54a10ea615 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH3" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH3": + + + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..1f25ac8e96d1ea4a9438f8fb22b56e4d92543396 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt @@ -0,0 +1,24 @@ +import "butane.lt" # <- defines the "Butane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + + + +# Generate an array of 864 = 12 x 12 x 6 Butane molecules +# which (more or less) uniformly fills the simulation box: + +molecules = new Butane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [6].move(10.4, 0, 0) + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt new file mode 100644 index 0000000000000000000000000000000000000000..ec9af62c4026f783a6300f671e6667c3debbe6d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt @@ -0,0 +1,103 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 10000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt new file mode 100644 index 0000000000000000000000000000000000000000..ea3ac4216763791c33c2c5fec23adb67b0b64d02 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ffefbc7f31af432202b5e9da33ca0f5ad562a58 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt @@ -0,0 +1,42 @@ +This example is a simple simulation of many long alkane chains (hexadecane) in a +box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". + +NOTE: This particular example uses the COMPASS force-field + However, moltemplate is not limited to COMPASS. + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains +use the COMPASS force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "compass_published.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "hexadecane.lt" files all refer to "compass_published.lt", +(as well as the "COMPASS" force-field object which it defines). Excerpt: + +import "compass_published.lt" +CH2 inherits COMPASS { ... +CH3 inherits COMPASS { ... +Hexadecane inherits COMPASS { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) + + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000000000000000000000000000000000..5957289da9592f8a25e6796ea16ceb5e7abde043 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..4871a06495cd92b8c5dd6a9d6397c2a2740fb983 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh @@ -0,0 +1,21 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.npt # minimization and simulation at constant pressure +lmp_mpi -i run.in.nvt # simulation at constant volume + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..15a3a963c860bbb7f0ca70c7ad13a16c5bc551aa --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3e3ed620ec8b32fb6da484368dc3fc299bad6de --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} + pbc box -shiftcenterrel {0.0 0.15 0.0} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt new file mode 100644 index 0000000000000000000000000000000000000000..ab508fc8948081f8d8899387d105c4afd04f3284 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt @@ -0,0 +1,13 @@ +# -------- WARNING: -------- + +This software is experimental, and the force-fields and equilbration protocols +have not been tested carefully by me. There is no gaurantee that the simulation +will reproduce the behavior of real hexadecane molecules, + +# -------- REQUEST FOR HELP: -------- + +However, if you notice a problem with this example, please report it. +Peer-review is the only way to improve this software (or any software). +Other suggestions are also welcome! + +(Contact jewett.aij@gmail.com, 2017-10-03) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b0d31f88453d4594681cc81791d66c5c1e8c0b99 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..f7c13d0989c124f0c1ecd791045fb525f14a3f3b Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..a4151a5fd34691d3986dd4e73f290c7bf41b1ae9 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000000000000000000000000000000000..db7ccabdc96ca5468dfc2c77f605b2ef5092fdc8 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH2" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH2": + + + + +CH2 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000000000000000000000000000000000..394080230a69111042d62d8aab289d54a10ea615 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt @@ -0,0 +1,70 @@ +# This file contains a definition for the "CH3" molecular subunit. +# First, load the COMPASS force field parameters we will need: + +import "compass_published.lt" # <-- defines the "COMPASS" force field + +# (The "compass_published.lt" file is located in the "force_fields" +# subdirectory distributed with moltemplate.) +# Then define "CH3": + + + + +CH3 inherits COMPASS { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# COMMENTS: +# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". +# 2) In this example, the atomic charge of an atom is calculated by summing +# partial charge contributions from neighboring atoms bonded to this atom. +# (according to the rules in "compass_published.lt"). For this reason, +# we can ignore the "charge" column in the "Data Atoms" section. Just +# leave theses charges as "0.0" for now. Moltemplate will recalculate them. +# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt new file mode 100644 index 0000000000000000000000000000000000000000..23d1c229a142f212019fb01ceacd3f10655aeb8a --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt @@ -0,0 +1,79 @@ +# This example looks complicated because I split the +# hexadecane molecule into individual CH2 and CH3 monomers. +# +# I defined it this way so that you can easily modify +# it to change the length of the alkane chain. + + +import "compass_published.lt" # load the "COMPASS" force-field information +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + + +Hexadecane inherits COMPASS { + + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + + # Now create an array of 16 "CH2" objects distributed along the X axis + + monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0) + + # Each monomer is rotated 180 degrees with respect to the previous + # monomer, and then moved 1.2533223 Angstroms down the X axis. + + # ---- Now, modify the ends: --- + # Delete the CH2 groups at the beginning and end, and replace them with CH3. + + delete monomers[0] + delete monomers[15] + + monomers[0] = new CH3 + monomers[15] = new CH3 + + # Move the CH3 groups to the correct location at either end of the chain: + + monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0) + # Note: 18.7998345 = (16-1) * 1.2533223 + + + # Now add a list of bonds connecting the carbon atoms together: + + write('Data Bond List') { + $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C + $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C + $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C + $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C + $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C + $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C + $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C + $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C + $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C + $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C + $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C + $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C + $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C + $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C + $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C + } + +} # Hexadecane + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..9d90d39c20028c8f114292bcdf9305eae214fe13 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt @@ -0,0 +1,20 @@ +import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + +molecules = new Hexadecane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [2].move(31.2, 0, 0) + + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt new file mode 100644 index 0000000000000000000000000000000000000000..2e9c49681741241532c5acfe5194d35946fa4adb --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt @@ -0,0 +1,102 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 50000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. We do that here: +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt new file mode 100644 index 0000000000000000000000000000000000000000..739396192469bc680f4e4624d92b87891bb348b7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..4a6377569d9f8ebc89afea32fac1c9e7951ffcc4 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt @@ -0,0 +1,37 @@ +This example is a simple simulation of many short alkane chains (butane) in a +box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". + +1) Create the "system.data", "system.in.init", and "system.in.settings" +files which LAMMPS will read by running: + +moltemplate.sh system.lt + + +2) Run LAMMPS in this order: + +lmp_mpi -i run.in.npt # running the simulation at constant pressure +lmp_mpi -i run.in.nvt # running the simulation at constant temperature + +(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) + +---- Details ---- + +The "Butane50" molecule, as well as the "CH2", and "CH3" monomers it contains +use the OPLSAA force-field. This means that when we define these molecules, +we only specify the atom names, bond list, and coordinates. +We do not have to list the atom charges, angles, dihedrals, or impropers. +The rules for creating atomic charge and angle topology are contained in +the "oplsaa.lt" file created by step 3) above. The "ch2group.lt", +"ch3group.lt", and "butane.lt" files all refer to "oplsaa.lt", +(as well as the "OPLSAA" force-field object which it defines). Excerpt: + +import "oplsaa.lt" +CH2 inherits OPLSAA { ... +CH3 inherits OPLSAA { ... +Butane inherits OPLSAA { ... + +Alternatively, you can manually define a list of angles, dihedrals, and +improper interactions in these files, instead of asking the force-field +to generate them for you. You can also specify some of the angles and +dihedrals explicitly, and let the force-field handle the rest. +(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh new file mode 100755 index 0000000000000000000000000000000000000000..5957289da9592f8a25e6796ea16ceb5e7abde043 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh @@ -0,0 +1,8 @@ + +# Note: By default, the system.data and system.in.settings files contain +# extra information for atoms defined in OPLSAA which you are not using +# in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: + +cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..94d6de972c4b228f570c2f203a03b08ef46cc024 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh @@ -0,0 +1,34 @@ +# --- Running LAMMPS --- +# +# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS +# input scripts which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.min # minimization +lmp_mpi -i run.in.nvt # minimization and simulation at constant volume + +#(Note: The constant volume simulation lacks pressure equilibration. These are +# completely separate simulations. The results of the constant pressure +# simulation might be ignored when beginning the simulation at constant +# volume. (This is because restart files in LAMMPS don't always work, +# and I was spending a lot of time trying to convince people it was a +# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) +# Read the "run.in.nvt" file to find out how to use the "read_restart" +# command to load the results of the pressure-equilibration simulation, +# before beginning a constant-volume run. + + + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..5cd2142a4128c41eb75945198e3fcdb8cf9e52b3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh @@ -0,0 +1,34 @@ + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # Optional: + # To check for missing angle,dihedral params run moltemplate this way instead: + # moltemplate.sh -checkff system.lt + + + # Moltemplate generates various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ + + + + +# Optional: +# Note: The system.data and system.in.settings files contain extra information +# for atoms defined in OPLSAA which you are not using in this simulation. +# This is harmless, but if you to delete this information from your +# system.in.settings and system.in.data files, run this script: +# +# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt new file mode 100644 index 0000000000000000000000000000000000000000..b39d8901ad7317dc16a3afbd97ce23b0156c3593 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt @@ -0,0 +1,87 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + Sometimes the solvent or membrane obscures the view of the solute. + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..093f557dd9011f11456a082bcfbe1340b94c5df6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg new file mode 100644 index 0000000000000000000000000000000000000000..a1bcb4aee6f85ffe4d15f1acbafa1161fccc2d9c Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg new file mode 100644 index 0000000000000000000000000000000000000000..39a88795579f33345539451daac4815f999961a6 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg new file mode 100644 index 0000000000000000000000000000000000000000..ab140a8f9ec82a71118681ba46b7b3ba8365ea7b Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..9fa7d195f3db76d596c4d37116daabbba0c40e39 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt new file mode 100644 index 0000000000000000000000000000000000000000..8c21db265c46332dbe7fa9b1520860f8c10063ad --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt @@ -0,0 +1,42 @@ +import "ch2group.lt" # load the definition of the "CH2" object +import "ch3group.lt" # load the definition of the "CH3" object + + +Butane inherits OPLSAA { + + create_var {$mol} # optional:force all monomers to share the same molecule-ID + + # Create an array of 4 objects distributed along the X axis + + monomer1 = new CH3 + monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) + monomer3 = new CH2.move(2.5066446,0,0) + monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) + + # Now add a list of bonds connecting the carbon atoms together: + # (Angles, dihedrals, impropers will be automatically added later.) + + write('Data Bond List') { + $bond:b1 $atom:monomer1/C $atom:monomer2/C + $bond:b2 $atom:monomer2/C $atom:monomer3/C + $bond:b3 $atom:monomer3/C $atom:monomer4/C + } + +} # Butane + + + + + + + + +######### (scratchwork calculations for the atomic coordinates) ######### +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163316030377 +# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 +# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt new file mode 100644 index 0000000000000000000000000000000000000000..665e8e6607286c8c81cc8cce31412e07ea9201b3 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt @@ -0,0 +1,67 @@ +# This file contains a definition for the "CH2" molecular subunit. + +# First, load the OPLS force field parameters we will need. +# This file is located in the "force_fields" subdirectory +# of the moltemplate distribution. + +import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field + + +# Then define "CH2": + + +CH2 inherits OPLSAA { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:81 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + } + +} # CH2 + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH2.move(0,0.4431163,0) + + + + +# ---- NOTES: ---- +# +# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", +# @atom:80 "Alkane CH3-" +# @atom:81 "Alkane -CH2-" +# @atom:85 "Alkane H-C CH3" +# @atom:85 "Alkane H-C CH2" +# In this example, atomic charges are generated by atom type (according to the +# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. +# The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. +# +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt new file mode 100644 index 0000000000000000000000000000000000000000..bf802b31627504efc7765fb24a277ed033b4ead0 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt @@ -0,0 +1,69 @@ +# This file contains a definition for the "CH3" molecular subunit. + +# First, load the OPLS force field parameters we will need. +# This file is located in the "force_fields" subdirectory +# of the moltemplate distribution. + +import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field + + +# Then define "CH3": + + +CH3 inherits OPLSAA { + + # atom-id mol-id atom-type charge x y z + + write("Data Atoms") { + $atom:C $mol:... @atom:80 0.0 0.000000 0.000000 0.000000 + $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 + $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 + $atom:H3 $mol:... @atom:85 0.0 -0.892431 -0.631044 0.000000 + } + + write('Data Bond List') { + $bond:CH1 $atom:C $atom:H1 + $bond:CH2 $atom:C $atom:H2 + $bond:CH3 $atom:C $atom:H3 + } + +} # CH3 + + + + +# Optional: Shift all the coordinates in the +Y direction by 0.4431163. +# This way, the carbon atom is no longer located at 0,0,0, but the +# axis of an alkane chain containing this monomer is at 0,0,0. +# (This makes it more convenient to construct a polymer later. +# If this is confusing, then simply add 0.4431163 to the Y +# coordinates in the "Data Atoms" section above.) + +CH3.move(0,0.4431163,0) + + + + +# ---- NOTES: ---- +# +# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", +# @atom:80 "Alkane CH3-" +# @atom:81 "Alkane -CH2-" +# @atom:85 "Alkane H-C CH3" +# @atom:85 "Alkane H-C CH2" +# In this example, atomic charges are generated by atom type (according to the +# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. +# The "..." in "$mol:..." tells moltemplate that this molecule may be part +# of a larger molecule, and (if so) to use the larger parent object's +# molecule id number as it's own. +# +######### (scratchwork calculations for the atomic coordinates) ######### +# +# Lcc = 1.5350 # length of the C-C bond (Sp3) +# Lch = 1.0930 # length of the C-H bond +# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) +# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 +# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 +# # 0.5*DeltaYc = 0.4431163 +# DeltaZh = Lch*sin(theta/2) # = 0.892431 +# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..52b5126494d0b58014e129b30c9659060d0e2ada --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt @@ -0,0 +1,25 @@ +import "butane.lt" # <- defines the "Butane" molecule type. + +# Periodic boundary conditions: +write_once("Data Boundary") { + 0.0 62.4 xlo xhi + 0.0 62.4 ylo yhi + 0.0 62.4 zlo zhi +} + + + +# Generate an array of 864 = 12 x 12 x 6 Butane molecules +# which (more or less) uniformly fills the simulation box: + +molecules = new Butane [12].move(0, 0, 5.2) + [12].move(0, 5.2, 0) + [6].move(10.4, 0, 0) + + + + +# NOTE: The spacing between molecules is large. There should be extra room to +# move during the initial stages of equilibration. However, you will have to +# run the simulation at NPT conditions later to compress the system to a +# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt new file mode 100644 index 0000000000000000000000000000000000000000..ec9af62c4026f783a6300f671e6667c3debbe6d7 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt @@ -0,0 +1,103 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + +read_data system.data + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, +# reorient, compress). The system (as defined in the "system.data" file) +# is already expanded. That means there are 3 steps left: + +dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz +thermo_style custom step temp pe etotal epair ebond eangle edihed press vol +thermo 50 +thermo_modify norm yes + +# -- Equilibration: part 1: initial minimization -- + +# Note: In general, it's always a good idea to minimize the system at first. + +minimize 1.0e-5 1.0e-7 100000 400000 +undump dumpeq1 + +write_data system_after_eq1_min.data + +# -- Equilibration part 2: reorienting the molecules (NVT) -- + +timestep 1.0 +dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz + +# Run the system at high temperature (at constant volume) to reorient the +# the molecules (which would otherwise be pointing in the same direction). + +# To speed it up, I randomize the atomic positions for a few thousand steps +# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). +# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) + + +fix fxlan all langevin 900.0 900.0 120 48279 +fix fxnve all nve + +run 4000 + +unfix fxlan +unfix fxnve +# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). +fix fxnvt all nvt temp 900.0 900.0 100.0 + +run 10000 +undump dumpeq2 + + +write_data system_after_eq2_reorient.data + +unfix fxnvt + + +# -- equilibration part 3: Equilibrating the density (NPT) -- + +# Originally, the simulation box (in "system.data" and "system.lt") was +# unrealistically large. The spacing between the molecules was large also. +# I did this to enable the molecules to move freely and reorient themselves. +# After doing that, we should run the simulation under NPT conditions to +# allow the simulation box to contract to it's natural size. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) + +dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 + +timestep 1.0 +run 100000 + +write_data system_after_eq3_npt.data + diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt new file mode 100644 index 0000000000000000000000000000000000000000..ea3ac4216763791c33c2c5fec23adb67b0b64d02 --- /dev/null +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt @@ -0,0 +1,45 @@ +# PREREQUISITES: +# +# 1) You must use moltemplate.sh to create 3 files: +# system.data system.in.init system.in.settings +# (Follow the instructions in README_setup.sh, +# or run the file as a script using ./README_setup.sh) +# 2) You must equilibrate the system beforehand using "run.in.npt". +# This will create the file "system_after_npt.data" which this file reads. +# (Note: I have not verified that this equilibration protocol works well.) + +# ------------------------------- Initialization Section -------------------- + +include system.in.init + +# ------------------------------- Atom Definition Section ------------------- + + +# Read the coordinates generated by an earlier NPT simulation + +read_data system_after_eq3_npt.data + +# (The "write_restart" and "read_restart" commands were buggy in 2012, +# but they should work also. I prefer "write_data" and "read_data".) + + +# ------------------------------- Settings Section -------------------------- + +include system.in.settings +include system.in.charges + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + + +timestep 1.0 +dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz +fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed +thermo 100 +thermo_modify norm yes + +run 50000 + +write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt index f744e1718fcbe3467f97ee691e801caa5b070929..470df8755090e6374c0d4a8a1727282f70ba654f 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt @@ -1,8 +1,5 @@ This is an example of how to use the OPLSAA force-field in LAMMPS -As of 2016-11-21, this code has not been tested for accuracy. -(See the WARNING.TXT file.) - step 1) To build the files which LAMMPS needs, follow the instructions in: README_setup.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt index a3e3ed620ec8b32fb6da484368dc3fc299bad6de..642c85c24cbad565ec7aeecd3e9ebf42ac285654 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} + pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.5 Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b9ff053fcb48e18052a81039fb4a3a8ab65cb1a2 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg deleted file mode 100644 index 00c82d3d9f5f13a5dd36eaee35d982557be2b1b1..0000000000000000000000000000000000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..65949a4684b3102a625d628e8760884493029781 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt index 1293cb1e4d2f7d3aac99aa6a3785476852c0b67a..5f5e8d904afe3647f7340a39130fc84e9c638899 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type @atom:90 corresponds to "Aromatic C" @@ -9,25 +9,32 @@ import "oplsaa.lt" Benzene inherits OPLSAA { - write('Data Atoms') { - $atom:C1 $mol @atom:90 0.00 5.274 1.999 -8.568 # "Aromatic C" - $atom:C2 $mol @atom:90 0.00 6.627 2.018 -8.209 # "Aromatic C" - $atom:C3 $mol @atom:90 0.00 7.366 0.829 -8.202 # "Aromatic C" - $atom:C4 $mol @atom:90 0.00 6.752 -0.379 -8.554 # "Aromatic C" - $atom:C5 $mol @atom:90 0.00 5.399 -0.398 -8.912 # "Aromatic C" - $atom:C6 $mol @atom:90 0.00 4.660 0.791 -8.919 # "Aromatic C" - $atom:H11 $mol @atom:91 0.00 4.704 2.916 -8.573 # "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 7.101 2.950 -7.938 # "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 8.410 0.844 -7.926 # "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 7.322 -1.296 -8.548 # "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 4.925 -1.330 -9.183 # "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 3.616 0.776 -9.196 # "Aromatic H-C" + # atom-id mol-id atom-type charge X Y Z # comment + + write("Data Atoms") { + $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" + $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" + $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" + $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" + $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" + $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" + $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" + $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" + $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" + $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" + $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" + $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" } # Note: You don't have to specify the charge in this example because # we are using the OPLSAA force-field assigns this by atom-type. # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 - write('Data Bond List') { + write("Data Bond List") { $bond:C12 $atom:C1 $atom:C2 $bond:C23 $atom:C2 $atom:C3 $bond:C34 $atom:C3 $atom:C4 @@ -42,4 +49,7 @@ Benzene inherits OPLSAA { $bond:C6H6 $atom:C6 $atom:H61 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt index 626c731b020f5ff7d5e12f51f92dc443c04effe2..3515702d1dda455ee5bda063cb74d847c947b8d7 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type 88 corresponds to "Alkene H2-C=" @@ -11,19 +11,24 @@ import "oplsaa.lt" Ethylene inherits OPLSAA { - # atom-id mol-id atom-type charge X Y Z + # atom-id mol-id atom-type charge X Y Z # comment write('Data Atoms') { - $atom:C1 $mol @atom:88 0.00 -0.6695 0.000000 0.000000 - $atom:C2 $mol @atom:88 0.00 0.6695 0.000000 0.000000 - $atom:H11 $mol @atom:89 0.00 -1.234217 -0.854458 0.000000 - $atom:H12 $mol @atom:89 0.00 -1.234217 0.854458 0.000000 - $atom:H21 $mol @atom:89 0.00 1.234217 -0.854458 0.000000 - $atom:H22 $mol @atom:89 0.00 1.234217 0.854458 0.000000 + $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" + $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" } # Note: You don't have to specify the charge in this example because # we are using the OPLSAA force-field assigns this by atom-type. # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 write('Data Bond List') { $bond:C12 $atom:C1 $atom:C2 @@ -33,11 +38,8 @@ Ethylene inherits OPLSAA { $bond:C2H2 $atom:C2 $atom:H22 } -} # Ethylene - + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -# Note: You don't need to supply the partial partial charges of the atoms. -# If you like, just fill the fourth column with zeros ("0.000"). -# Moltemplate and LAMMPS will automatically assign the charge later +} # Ethylene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt index 49458a5b42d9d8852bc8ae3883a3bbdbde46f689..a28fd9f4afa0ac1965b3f510d24e77e848681158 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt @@ -4,20 +4,20 @@ import "benzene.lt" # <- defines the "Benzene" molecule type. # Periodic boundary conditions: write_once("Data Boundary") { - 0.0 80.00 xlo xhi - 0.0 80.00 ylo yhi - 0.0 80.00 zlo zhi + 0.0 48.00 xlo xhi + 0.0 48.00 ylo yhi + 0.0 48.00 zlo zhi } -# Create 1000 ethylenes and 500 benzenes +# Create 216 ethylenes and 108 benzenes -ethylenes = new Ethylene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [10].move(0, 0, 8.0) +ethylenes = new Ethylene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [6].move(0, 0, 8.0) -benzenes = new Benzene[10].move(8.0, 0, 0) - [10].move(0, 8.0, 0) - [5].move(0, 0, 16.0) +benzenes = new Benzene[6].move(8.0, 0, 0) + [6].move(0, 8.0, 0) + [3].move(0, 0, 16.0) # Now shift the positions of all of the benzene molecules, # to reduce the chance that they overlap with the ethylene molecules. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt index 2f3b81c18690095aae3cfff3e5a9541ae8b61582..09b6a6b1469adc545f313540a357824eef52524d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt @@ -40,7 +40,7 @@ include system.in.settings # -- simulation protocol -- -timestep 1.0 +timestep 2.0 dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 thermo 500 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt index f240a091fe47648a9bd7f645314329ad960fc1ac..5f5e8d904afe3647f7340a39130fc84e9c638899 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type @atom:90 corresponds to "Aromatic C" @@ -9,31 +9,32 @@ import "oplsaa.lt" Benzene inherits OPLSAA { - # We just need a list of atom types and bonds. - # - # You don't have to specify the charge in this example because we are - # using the OPLSAA force-field assigns this by atom-type. - # - # You also don't have to specify the coordinates, because - # you are using PACKMOL to generate them for you. - # Just leave these numbers as 0.00 for now.. - - write('Data Atoms') { - $atom:C1 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C2 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C3 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C4 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C5 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:C6 $mol @atom:90 0.00 0.00 0.00 0.00 # "Aromatic C" - $atom:H11 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 0.00 0.00 0.00 # "Aromatic H-C" + # atom-id mol-id atom-type charge X Y Z # comment + + write("Data Atoms") { + $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" + $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" + $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" + $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" + $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" + $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" + $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" + $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" + $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" + $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" + $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" + $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" } + # Note: You don't have to specify the charge in this example because + # we are using the OPLSAA force-field assigns this by atom-type. + # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 - write('Data Bond List') { + write("Data Bond List") { $bond:C12 $atom:C1 $atom:C2 $bond:C23 $atom:C2 $atom:C3 $bond:C34 $atom:C3 $atom:C4 @@ -48,4 +49,7 @@ Benzene inherits OPLSAA { $bond:C6H6 $atom:C6 $atom:H61 } + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") + } # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt index 45adb1faefd80203cba7b24117e84b1671093177..3515702d1dda455ee5bda063cb74d847c947b8d7 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt @@ -1,7 +1,7 @@ import "oplsaa.lt" -# The "oplsaa.lt" file contains force-field definitions and masses for the -# atoms in your system. See oplsaa_lt_generator/README.TXT for details. +# The "oplsaa.lt" file contains force-field definitions, +# partial charges and masses for the atoms in your system. # Note: # Atom type 88 corresponds to "Alkene H2-C=" @@ -11,16 +11,24 @@ import "oplsaa.lt" Ethylene inherits OPLSAA { - # atom-id mol-id atom-type charge X Y Z + # atom-id mol-id atom-type charge X Y Z # comment write('Data Atoms') { - $atom:C1 $mol @atom:88 0.000 -0.6695 0.000000 0.000000 - $atom:C2 $mol @atom:88 0.000 0.6695 0.000000 0.000000 - $atom:H11 $mol @atom:89 0.000 -1.234217 -0.854458 0.000000 - $atom:H12 $mol @atom:89 0.000 -1.234217 0.854458 0.000000 - $atom:H21 $mol @atom:89 0.000 1.234217 -0.854458 0.000000 - $atom:H22 $mol @atom:89 0.000 1.234217 0.854458 0.000000 + $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" + $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" + $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" + $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" } + # Note: You don't have to specify the charge in this example because + # we are using the OPLSAA force-field assigns this by atom-type. + # Just leave these numbers as 0.00 for now. + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you + + # A list of the bonds in the molecule + # BondID AtomID1 AtomID2 write('Data Bond List') { $bond:C12 $atom:C1 $atom:C2 @@ -30,11 +38,8 @@ Ethylene inherits OPLSAA { $bond:C2H2 $atom:C2 $atom:H22 } -} # Ethylene - + # In the "Data Bond List" section we don't have to specify the bond type. + # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -# Note: You don't need to supply the partial partial charges of the atoms. -# If you like, just fill the fourth column with zeros ("0.000"). -# Moltemplate and LAMMPS will automatically assign the charge later +} # Ethylene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz index 1a727ff40c75dd3956ef49090db30200038af9dc..76af48514499cec8c4b1882711fb8f253f12ab9c 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz @@ -1,14 +1,14 @@ 12 Benzene -C1 5.274 1.999 -8.568 -C2 6.627 2.018 -8.209 -C3 7.366 0.829 -8.202 -C4 6.752 -0.379 -8.554 -C5 5.399 -0.398 -8.912 -C6 4.660 0.791 -8.919 -H11 4.704 2.916 -8.573 -H21 7.101 2.950 -7.938 -H31 8.410 0.844 -7.926 -H41 7.322 -1.296 -8.548 -H51 4.925 -1.330 -9.183 -H61 3.616 0.776 -9.196 +C1 -0.739 1.189 -0.00733 +C2 0.614 1.208 0.35167 +C3 1.353 0.019 0.35867 +C4 0.739 -1.189 0.00667 +C5 -0.614 -1.208 -0.35133 +C6 -1.353 -0.019 -0.35833 +H11 -1.309 2.106 -0.01233 +H21 1.088 2.14 0.62267 +H31 2.397 0.034 0.63467 +H41 1.309 -2.106 0.01267 +H51 -1.088 -2.14 -0.62233 +H61 -2.397 -0.034 -0.63533 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt index 1450f1dd59d42494f2cbedc0a516bb79ec282dc3..bfd39e8f47e081c8c8ad99fc987dad2ecea1349d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt @@ -1,5 +1,5 @@ This example is a simple simulation of many long alkane chains (hexadecane) in a -box at room temperature and atmospheric pressure. Please read "WARNING.TXT". +box near the boiling point atmospheric pressure. Please read "WARNING.TXT". NOTE: This particular example uses the OPLSAA force-field However, moltemplate is not limited to OPLSAA. @@ -12,7 +12,6 @@ moltemplate.sh system.lt 2) Run LAMMPS in this order: -lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... lmp_mpi -i run.in.npt # running the simulation at constant pressure lmp_mpi -i run.in.nvt # running the simulation at constant temperature diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt index e06bf0caa1402ceaba9bbfb628452be8025d8c39..215e7fcf913663ab4d5c9284d41c8e767b724a3d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt @@ -2,9 +2,7 @@ This software is experimental, and the force-fields and equilbration protocols have not been tested carefully by me. There is no gaurantee that the simulation -will reproduce the behavior of real hexadecane molecules, -(or even of hexadecane molecules simulated using AMBER, which should - be using the same force-field). +will reproduce the behavior of real hexadecane molecules # -------- REQUEST FOR HELP: -------- diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..5a5a188aed02493aa5fd49b20439f84ad127f489 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..65e20353ca70955d22afffc5f07709f828d3d561 Binary files /dev/null and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg index 3ad353dbb4e083ccc07be687ea044170e86ec952..a4151a5fd34691d3986dd4e73f290c7bf41b1ae9 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg and b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt index 05091ba39c8bb1d27bd3c8e050d4a8f6cbc91380..c800d56679dcd07557883078c334077cb550fdaa 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt @@ -2,7 +2,7 @@ # First, load the OPLS force field parameters we will need. # These 2 files are located in the "force_fields" subdirectory -# of the moltemplate distribution. +# distributed with moltemplate. import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt index 1b1a28fabc413c1dda4410bfb5b1317370c37325..f30c796b475c7f8b7e124a5f3ebaedfa13bb876d 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt @@ -74,11 +74,24 @@ unfix fxnvt # I did this to enable the molecules to move freely and reorient themselves. # After doing that, we should run the simulation under NPT conditions to # allow the simulation box to contract to it's natural size. We do that here: -# We begin the simulation at 100 barr (a relatively low pressure), and -# slowly decrease it to 1 barr, maintianing the temperature at 300K. +# To help it collapse, we begin the simulation at a relatively high pressure +# Later on, we will slowly decrease it to 1 bar. + +# First cool the system. (Do this at high pressure to avoid bubble formation.) dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 +fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 + +timestep 1.0 +run 20000 + +# At the very end of the previous simulation, the temperature dropped below +# the boiling point. Run the simulation for longer at these conditions to +# give it a chance for the vapor -> liquid transition to complete. +# We will also slowly decrease the pressure to 1 bar. + +unfix fxnpt +fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 timestep 1.0 run 100000 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt index 38815745c5a0306fb7e3b80471ffa34e58527ce6..6f74ef0870ab0a98b1aa612ae9a24c8ccfe72bf7 100644 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt +++ b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt @@ -35,9 +35,10 @@ include system.in.charges timestep 1.0 dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 +fix fxnvt all nvt temp 270.0 270.0 500.0 tchain 1 +thermo_style custom step temp pe etotal epair ebond eangle edihed thermo 100 -#thermo_modify flush yes +thermo_modify norm yes run 50000 diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt index 2b550b6309edff76abe50c23b74e8ab6d95f0f24..1f0f0f61b58f3fad880fe28429b44a551c5756d6 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt @@ -6,18 +6,6 @@ SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - write("Data Atoms") { $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 @@ -39,13 +27,25 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) + fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH + # (Remember to "unfix" fShakeSPCE during minimization.) + } + + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt index c10893b4117b6f6bc7671eb7d6b65dfa6df4c434..efa4fca484228a0b1a47a60c7ac48b95cfa101de 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt @@ -27,7 +27,7 @@ include system.in.settings # Note: The minimization step is not necessary in this example. However # in general, it's always a good idea to minimize the system beforehand. # fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE +unfix fShakeSPCE minimize 1.0e-5 1.0e-7 100000 400000 # Now read "system.in.settings" in order to redefine fSHAKE again: include system.in.settings diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt index e1bf2390a058fb5bc6c6f625c908471211258d77..d40da62b992c818dc06a77bc948d4b4706bad73b 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt @@ -29,8 +29,8 @@ SPCE { write_once("In Settings") { bond_coeff @bond:OH harmonic 600.0 1.0 angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 + pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 + pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt deleted file mode 100644 index c7aaecebbc664f632d12db6400f4cc4d3b70bf18..0000000000000000000000000000000000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/watmw.lt +++ /dev/null @@ -1,54 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt index a3e3ed620ec8b32fb6da484368dc3fc299bad6de..e345be951d0885ac3fc4ee7f9ea8be4f473bfa40 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt @@ -60,8 +60,8 @@ d) Try entering these commands: It can help to shift the location of the periodic boundary box To shift the box in the y direction (for example) do this: - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} + pbc wrap -compound res -all -shiftcenterrel {-0.05 0.14 -0.05} + pbc box -shiftcenterrel {-0.05 0.14 -0.05} -width 0.5 -style tubes Distances are measured in units of box-length fractions, not Angstroms. diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg index 2c34754c4c2754c75502a87245bf882f555b1def..bf00edc9c40a6c506d16c7c51b442facf810aa01 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg and b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg index 220a717271c2e5fd6a8e9eb6ec47cd3851062339..af70c239978f5205d2ed874be9e3569adb8f6726 100644 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg and b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt index 8d363412536d8941d9781a661c3e5994045c204e..ff52a7db97216d245a0319cd2ca96ab6268a8dcf 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt @@ -1,67 +1,68 @@ # We define two molecule classes to represent Na+ and Cl- ions, respectively. -# This may seem like overkill since they both only consist of one atom each. +# They both contain only one atom. - -# Note: Monovalent ion parameters for Ewald and SPC/E water -# are from: Joung & Cheatham JPCB (2008) -# These Lennard Jones parameters match the parameters for ions -# in SPC/E water in the "frcmod.ionsjc_spce" file distributed -# with Amber (the 2010 version). +# In moltemplate each molecule type is stored in a file whose format mimics the +# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. +# Once defined, these molecules may be copied and moved to build larger systems. NaIon { - # The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. - # However sigma must be divided by 2^(1/6), because they use the alternate - # Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and - # pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) - # (Note: This change does not effect the epsilon parameter.) + # ---- Definition of "NaIon" ---- - write_once("In Settings") { - pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.079769246386 + # AtomID MolID AtomType charge X Y Z + write("Data Atoms") { + $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 } write_once("Data Masses") { @atom:Na 22.9898 } - # assumes "full" atom style - write("Data Atoms") { - $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 + write_once("In Settings") { + pair_coeff @atom:Na @atom:Na 0.3526418 1.079769246386 } + # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) + } # NaIon + + ClIon { - write_once("In Settings") { - pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 + + # ---- Definition of "ClIon" ---- + + # AtomID MolID AtomType charge X Y Z + write("Data Atoms") { + $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 } write_once("Data Masses") { @atom:Cl 35.453 } - # assumes "full" atom style - write("Data Atoms") { - $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 + write_once("In Settings") { + pair_coeff @atom:Cl @atom:Cl 0.0127850 2.711 } + # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) + } # ClIon -write_once("In Init") { - # -- Default styles for ions -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - kspace_style pppm 0.0001 - pair_modify mix arithmetic -} - -# Optional: Define a group named "ions" consisting of either Na or Cl ions. -write_once("In Settings") { - group ionNa type @atom:NaIon/Na @atom:NaIon/Na - group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl - group ions type @atom:NaIon/Na @atom:ClIon/Cl -} + + + + +# Note: Monovalent ion parameters for Ewald and SPC/E water +# are from: Joung & Cheatham JPCB (2008) +# These Lennard Jones parameters match the parameters for ions +# in SPC/E water in the "frcmod.ionsjc_spce" file distributed +# with Amber (the 2010 version). +# +# The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. +# However sigma must be divided by 2^(1/6), because they use the alternate +# Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and +# pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) +# (Note: This change does not effect the epsilon parameter.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt index 019911c19b8e5ce3fd0096b04ee2fd4fc7f40172..db5e7df3b3a785c034b9278ceb6d6d2d51c2c541 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt @@ -1,51 +1,113 @@ +# In moltemplate each molecule type is stored in a file whose format mimics the +# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. +# Once defined, these molecules can be copied and moved to build larger systems. +# +# "SPCE" ("extended simple point charge") is one of several popular water models +# (See Berendsen H.J.C et al., J.Phys.Chem. Vol91 pp.6269-6271,1987 for details) +# # file "spce.lt" # # H1 H2 # \ / # O + SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } + # ---- Definition of the "SPCE" (water molecule type) ---- + + # The "Data Atoms" section is a list of atom attributes (type, charge, x,y,z) + # AtomID MoleculeID AtomType Charge X Y Z write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 + $atom:o $mol @atom:O -0.8476 0.0000000 0.00000 0.000000 + $atom:h1 $mol @atom:H 0.4238 0.8164904 0.00000 0.5773590 + $atom:h2 $mol @atom:H 0.4238 -0.8164904 0.00000 0.5773590 } + # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). + # If we put "$mol" there, moltemplate will generate this integer for you - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } + # A list of the bonds in the molecule: + # BondID BondType AtomID1 AtomID2 write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 + $bond:OH1 @bond:OH $atom:o $atom:h1 + $bond:OH2 @bond:OH $atom:o $atom:h2 } + # A list of the angles in the molecule: + # AngleID AngleType AtomID1 AtomID2 AtomID3 + write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 + $angle:HOH @angle:HOH $atom:h1 $atom:o $atom:h2 + } + + # The mass of each atom type: + + write_once("Data Masses") { + @atom:O 15.9994 + @atom:H 1.008 } + + # ---- Where to put force field parameters? ---- + # Moltemplate allows you to specify force-field parameters anywhere you want. + # Sometimes it is convenient to nest them within a molecule's definition. + # For more complicated simulations, it's convenient to define a "ForceField" + # object containing force field parameters shared by many different types of + # molecules. (Since this is a simple example, there is no need to do that.) + + # The "In Settings" section contains LAMMPS commands which typically define + # force-field parameters (eg "pair_coeff") and constraints (eg "fix shake") + write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) + bond_coeff @bond:OH 1000.0 1.0 + # explanation: http://lammps.sandia.gov/doc/bond_harmonic.html + + angle_coeff @angle:HOH 1000.0 109.47 + # explanation: http://lammps.sandia.gov/doc/angle_harmonic.html + + pair_coeff @atom:O @atom:O 0.1553 3.166 + pair_coeff @atom:H @atom:H 0.0 2.058 + # explanation: http://lammps.sandia.gov/doc/pair_charmm.html + + # OPTIONAL: We want the water molecules to behave like rigid objects, so + # we apply the "SHAKE" constraint to the group of atoms in water molecules. + # (SHAKE is used to make bonds and angles rigid.) + + group gSPCE type @atom:O @atom:H + # explanation: http://lammps.sandia.gov/doc/group.html + + fix fShakeSPCE gSPCE shake 0.0001 10 100 b @bond:OH a @angle:HOH + # explanation: http://lammps.sandia.gov/doc/fix_shake.html + # (Remember to "unfix" fSHAKE during minimization.) + + } + + # LAMMPS requires that some commands must be issued in a certain order. + # (IE. You must inform LAMMPS the kind of simulation you wish to run + # before supplying LAMMPS with numeric parameters for that simulation.) + # The "In Init" section is where you put commands which must be run before + # all other commands in the simulation (such as the commands in "In Settings") + + write_once("In Init") { + + units real + # explanation: http://lammps.sandia.gov/doc/units.html + + # Specify the attributes of the particles in our system (eg. "full") + atom_style full + # explanation: http://lammps.sandia.gov/doc/atom_style.html + + # Specify the kinds of formulas we want to use to calculate + # the forces in our system (ie. force-field "styles") + bond_style harmonic + angle_style harmonic + pair_style lj/charmm/coul/long 9.0 10.0 10.0 + pair_modify mix arithmetic + # explanation: http://lammps.sandia.gov/doc/pair_modify.html + kspace_style pppm 0.0001 + # explanation: http://lammps.sandia.gov/doc/kspace_style.html } } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt index af38795022a227f5ea7dd50c143595c8eb744b19..284d042d7313067b596325a870791ccb26ee63c2 100644 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt +++ b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt @@ -1,6 +1,4 @@ -import "spce.lt" # <- This defines the SPCE water molecule. This file is - # located in the "force_fields" subdirectory - # distributed with moltemplate +import "spce.lt" # <- This defines the SPCE water molecule. import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". @@ -16,8 +14,8 @@ write_once("Data Boundary") { # spacing 3.45 Angstroms. (The pressure must be equilibrated later.) wat = new SPCE [10].move(0.00, 0.00, 3.45) - [10].move(0.00, 3.45, 0.00) - [10].move(3.45, 0.00, 0.00) + [10].move(0.00, 3.45, 0.01) + [10].move(3.45, 0.01, 0.01) # We now create a 2x2x2 lattice of Na+ and Cl- ions: @@ -30,14 +28,16 @@ cl = new ClIon [2].move(0,0,17.25) [2].move(0,17.25,0) [2].move(17.25,0,0) -na[*][*][*].move(5.175,5.175,5.6) -cl[*][*][*].move(12.075,12.075,12.5) +na[*][*][*].move(5,5,5) +cl[*][*][*].move(12,12,12) -# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts +# (The (5,5,5) and (12,12,12) translational shifts # prevent the Na and Cl ions from overlapping # with the water molecules or each other.) + + # Comment: Fortunately the ions and the water in this example share the # same force-field styles (so their was no need to use "hybrid" styles). # If this were not the case, you might need to add something like this. diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..b2996dab29dbcf66b82204c9670ed0cb08d9aa71 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt @@ -0,0 +1,11 @@ +This is an example of all-atom methanol immersed in coarse grained ELBA water. +It was provided by Oscar Matus Rivas at McGill University. + + +References: +1. Orsi, Mario, Wei Ding, and Michail Palaiokostas. "Direct mixing of atomistic solutes and coarse-grained water." Journal of chemical theory and computation 10.10 (2014): 4684-4693. + +2. Orsi, Mario. "Comparative assessment of the ELBA coarse-grained model for water." Molecular Physics 112.11 (2014): 1566-1576. + +3. ELBA coarse-grained water model tutorial: +https://github.com/orsim/elba-lammps/tree/master/examples/water-bulk diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh new file mode 100644 index 0000000000000000000000000000000000000000..91e79124e1f8ec4b25bb961b1e8cf0ee77266c88 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# +# The file "run.in.npt" is a LAMMPS +# input script which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_mpi -i run.in.npt # simulation at constant pressure + +# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", +# and has many other names depending upon how it was compiled.) + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..20d5eac2314a339a38f5f3a1bbcb7e7f4674ed1e --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh @@ -0,0 +1,28 @@ + +# Create the coordinates of the atoms using PACKMOL +cd packmol_files + + packmol < input.packmol + mv -f system.xyz ../moltemplate_files/ + +cd .. + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + moltemplate.sh -atomstyle "hybrid sphere dipole molecular" \ + -xyz system.xyz system.lt + + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ system.xyz + +cd ../ + diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg new file mode 100644 index 0000000000000000000000000000000000000000..88773055a10ba0a6ec73085d6d49ffb2d14a50db Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt new file mode 100644 index 0000000000000000000000000000000000000000..e5a35fbfd9901123ed793c2f306bc328f2e95a90 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt @@ -0,0 +1,39 @@ + +ElbaFF { + + write_once("Data Masses") { + @atom:W 18.0153 # Water + } + + write_once("In Settings") { + pair_coeff @atom:W @atom:W lj/sf/dipole/sf 0.55 3.05 + } + + # select the LAMMPS force field styles and other settings we will need + write_once("In Init") { + units real + atom_style hybrid sphere dipole molecular + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid harmonic + pair_style hybrid lj/sf/dipole/sf 12.0 lj/charmm/coul/long 11.0 12.0 + kspace_style pppm/cg 1.0e-5 + pair_modify mix arithmetic + special_bonds amber + } + +} # end of definition of "ElbaFF" + + +ElbaWater inherits ElbaFF { + + # atom-ID atom-Type x y z diameter density q mux muy muz molecule-ID + write("Data Atoms") { + $atom:id1 @atom:W 0.0 0.0 0.0 4.080749 0.5063179 0.0 0.541 0.0 0.0 $mol:. + } + + write_once("In Settings") { + group gElbaWater type @atom:W + } + +} # end of definition of "ElbaWater" diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt new file mode 100644 index 0000000000000000000000000000000000000000..1d556ab13b2168e02fb5069a0f711a5db6a8bf82 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt @@ -0,0 +1,84 @@ +# This version of the methanol molecule uses the GAFF force +# field. (BCC) Charges were assigned using AmberTools + +Methanol { + + write_once("In Settings") { + pair_coeff @atom:type1 @atom:type1 lj/charmm/coul/long 0.2104000002486992 3.066473387458142 0.2104000002486992 3.066473387458142 + pair_coeff @atom:type2 @atom:type2 lj/charmm/coul/long 0.10939999991572773 3.399669508450741 0.10939999991572773 3.399669508450741 + pair_coeff @atom:type3 @atom:type3 lj/charmm/coul/long 0.01570000009846142 2.4713530426421655 0.01570000009846142 2.4713530426421655 + pair_coeff @atom:type4 @atom:type4 lj/charmm/coul/long 0.0 0.0 0.0 0.0 + } + + write_once("In Settings") { + bond_coeff @bond:type1 harmonic 316.7 1.4233 + bond_coeff @bond:type2 harmonic 371.4 0.973 + bond_coeff @bond:type3 harmonic 330.6 1.0969 + } + + write_once("In Settings") { + angle_coeff @angle:type1 harmonic 50.93 110.260047369346 + angle_coeff @angle:type2 harmonic 47.38 107.26004608361897 + angle_coeff @angle:type3 harmonic 39.24 108.46004659790978 + } + + write_once("In Settings") { + dihedral_coeff @dihedral:type1 harmonic 0.166666667 1 3 + } + + + ### DATA sections + + + write_once("Data Masses") { + @atom:type1 16.0 + @atom:type2 12.01 + @atom:type3 1.008 + @atom:type4 1.008 + } + + + # NOTE: This molecule uses atom_style hybrid sphere dipole molecular + # (This is the same atom_style used by ELBA.) Hence the extra + # columns for "diam", "mux", "muy", "muz" are not relevant + # for this molecule and can be ignored. + + write("Data Atoms") { + # atom-ID atom-Type x y z diam dens q mux muy muz molecule-ID + $atom:id1 @atom:type1 0.708 0.0 0.0 0.0 16.0 -0.598800 0.0 0.0 0.0 $mol:id0 + $atom:id2 @atom:type2 -0.708 0.0 0.0 0.0 12.01 0.116700 0.0 0.0 0.0 $mol:id0 + $atom:id3 @atom:type3 -1.073 -0.769 0.685 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id4 @atom:type3 -1.073 -0.195 -1.011 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id5 @atom:type3 -1.063 0.979 0.331 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 + $atom:id6 @atom:type4 0.994 -0.88 -0.298 0.0 1.008 0.396000 0.0 0.0 0.0 $mol:id0 + } + + write("Data Bonds") { + $bond:id1 @bond:type2 $atom:id1 $atom:id6 + $bond:id2 @bond:type3 $atom:id2 $atom:id3 + $bond:id3 @bond:type3 $atom:id2 $atom:id4 + $bond:id4 @bond:type3 $atom:id2 $atom:id5 + $bond:id5 @bond:type1 $atom:id1 $atom:id2 + } + + write("Data Angles") { + $angle:id1 @angle:type1 $atom:id1 $atom:id2 $atom:id3 + $angle:id2 @angle:type1 $atom:id1 $atom:id2 $atom:id4 + $angle:id3 @angle:type1 $atom:id1 $atom:id2 $atom:id5 + $angle:id4 @angle:type2 $atom:id2 $atom:id1 $atom:id6 + $angle:id5 @angle:type3 $atom:id3 $atom:id2 $atom:id4 + $angle:id6 @angle:type3 $atom:id3 $atom:id2 $atom:id5 + $angle:id7 @angle:type3 $atom:id4 $atom:id2 $atom:id5 + } + + write("Data Dihedrals") { + $dihedral:id1 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id3 + $dihedral:id2 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id4 + $dihedral:id3 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id5 + } + + write_once("In Settings") { + group gMethanol type @atom:type1 @atom:type2 @atom:type3 @atom:type4 + } + +} # end of "Methanol" type definition diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..1a077a92f1b3a07862305986fb61dfe77f890df7 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt @@ -0,0 +1,29 @@ +import "methanol.lt" + +import "elba.lt" + +write_once("Data Boundary") { + -15.5 15.5 xlo xhi + -15.5 15.5 ylo yhi + -15.5 15.5 zlo zhi +} + +solute = new Methanol [1] + +solvent = new ElbaWater [1000] + +# Lorentz-Berthelot mixing +write_once("In Settings") { + pair_coeff @atom:Methanol/type1 @atom:Methanol/type2 lj/charmm/coul/long 0.151716 3.233071 0.151716 3.233071 + pair_coeff @atom:Methanol/type1 @atom:Methanol/type3 lj/charmm/coul/long 0.057474 2.768913 0.057474 2.768913 + pair_coeff @atom:Methanol/type1 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.533237 0.000000 1.533237 + pair_coeff @atom:Methanol/type1 @atom:ElbaFF/W lj/sf/dipole/sf 0.340176 3.058237 + pair_coeff @atom:Methanol/type2 @atom:Methanol/type3 lj/charmm/coul/long 0.041444 2.935511 0.041444 2.935511 + pair_coeff @atom:Methanol/type2 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.699835 0.000000 1.699835 + pair_coeff @atom:Methanol/type2 @atom:ElbaFF/W lj/sf/dipole/sf 0.245296 3.224835 + pair_coeff @atom:Methanol/type3 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.235677 0.000000 1.235677 + pair_coeff @atom:Methanol/type3 @atom:ElbaFF/W lj/sf/dipole/sf 0.092925 2.760677 + pair_coeff @atom:Methanol/type4 @atom:ElbaFF/W lj/sf/dipole/sf 0.000000 1.525000 +} + +} diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d310d44d30207737d4efd0baf2f6e9cb67602e4 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt @@ -0,0 +1,12 @@ +Packmol is a program that generates non-overlapping atomic coordinates for +mixtures of molecules. + +Usage: + + packmol < input.packmol + +Ouput: + + system.xyz + +(a file containing the coordinates of all of the molecules packed together.) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz new file mode 100644 index 0000000000000000000000000000000000000000..fc495c05648bd8f75ef71095c2204bb04b60daa7 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz @@ -0,0 +1,1008 @@ + 1006 + Built with Packmol + O 1.077217 0.144250 0.048817 + C -0.338583 0.144250 0.048817 + H -0.703883 -0.624750 0.734017 + H -0.703783 -0.050450 -0.962483 + H -0.693883 1.122850 0.380017 + H 1.362917 -0.736150 -0.249183 + OW -1.412297 -7.446504 10.904602 + OW 4.452292 7.235571 -6.250955 + OW -6.020558 -4.280954 1.868432 + OW -5.179618 11.632347 -13.999700 + OW 3.301355 8.558586 5.180801 + OW -12.174570 -4.025488 11.826522 + OW 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0000000000000000000000000000000000000000..9c640263d992cb95f69f18f42576ddd225872191 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol @@ -0,0 +1,17 @@ +tolerance 2.5 +filetype xyz +output system.xyz + +# Methanol +structure methanol.xyz + number 1 + center + fixed 0. 0. 0. 0. 0. 0. +end structure + +# ELBA Solvent +structure elba_water.xyz + number 1000 + inside box -14.0 -14.0 -14.0 14.0 14.0 14.0 +end structure + diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz new file mode 100644 index 0000000000000000000000000000000000000000..b06d93fa5f68913f305165d90a27d908104ce01c --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz @@ -0,0 +1,8 @@ +6 + +O 0.70790 0.00000 0.00000 +C -0.70790 0.00000 0.00000 +H -1.07320 -0.76900 0.68520 +H -1.07310 -0.19470 -1.01130 +H -1.06320 0.97860 0.33120 +H 0.99360 -0.88040 -0.29800 diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt new file mode 100644 index 0000000000000000000000000000000000000000..ad8076d7fdc88277423bdd88db3200ff7d6c2f8b --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt @@ -0,0 +1,54 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh (& packmol?) to create 3 files: +# system.data system.in.init system.in.settings +# +# See "README_setup.sh" for instructions how to use moltemplate.sh +# Note: This input script file only covers equilibration of the system. +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + +# -- simulation protocol -- + +# (Groups "gElbaWater" and "gMethanol" are defined in "system.in.settings" +# Rename them to "gSolvent" and "gSolute") +group gSolvent union gElbaWater gElbaWater +group gSolute union gMethanol gMethanol + +# Randomize the direction of the solvent dipoles +set group gSolvent dipole/random 9876 0.541 + +velocity all create 298.0 9876 + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 2.0 + +fix 1 gSolute nve # integrate gSolute +fix 2 gSolvent nve/sphere update dipole # integrate gSolvent +fix 3 gSolute langevin 298.0 298.0 1000 9876 # thermostat gSolute +fix 4 gSolvent langevin 298.0 298.0 1000 9876 omega yes zero yes # thermostat gSolvent +fix 5 all press/berendsen iso 1.0 1.0 1000 modulus 21740 # barostat +fix 6 all momentum 500 linear 1 1 1 +fix 7 gSolute shake 1.0e-6 100 0 m 1.0 + +dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z mux muy muz ix iy iz + +thermo_style custom step temp etotal pe epair press +thermo_modify norm yes flush yes +thermo 100 + +run 10000 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..c61369a2258e6ced9098258f14439171538d6870 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt @@ -0,0 +1,8 @@ +You can use packmol to create a file containing the atomic coordinates +for a system of coarse-grained lipids mixed with water using this command: + +If it takes too long for packmol to run, try lowering the tolerance. +(tolerance 2.0 should work) + +packmol < mix_lipids+water.inp + diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz new file mode 100644 index 0000000000000000000000000000000000000000..7caffdc1595dced0e20a2ce90b6d9074cc8cfd8a --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz @@ -0,0 +1,14 @@ +12 + DOPC +Q0 0.596 0.518 2.453 +Qa 0.413 0.591 2.167 +Na 0.525 0.626 1.829 +Na 0.749 0.434 1.795 +C1 0.428 0.686 1.448 +C3 0.395 0.491 1.197 +C1 0.389 0.575 0.899 +C1 0.423 0.497 0.555 +C1 0.944 0.505 1.503 +C3 0.906 0.476 1.192 +C1 0.899 0.567 0.905 +C1 0.921 0.637 0.557 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp new file mode 100644 index 0000000000000000000000000000000000000000..9e1388a137c216bb6e4518f67acffa441109b322 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp @@ -0,0 +1,35 @@ +# +# A mixture of coarse-grained (martini) DPPC (lipid) and water. +# + +# All the atoms from diferent molecules will be separated at least 3.0 +# Anstroms at the solution. + +tolerance 3.0 # minimal distance between atoms in different molecules + # (you should also consider changing the "discale" + # parameter. I think discale=1.0 by default.) + +seed 12345 # seed for random number generator + +# The file type of input and output files is XYZ + +filetype xyz + +# The name of the output file + +output system.xyz + +# DPPC (lipid) molecules and water molecules will be put in a box +# defined by the minimum coordinates x, y and z = 0 0 0. and maximum +# coordinates 100 100 100. (Box size: 100x100x100) + +structure dopc.xyz + number 300 + inside box 0.0 0.0 0.0 100.0 100.0 100.0 +end structure + +structure water.xyz + number 6000 + inside box 0.0 0.0 0.0 100.0 100.0 100.0 +end structure + diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz new file mode 100644 index 0000000000000000000000000000000000000000..84fe1f74c26574f6c3c28e2de8239449c5a2684e --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz @@ -0,0 +1,3 @@ +1 + water +W 0 0 0 diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt index aad330df20b50a9de3ebe889d8281378e8c8dfea..e177c136e3b70f64af931db563542ce51b39d627 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt @@ -1,8 +1,11 @@ -# The "HPForceField" is a force-field environment object containing -# force-field data, atomic masses, and bond rules. -# Later, when we define molecules (such as "H" and "P"), we can inherit -# atom types and bond-rules from this force-field. This will automatically -# assign bonds and angular interactions according to atom (and bond) type. +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later, when we define molecules (such as "H" and "P"), we can +# borrow these atom types, bond-rules and force field parameters. This way, +# bonds and angular interactions are generated automatically according to +# atom (and bond) type. # (You can also assign charge by atom type. However in this example I assigned # charge to each atom manually (not by type). The OPLSAA examples in the # "all_atoms" directory demonstrate how to assign charge by atom type.) @@ -11,6 +14,31 @@ HPForceField { + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style charmm + pair_style lj/cut 11.0 + + # If charges are needed, (assuming biopolymers), try one of: + #dielectric 80.0 + #pair_style lj/cut/coul/debye 0.1 11.0 + # or (for short distances, below a couple nm) + #pair_style lj/charmm/coul/charmm/implicit 9.0 11.0 + + pair_modify mix arithmetic + special_bonds lj 0.0 0.0 0.0 + } + + # There are 3 atom types: write_once("Data Masses") { @@ -22,16 +50,17 @@ HPForceField { # 2-body (non-bonded) interactions: # # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) # # Hydrophobic side-chain (R) atoms are attractive (large epsilon parameter). # Polar side-chains and backbone atoms are not attractive (small epsilon). # - # i j pairstylename eps sig + # i j eps sig # write_once("In Settings") { - pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 - pair_coeff @atom:HR @atom:HR lj/cut 2.50 3.6 - pair_coeff @atom:PR @atom:PR lj/cut 0.10 3.6 + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:HR @atom:HR 2.50 3.6 + pair_coeff @atom:PR @atom:PR 0.10 3.6 } # (By default, interactions between different AtomTypes use "arithmetic"rules: @@ -50,15 +79,16 @@ HPForceField { # 2-body (bonded) interactions: # # Ubond(r) = (k/2)*(r-0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) # # The corresponding command is: # - # bond_coeff bondType bondstylename k r0 + # bond_coeff bondType k r0 # write_once("In Settings") { - bond_coeff @bond:Sidechain harmonic 30.0 3.4 - bond_coeff @bond:Backbone harmonic 30.0 3.7 + bond_coeff @bond:Sidechain 30.0 3.4 + bond_coeff @bond:Backbone 30.0 3.7 } @@ -83,14 +113,15 @@ HPForceField { # # Uangle(theta) = (k/2)*(theta-theta0)^2 # (k in kcal/mol/rad^2, theta0 in degrees) + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) # # The corresponding command is: # - # angle_coeff angleType anglestylename k theta0 + # angle_coeff angleType k theta0 write_once("In Settings") { - angle_coeff @angle:Backbone harmonic 30.00 114 - angle_coeff @angle:Sidechain harmonic 30.00 123 + angle_coeff @angle:Backbone 30.00 114 + angle_coeff @angle:Sidechain 30.00 123 } @@ -100,40 +131,16 @@ HPForceField { # Udihedral(phi) = K * (1 + cos(n*phi - d)) # # The d parameter is in degrees, K is in kcal/mol/rad^2. + # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) # # The corresponding command is - # dihedral_coeff dihedralType dihedralstylename K n d w (ignore "w") + # dihedral_coeff dihedralType K n d w (ignore "w") write_once("In Settings") { - dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 + dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 } # write_once("In Settings") - # LAMMPS supports a large number of force-field styles. We must select - # which ones we need. This information belongs in the "In Init" section. - # (Hybrid styles used for portability. These choices can be overridden later.) - - write_once("In Init") { - # -- Default styles for "2bead" -- - # (Hybrid force fields were not necessary but are used for portability.) - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/cut 11.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 11.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - } # HPForceField diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..eca0a1b7f41944910a01eb84dd046b3773a0d5cd --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt @@ -0,0 +1,17 @@ + +This directory contains an example of a couarse-grained (vaguely protein-like) +heteropolymer consisting of 14 residues, each of which has 2 atoms +(one backbone atom, one residue atom.) + +There are two types of residues, H and P. +The R-atom for the H residue are attracted to eachother. +All other atoms are repulsive. + +Instructions on how to build LAMMPS input files and +run a short simulation are provided in other README files. + +step 1) +README_setup.sh + +step2) +README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..8bf8e27648d1ed6928de2d4fc2feacf1999d38ae --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# -- Prerequisites: -- +# The "run.in.nvt" file is a LAMMPS input script containing +# references to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + + +lmp_mpi -i run.in.nvt + + + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.nvt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..cf22ee0fa1868664c5f3cc786d382d1b511097d5 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh @@ -0,0 +1,23 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): + + +# Create LAMMPS input files this way: +cd moltemplate_files + + # run moltemplate + + moltemplate.sh system.lt + + # This will generate various files with names ending in *.in* and *.data. + # These files are the input files directly read by LAMMPS. Move them to + # the parent directory (or wherever you plan to run the simulation). + + mv -f system.in* system.data ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt new file mode 100644 index 0000000000000000000000000000000000000000..518df2c20a6b3a9ea7c31fd8edd40fd580bc721c --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt @@ -0,0 +1,86 @@ + + ------- To view a lammps trajectory in VMD -------- + + +1) Build a PSF file for use in viewing with VMD. + +This step works with VMD 1.9 and topotools 1.2. +(Older versions, like VMD 1.8.6, don't support this.) + + +a) Start VMD +b) Menu Extensions->Tk Console +c) Enter: + +(I assume that the the DATA file is called "system.data") + + topo readlammpsdata system.data full + animate write psf system.psf + +2) + +Later, to Load a trajectory in VMD: + + Start VMD + Select menu: File->New Molecule + -Browse to select the PSF file you created above, and load it. + (Don't close the window yet.) + -Browse to select the trajectory file. + If necessary, for "file type" select: "LAMMPS Trajectory" + Load it. + + ---- A note on trajectory format: ----- +If the trajectory is a DUMP file, then make sure the it contains the +information you need for pbctools (see below. I've been using this +command in my LAMMPS scripts to create the trajectories: + + dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz + +It's a good idea to use an atom_style which supports molecule-ID numbers +so that you can assign a molecule-ID number to each atom. (I think this +is needed to wrap atom coordinates without breaking molecules in half.) + +Of course, you don't have to save your trajectories in DUMP format, +(other formats like DCD work fine) I just mention dump files +because these are the files I'm familiar with. + +3) ----- Wrap the coordinates to the unit cell + (without cutting the molecules in half) + +a) Start VMD +b) Load the trajectory in VMD (see above) +c) Menu Extensions->Tk Console +d) Try entering these commands: + + pbc wrap -compound res -all + pbc box + + ----- Optional ---- + It can help to shift the location of the periodic boundary box + To shift the box in the y direction (for example) do this: + + pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.15 -0.05} + pbc box -shiftcenterrel {-0.05 -0.15 -0.05} -width 1.6 -style tubes + + Distances are measured in units of box-length fractions, not Angstroms. + + Alternately if you have a solute whose atoms are all of type 1, + then you can also try this to center the box around it: + + pbc wrap -sel type=1 -all -centersel type=2 -center com + +4) + You should check if your periodic boundary conditions are too small. + To do that: + select Graphics->Representations menu option + click on the "Periodic" tab, and + click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. + +5) Optional: If you like, change the atom types in the PSF file so + that VMD recognizes the atom types, use something like: + +sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf +sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf +sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf + +(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg new file mode 100644 index 0000000000000000000000000000000000000000..35af99387ec987f274dc91c837cd4a6fb23a21ee Binary files /dev/null and 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b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_array3x3x3_LR.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg new file mode 100644 index 0000000000000000000000000000000000000000..18ca16001c4d3a58b3cc264278aa6a83b7ee3317 Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh new file mode 100755 index 0000000000000000000000000000000000000000..bcc5947b1fa03f5c5baa8423fef0d1a2eca76d0d --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh @@ -0,0 +1,6 @@ +# Use these commands to generate the LAMMPS input script and data file +# (and other auxilliary files): +moltemplate.sh system.lt + +# This will generate various files with names ending in *.in* and *.data. + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..3d9fdab3206440fd5a9b6d2917b03b3a2703d658 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt @@ -0,0 +1,19 @@ +# In this example, we construct a large molecule ("Polymer") +# from multiple smaller molecular subunits ("Monomer"). +# The "Monomer" molecule contains two atoms (type "CA", and "R") +# +# "Monomer" +# +# @R +# | +# @CA +# +# Eventually, we will connect multiple "Monomer" molecular subunits +# together to form a polymer, as shown below: +# +# @R @R +# | | +# _@CA_ _@CA_ +# ... -.@CA-' `-@CA-' ` ... +# | | +# @R @R diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt new file mode 100644 index 0000000000000000000000000000000000000000..8dfdf98a415c39f4e339a0f7ddbf899485f070cc --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt @@ -0,0 +1,110 @@ + +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later on when we define molecule objects, we can access all +# of the atom types and force field parameters here using "inherits ForceField". +# (See "monomer.lt" for example.) + + +ForceField { + + + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + # -- Styles used in "ForceField" -- + # -- (Changing these styles will change the formulas above) -- + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style charmm + pair_style lj/cut 11.0 + } + + + # There are 2 atom types: "CA" and "R" + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # ---- 2-body (non-bonded) interactions: ---- + # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + # Pairwise (non-bonded) interactions: + # atomType1 atomType2 epsilon sigma + pair_coeff @atom:CA @atom:CA 0.10 2.0 + pair_coeff @atom:R @atom:R 0.50 3.6 + # (Interactions between different atoms are determined by mixing rules.) + } + + # ---- 2-body (bonded) interactions: ---- + # + # Ubond(r) = k*(r-r0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) + # + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:Sidechain 15.0 3.4 + bond_coeff @bond:Backbone 15.0 3.7 + } + + # ---- 3-body angle (hinge) interactions: ---- + + # Rules for determining 3-body (angle) interactions by atom & bond type: + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:Backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:Sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + } + + # Force-field parameters for 3-body (angle) interactions: + # + # Uangle(theta) = k*(theta-theta0)^2 + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) + # + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:Backbone 30.00 114 + angle_coeff @angle:Sidechain 30.00 132 + } + + # ---- 4-body dihedral interactions ---- + + # 4-body interactions in this example are listed by atomType + # Rules for determining 4-body (dihedral) interactions by atom & bond type: + write_once("Data Dihedrals By Type") { + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 + @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* + } + + # The forumula used is: + # + # Udihedral(phi) = K * (1 + cos(n*phi - d)) + # + # The d parameter is in degrees, K is in kcal/mol/rad^2. + # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) + # + # The corresponding command is + # dihedral_coeff dihedralType K n d w(ignored) + + write_once("In Settings") { + dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 + dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 + } + +} # "ForceField" + + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt new file mode 100644 index 0000000000000000000000000000000000000000..286eb12ff4cdec2f12b69b83c6e1488849bb8415 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt @@ -0,0 +1,20 @@ +import "forcefield.lt" # contains force-field parameters + +Monomer inherits ForceField { + + write("Data Atoms") { + # atomId molId atomType charge x y z + $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 + $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 + } + write("Data Bonds") { + # bond-id bond-type atom-id1 atom-id2 + $bond:cr @bond:Sidechain $atom:ca $atom:r + } +} + + + +# NOTE: The "..." in "$mol:..." tells moltemplate that this molecule is part +# of a larger molecule, and to use the larger parent object's +# molecule id number as it's own. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt new file mode 100644 index 0000000000000000000000000000000000000000..5ca8eb03e96e247cd9f758c98602eb0123c009b8 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt @@ -0,0 +1,27 @@ +import "monomer.lt" # <-- defines "Monomer" and "ForceField" + +Polymer inherits ForceField { + + # The next line is optional + create_var {$mol} # force all monomers to share the same molecule-ID + + # Now create some monomers + + mon1 = new Monomer + mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) + mon3 = new Monomer.move(6.4,0,0) + mon4 = new Monomer.rot(180.0, 1,0,0).move(9.6,0,0) + mon5 = new Monomer.move(12.8,0,0) + mon6 = new Monomer.rot(180.0, 1,0,0).move(16.0,0,0) + mon7 = new Monomer.move(19.2,0,0) + + # Now, link the monomers together this way: + write("Data Bonds") { + $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca + $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca + $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca + $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca + $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca + $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca + } +} diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..480f8c021648643484d79f00daae8dc7e694b656 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt @@ -0,0 +1,29 @@ +import "polymer.lt" + + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 90.0 xlo xhi + 0 90.0 ylo yhi + 0 90.0 zlo zhi +} + +# Create 27 polymers in a rectangular grid + +polymers = new Polymer [3].move(0, 0, 30.0) + [3].move(0, 30.0, 0) + [3].move(30.0, 0, 0) + + + +# ------------ Optional: ------------ +# Now (for fun) shift some of the polymers +# in the x direction by a distance of 20.0 +# Suppose we want to move the middle slice +# (which has constant Z). We do that this way: +# polymers[1][*][*].move(20,0,0) +# more examples: +# polymers[*][1][*].move(0,0,20) +# polymers[*][*][1].move(0,20,0) + + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt new file mode 100644 index 0000000000000000000000000000000000000000..e9fdbf41fd08f63d90ee4bba4eb5d5ec11ffbde7 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt @@ -0,0 +1,32 @@ +# -- Init Section -- + +include system.in.init + +# -- Atom Definition Section -- + +read_data system.data + +# -- Settings Section -- + +include system.in.settings + +# -- Run Section -- + + +timestep 2.0 +dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz + +# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". +# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) + +fix fxlan all langevin 300.0 300.0 5000.0 48279 +fix fxnve all nve + + +thermo_style custom step temp pe etotal press vol epair ebond eangle edihed +thermo 1000 # time interval for printing out "thermo" data + +run 40000000 + +write_data system_after_nvt.data + diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt index a8a35339f5f2c1629defe228505f89f22c94aa1d..88c1f6e3226ccbe2e7cd8724cf1b8e72c0361016 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt @@ -10,7 +10,10 @@ # ---------------------------------------------------------------------- -Monomer { +import "polymer_forcefield.lt" # contains force-field parameters + + +Monomer inherits ForceField { # atom-id mol-id atom-type charge x y z @@ -24,88 +27,14 @@ Monomer { # be a part of a larger molecule, and (if so) to use the larger # parent object's molecule id number as it's own - - # atom-type mass - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.05 2.0 - pair_coeff @atom:R @atom:R 0.50 2.0 - } - # bond-id bond-type atom-id1 atom-id2 write("Data Bonds") { $bond:CR1 @bond:sidechain $atom:CA $atom:R1 $bond:CR2 @bond:sidechain $atom:CA $atom:R2 } - - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:sidechain 30.0 1.2 - bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" - } - - # For a compound molecule consisting of smaller building blocks (such as a - # polymer built from monomers), it is tedious to explicitly list all of the - # angles, dihedrals in the entire molecule. Instead, you can define rules - # for automatically generating all the angular interactions between bonded - # atoms according to their connectivity and the atom/bond type. - # Later, when you connect multiple monomers together to form a polymer, - # appropriate bond-angle forces will be applied to these atoms automatically - # (as well as dihedral and improper forces, if defined). - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* - } - - # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. - # The other angular interactions are between atoms in neighboring monomers.) - - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - } - - # Parameters for these new angular interactions must be defined. (I recommend - # putting all force-field parameters (coeffs) in the "In Settings" section.) - - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:backbone 50.00 160 - angle_coeff @angle:sidechain 50.00 120 - angle_coeff @angle:RCR 50.00 120 - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 - } + # atom-type mass } # Monomer - - - - -# ------------------------------------------------------------------------- -# Heteropolymers: -# -# There is a similar example for heteropolymers which is distributed online -# bundled with the moltemplate software. It is named "2bead_heteropolymer", -# and it demonstrates how to share backbone (CA) atoms, bonds and angles -# (so that you don't have to define them seperately for each type of monomer). -# ------------------------------------------------------------------------- - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt index 31a36d07ced22baa39a2eacce31e3c8d0b888ef7..5eae2abe29aa9ee046fda805eff219d7f2477656 100644 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt @@ -1,9 +1,9 @@ -import "monomer.lt" +import "monomer.lt" # <-- defines "Monomer" and "ForceField" -Polymer { +Polymer inherits ForceField { create_var {$mol} # optional:force all monomers to share the same molecule-ID - # (The "Data Atoms" in Monomer must use "$mol:..." notation.) + #(The "Data Atoms" in Monomer must use "$mol:..." notation.) # Make a chain of monomers monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) @@ -29,4 +29,4 @@ Polymer { # Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomer.lt" +# automatically according to the instructions in "forcefield.lt" diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt new file mode 100644 index 0000000000000000000000000000000000000000..ef7efe24e45ceb539186c8e4c278ce7f5ac6ce46 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt @@ -0,0 +1,120 @@ +# Define a "ForceField" object. +# A force field in moltemplate is any object containing mostly pair_coeff, +# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", +# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") +# information. Later on when we define molecule objects, we can access all +# of the atom types and force field parameters here using "inherits ForceField". +# (See "monomer.lt" for example.) + + +ForceField { + + # LAMMPS supports a large number of "styles" (ie. equations for calculating + # forces between particles). At some point, we must eventually select the + # formulas we want to use. This can be done anywhere, but we might as + # well specify that now. Later on we will specify the parameters + # which go into these equations. + + write_once("In Init") { + # -- Styles used in "ForceField" -- + # -- (Changing these styles will change the formulas above) -- + units real + atom_style full + bond_style harmonic + angle_style harmonic + dihedral_style opls + pair_style lj/cut 11.0 + } + + + # There are 2 atom types: "CA" and "R" + + write_once("Data Masses") { + @atom:CA 13.0 + @atom:R 50.0 + } + + # ---- 2-body (non-bonded) interactions: ---- + # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) + # (for details see http://lammps.sandia.gov/doc/pair_lj.html) + # atom-type atom-type epsilon sigma + + write_once("In Settings") { + pair_coeff @atom:CA @atom:CA 0.05 2.0 + pair_coeff @atom:R @atom:R 0.50 2.0 + # (Interactions between different atoms are determined by mixing rules.) + } + + # ---- 2-body (bonded) interactions: ---- + # + # Ubond(r) = k*(r-r0)^2 + # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) + # + write_once("In Settings") { + # bond-type k r0 + bond_coeff @bond:sidechain 30.0 1.2 + bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" + } + + # For a compound molecule consisting of smaller building blocks (such as a + # polymer built from monomers), it is tedious to explicitly list all of the + # angles, dihedrals in the entire molecule. Instead, you can define rules + # for automatically generating all the angular interactions between bonded + # atoms according to their connectivity and the atom/bond type. + # Later, when you connect multiple monomers together to form a polymer, + # appropriate bond-angle forces will be applied to these atoms automatically + # (as well as dihedral and improper forces, if defined). + + # ---- 3-body angle (hinge) interactions ---- + # Rules for determining 3-body interactions by type + + # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 + + write_once("Data Angles By Type") { + @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* + @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* + @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* + } + + # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. + # The other angular interactions are between atoms in neighboring monomers.) + + # Force-field parameters for 3-body (angle) interactions: + # + # Uangle(theta) = k*(theta-theta0)^2 + # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) + # + write_once("In Settings") { + # angle-type k theta0 + angle_coeff @angle:backbone 50.00 160 + angle_coeff @angle:sidechain 50.00 120 + angle_coeff @angle:RCR 50.00 120 + } + + # ---- 4-body dihedral interactions ---- + + # Rules for determining 4-body (dihedral) interactions by atom & bond type: + # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 + + write_once("Data Dihedrals By Type") { + @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* + } + # (A more realistic force field would have more dihedral and angle types) + + + # The forumula used for dihedral interactions is: + # + # Udihedral(phi) = (K1/2)*(1+cos(phi)) + (K2/2)*(1+cos(2*phi)) + + # ... (K3/2)*(1+cos(3*phi)) + (K4/2)*(1+cos(4*phi)) + # (for details, see http://lammps.sandia.gov/doc/dihedral_opls.html) + # + # The corresponding command is + + write_once("In Settings") { + # dihedral-type K1 K2 K3 K4 + dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 + } + +} # "ForceField" + + diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..c3c4faecb190332c8b7f633ea172f115eddbd9d9 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt @@ -0,0 +1,20 @@ +# CG model of benzene where each molecule is represented as an ellipsoid +# and the intermolecular interactions are described with the Gay-Berne potential +# +# Do not expect realistic behaviour from this example. +# The long-range electrostatic interactions are missing. +# +# To build the files which LAMMPS needs, follow the instructions in +# README_setup.sh +# +# To run the simulation in LAMMPS, follow the instructions in: +# README_run.sh +# +# Finally, to view the simulation results in OVITO, follow the instructions in: +# README_visualization_OVITO.txt +# README_visualization_OVITO_ellipsoids.png +# +# +# This example was provided by Otello M. Roscion (U.Southampton) +# and Matteo Ricci(U.Bologna) Many thanks for editing and debugging +# moltemplate code to get this working! diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..91e79124e1f8ec4b25bb961b1e8cf0ee77266c88 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh @@ -0,0 +1,20 @@ +# --- Running LAMMPS --- +# +# The file "run.in.npt" is a LAMMPS +# input script which link to the input scripts and data files +# you hopefully have created earlier with moltemplate.sh: +# system.in.init, system.in.settings, system.data +# If not, carry out the instructions in "README_setup.sh". +# +# -- Instructions: -- +# If "lmp_mpi" is the name of the command you use to invoke lammps, +# then you would run lammps on these files this way: + +lmp_mpi -i run.in.npt # simulation at constant pressure + +# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", +# and has many other names depending upon how it was compiled.) + +# If you have compiled the MPI version of lammps, you can run lammps in parallel +#mpirun -np 4 lmp_mpi -i run.in.npt +# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh new file mode 100755 index 0000000000000000000000000000000000000000..3a5a6d2e67c268a7922e56aeb84743408b3779a6 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh @@ -0,0 +1,19 @@ +# Create LAMMPS input files this way: +cd moltemplate_files + + # Run moltemplate with the "-allow-wildcards" and "-nocheck" arguments + # as well as a custom -atomstyle + + moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt \ + -allow-wildcards -nocheck + + # This will generate various files with names ending in *.in* and *.data. + # Move them to the directory where you plan to run LAMMPS (in this case "../") + mv -f system.data system.in* ../ + + # Optional: + # The "./output_ttree/" directory is full of temporary files generated by + # moltemplate. They can be useful for debugging, but are usually thrown away. + rm -rf output_ttree/ + +cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt new file mode 100644 index 0000000000000000000000000000000000000000..cd2498b1a15cde0c4d41767207b3279b935fb145 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt @@ -0,0 +1,12 @@ +You can visualize the trajectory (dump file) with the program OVITO (www.ovito.org). You will have to define few parameters, thought. Invoke ovito using: + +ovito traj.lammpstrj + +On the right panel of ovito, under the section "LAMMPS dump" click on the button "Edit column mapping" and enter the fields as specified in the attached png file. On the same panel, tick "File contains a time series" to display the entire trajectory. + +A screenshot of these settings is available: +README_visualization_OVITO_ellipsoids.png + + +Otello M. Roscioni +roscioni@gmail.com diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png new file mode 100644 index 0000000000000000000000000000000000000000..15e5e77c4bb87793f3e7a9cfe81b5be5616dc39b Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png new file mode 100644 index 0000000000000000000000000000000000000000..89629bde4840d81a79c07a3d65c0ff48c3cd7cf3 Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg new file mode 100644 index 0000000000000000000000000000000000000000..b3514f4c8ab106b4a72227760638be21f692812a Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg new file mode 100644 index 0000000000000000000000000000000000000000..7c35039c01494d4d4aba7383d81b9b1d0187859e Binary files /dev/null and b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt new file mode 100644 index 0000000000000000000000000000000000000000..036847ea4a4c41de412b0b5ad1c019ebc48f1ef2 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt @@ -0,0 +1,62 @@ +# CG model of benzene where each molecule is represented as an ellipsoid +# and the intermolecular interactions are described with the Gay-Berne potential +# +# Do not expect a physical behaviour from this sample: long-range electrostatic +# interactions are missing. +# +# Otello M. Roscioni +# roscioni@gmail.com + +# Run with the command: +# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt -allow-wildcards -nocheck + + +BENZ { + + # atom-ID atom-type ellipsoidflag density x y z + write("Data Atoms"){ + $atom:ben @atom:b1 1 1.14337 0.0 0.0 0.0 + } + + # atom-ID width1 width2 width3 qw qx qy qz + write("Data Ellipsoids"){ + $atom:ben 6.3888 6.3888 3.1967 1.0 0.0 0.0 0.0 + } + + write_once("In Init") { + units real + atom_style ellipsoid + pair_style gayberne 1.0 1.0 -3.0 25.0 + pair_modify mix arithmetic + + # Neighbour list. (Can be overridden) + neighbor 1.0 bin + neigh_modify check yes one 5000 + } + + + write_once("In Settings") { + # Gay-Berne parameters. + pair_coeff @atom:b1 @atom:b1 1.0 3.7275 0.7797 0.7797 3.6200 0.7797 0.7797 3.6200 25.0 + } + + + write_once("In Settings") { # <-- append to "In Settings" + + # It's probably useful to put the following computes and settings here since + # I imagine that most people who use this model would find them useful: + + compute q all property/atom quatw quati quatj quatk + compute shape all property/atom shapex shapey shapez + compute temp_trasl all temp + compute temp_rototrasl all temp/asphere dof all + compute press_trasl all pressure temp_trasl + compute myMSD all msd com yes + + # Modify temperature to include ellipsoidal degrees of freedom. + thermo_modify temp temp_rototrasl + thermo_modify press press_trasl + } + +} #BENZ + diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt new file mode 100644 index 0000000000000000000000000000000000000000..00d669063b5d4e5d76786ea93ead62d665e73c39 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt @@ -0,0 +1,24 @@ +# Run with the command: +# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" benzene_sample01.lt -allow-wildcards -nocheck + +import "benzene_cg.lt" + +# Specify the periodic boundary conditions: +write_once("Data Boundary") { + 0 35.0 xlo xhi + 0 35.0 ylo yhi + 0 35.0 zlo zhi +} + +bulk = new BENZ [5].move(7, 0, 0) + [5].move(0, 7, 0).rot(10,0,1,0) + [5].move(0, 0, 7) + +# NOTE: +# I included a .rot() rotation command above in order to demonstrate +# that moltemplate can control ellipsoid orientation as well as position. +# Unfortunately, this example may be difficult to understand. Explanation: +# When ".rot(10,0,1,0)" appears in the middle of a 3-D array declaration, +# it applies a rotation of 10 degrees around the y axis ("0,1,0", into the +# screen) each time the middle index ("j" in "BENZ[i][j][k]") increases by one. +# This will cause the k-columns to be twisted around the y axis as y increases. diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in new file mode 100644 index 0000000000000000000000000000000000000000..94ad81659be2b774425727309ca29ec866ddfa30 --- /dev/null +++ b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in @@ -0,0 +1,37 @@ +# PREREQUISITES: +# +# You must use moltemplate.sh (& packmol?) to create 3 files: +# system.data system.in.init system.in.settings +# +# See "README_setup.sh" for instructions how to use moltemplate.sh +# Note: This input script file only covers equilibration of the system. +# +# ------------------------------- Initialization Section -------------------- + +include "system.in.init" +boundary p p p + +# ------------------------------- Atom Definition Section ------------------- + +read_data "system.data" + +# ------------------------------- Settings Section -------------------------- + +include "system.in.settings" + +# ------------------------------- Run Section ------------------------------- + +# Output: +thermo 100 +thermo_style custom step etotal evdwl ke pe temp press vol density & + c_myMSD[1] c_myMSD[2] c_myMSD[3] c_myMSD[4] cpu +dump 1 all custom 100 traj.lammpstrj & +id type x y z c_q[1] c_q[2] c_q[3] c_q[4] & +c_shape[1] c_shape[2] c_shape[3] & +angmomx angmomy angmomz + +# Dynamics: +timestep 10.0 +fix 2 all npt/asphere temp 300. 300. 1000. iso 1. 1. 10000. +fix_modify 2 press press_trasl +run 20000 diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min index 2fc8fbba759b53abe2eecd9c8cdf025d18913360..9e1ccb360ae99e5ab8e9ecd55152300e15d93699 100644 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min +++ b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min @@ -28,7 +28,7 @@ include system.in.settings # -- Run section -- -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz +dump 1 all custom 50 traj.lammpstrj id mol type x y z ix iy iz minimize 1.0e-5 1.0e-7 500 2000 diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt index 019911c19b8e5ce3fd0096b04ee2fd4fc7f40172..1f0f0f61b58f3fad880fe28429b44a551c5756d6 100644 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt +++ b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt @@ -6,18 +6,6 @@ SPCE { - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - write("Data Atoms") { $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 @@ -39,14 +27,26 @@ SPCE { } write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 + bond_coeff @bond:OH harmonic 600.0 1.0 + angle_coeff @angle:HOH harmonic 75.0 109.47 pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 + pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 group spce type @atom:O @atom:H fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH # (Remember to "unfix" fShakeSPCE during minimization.) } + write_once("In Init") { + # -- Default styles (for solo "SPCE" water) -- + units real + atom_style full + # (Hybrid force fields were not necessary but are used for portability.) + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + bond_style hybrid harmonic + angle_style hybrid harmonic + kspace_style pppm 0.0001 + #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! + } + } # end of definition of "SPCE" water molecule type diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f5fd61bd3135c3adf713a63a6689a42f9745f02 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt @@ -0,0 +1,25 @@ +This example using the electron Force Field (eFF) was created by +Andres Jaramillo-Botero and distributed with LAMMPS in the +"examples/USERS/eff/CH4" subdirectory. +The files from that example were converted into moltemplate format using +"ltemplify.py" and then edited by hand (to rename the atom types, +and replace all of the "pair_coeff ..." commands with "pair_coeff * *") + + +--- Original README: --- +Methane, valence electron ionization and full molecule tests (spe, dynamics). +Note: electron mass set to 1 + + +----- +WARNING: Regarding the "run.in.ch4_ionized" file + As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command + located in "orig_files/in.ch4_ionized.dynamics" (as well as the + files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", + which are both derived from it) causes LAMMPS to hang. + Running LAMMPS on Andres' original eFF example has the same behavior. + This appears to be an eFF/LAMMPS issue (not a moltemplate issue). + The "pair_style eff/cut 100" command works, so + try reducing the cutoff (or ask Andres Jaramillo-Botero for help). + Please let me know if you solve this issue (jewett.aij -at- g mail) + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh new file mode 100644 index 0000000000000000000000000000000000000000..527ff194424bda3a3ff0f46b126d1dc67a9be13f --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh @@ -0,0 +1,3 @@ + +lmp_mpi -i run.in.ch4 + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh new file mode 100644 index 0000000000000000000000000000000000000000..8433d10fa285e72cc21c2853e37a29198d82e2ab --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh @@ -0,0 +1,14 @@ +cd moltemplate_files/ + + moltemplate.sh -atomstyle electron system_ch4.lt + + # This will generate 3 files: + # "system_ch4.data", "system_ch4.in.init", "system_ch4.in.settings" + + mv -f system_ch4.data system_ch4.in.init system_ch4.in.settings ../ + + # optional: delete temporary files + + rm -rf output_ttree + +cd ../ diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt new file mode 100644 index 0000000000000000000000000000000000000000..b5989e5a1b951b2ab3e93b565f70fe10c67a4ec2 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt @@ -0,0 +1,45 @@ + +CH4 { + + write_once("Data Masses") { + @atom:C 12.01070 + @atom:H 1.000794 + @atom:e 1.000000 + } + + # id type q spin eradius x y z + + write("Data Atoms") { + $atom:c @atom:C 6.0 0 0.0 0.0 0.0 0.0 + $atom:h1 @atom:H 1.0 0 0.0 1.0 1.0 1.0 + $atom:h2 @atom:H 1.0 0 0.0 -1.0 -1.0 1.0 + $atom:h3 @atom:H 1.0 0 0.0 1.0 -1.0 -1.0 + $atom:h4 @atom:H 1.0 0 0.0 -1.0 1.0 -1.0 + $atom:esr @atom:e 0.0 -1 0.5 0.0 0.0 0.0 + $atom:esR1 @atom:e 0.0 -1 1.0 1.0 1.0 1.0 + $atom:esR2 @atom:e 0.0 -1 1.0 -1.0 -1.0 1.0 + $atom:esR3 @atom:e 0.0 -1 1.0 1.0 -1.0 -1.0 + $atom:esR4 @atom:e 0.0 -1 1.0 -1.0 1.0 -1.0 + $atom:eSr @atom:e 0.0 1 0.5 0.0 0.0 0.0 + $atom:eSR1 @atom:e 0.0 1 1.0 1.0 1.0 1.0 + $atom:eSR2 @atom:e 0.0 1 1.0 -1.0 -1.0 1.0 + $atom:eSR2 @atom:e 0.0 1 1.0 1.0 -1.0 -1.0 + $atom:eSR3 @atom:e 0.0 1 1.0 -1.0 1.0 -1.0 + } + + # -- styles and force-field parameters -- + # (these can be overridden later) + + write_once("In Init") { + atom_style electron + units electron + pair_style eff/cut 100.0 + newton on + comm_modify vel yes + } + write_once("In Settings") { + pair_coeff * * + } + +} # end of "CH4" object definition + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt new file mode 100644 index 0000000000000000000000000000000000000000..62865418e8ce7190fddfd08c24eb84d61d11dd7f --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt @@ -0,0 +1,55 @@ +# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command +# located in "orig_files/in.ch4_ionized.dynamics" (as well as the +# files "moltemplate_files/ch4_ionized.lt" (this file) +# ...causes LAMMPS to hang. +# Running LAMMPS on Andres' original eFF example has the same behavior. +# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. +# The "pair_style eff/cut 100" command works, so +# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). +# Please let me know if you solve this issue (jewett.aij -at- g mail ) + + +CH4_ionized { + + write_once("Data Masses") { + @atom:C 12.01070 + @atom:H 1.000794 + @atom:e 1.000000 + } + + # id type q spin eradius x y z + + write("Data Atoms") { + $atom:c @atom:C 6.000000 0 0.0 0.000000 -0.000000 0.000000 + $atom:h1 @atom:H 1.000000 0 0.0 1.247211 1.247211 1.247211 + $atom:h2 @atom:H 1.000000 0 0.0 -1.247211 -1.247211 1.247211 + $atom:h3 @atom:H 1.000000 0 0.0 1.247211 -1.247211 -1.247211 + $atom:h4 @atom:H 1.000000 0 0.0 -1.247211 1.247211 -1.247211 + $atom:esr @atom:e 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 + $atom:esR1 @atom:e 0.000000 -1 1.486181 0.979221 0.979221 0.979221 + $atom:esR2 @atom:e 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 + $atom:esR3 @atom:e 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 + $atom:esR4 @atom:e 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 + $atom:eSr @atom:e 0.000000 1 0.329128 -0.000000 0.000000 0.000000 + $atom:eSR1 @atom:e 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 + $atom:eSR2 @atom:e 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 + $atom:eSR3 @atom:e 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 + } + + # -- styles and force-field parameters -- + # (these can be overridden later) + + write_once("In Init") { + atom_style electron + units electron + pair_style eff/cut 5000.0 0 0 + newton on + comm_modify vel yes + } + + write_once("In Settings") { + pair_coeff * * + } + +} # end of "CH4_ionized" object definition + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in new file mode 100644 index 0000000000000000000000000000000000000000..8ba9365a9bfa6aaee2452ed566cdeb74f6ac24ae --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in @@ -0,0 +1,42 @@ + + +# ----------------- Init Section ----------------- + +include "system_ch4.in.init" + + +# ----------------- Atom Definition Section ----------------- + +read_data "system_ch4.data" + +# ----------------- Settings Section ----------------- + +include "system_ch4.in.settings" + + +# ----------------- Run Section ----------------- + +# The lines above define the system you want to simulate. +# What you do next is up to you. +# Typically a user would minimize and equilibrate +# the system using commands similar to the following: +# ---- examples ---- +# +# -- minimize -- +# minimize 1.0e-5 1.0e-7 1000 10000 +# (Note: Some fixes, for example "shake", interfere with the minimize command, +# You can use the "unfix" command to disable them before minimization.) +# -- declare time step for normal MD -- +# timestep 1.0 +# -- run at constant pressure (Nose-Hoover)-- +# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 +# -- ALTERNATELY, run at constant volume (Nose-Hoover) -- +# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 +# -- ALTERNATELY, run at constant volume using Langevin dynamics. -- +# -- (This is good for sparse CG polymers in implicit solvent.) -- +# fix fxLAN all langevin 300.0 300.0 5000 48279 +# fix fxNVE all nve #(<--needed by fix langevin) +# -- Now, finally run the simulation -- +# run 50000 +# ---- (end of examples) ---- + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt new file mode 100644 index 0000000000000000000000000000000000000000..3b0e6d7894fecf19352a36ce2e38043a163fc5d6 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt @@ -0,0 +1,28 @@ + +import "ch4.lt" # <-- defines "CH4" + + +# instantiate one or more copies of the "CH4" object: + +# Instantiate two copies of CH4: + +molecule1 = new CH4.move(-5.0,0,0) +molecule2 = new CH4.move(5.0,0,0) +# : : : + + +# alternate example: +# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: +# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) +# molecules[*][*][*].move(-5,-5,-5) + + +# optional "Boundary" (goes in header of generated DATA file) +# (-200 200 by default) + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt new file mode 100644 index 0000000000000000000000000000000000000000..cd44be380e014233410bb50fde9837807feedd16 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt @@ -0,0 +1,29 @@ + +import "ch4.lt" # <-- defines "CH4" +import "ch4_ionized.lt" # <-- defines "CH4_ionized" + + +# instantiate one or more copies of the "CH4" object: + +# Instantiate two copies of CH4: + +molecule1 = new CH4_ionized.move(-5.0,0,0) +molecule2 = new CH4_ionized.move(5.0,0,0) +# : : : + + +# alternate example: +# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: +# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) +# molecules[*][*][*].move(-5,-5,-5) + + +# optional "Boundary" (goes in header of generated DATA file) +# (-200 200 by default) + +write_once("Data Boundary") { + -500.0 500.0 xlo xhi + -500.0 500.0 ylo yhi + -500.0 500.0 zlo zhi +} + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README new file mode 100644 index 0000000000000000000000000000000000000000..20714b24c0bf66bee997600a265e54fce8f89870 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README @@ -0,0 +1,2 @@ +Methane, valence electron ionization and full molecule tests (spe, min, dynamics). +Note: electron mass set to 1 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 new file mode 100644 index 0000000000000000000000000000000000000000..ebe29be4ed1c5080df4083c959aaeda2ab8f6c4d --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 @@ -0,0 +1,32 @@ +Created by AJB + +15 atoms +3 atom types + +-500.0 500.0 xlo xhi +-500.0 500.0 ylo yhi +-500.0 500.0 zlo zhi + +Masses + +1 12.01070 # C nuclei mass +2 1.000794 # H nuclei mass +3 1.000000 # electron mass + +Atoms +#id|type|q|spin|eradius|x|y|z| +1 1 6.0 0 0.0 0.0 0.0 0.0 +2 2 1.0 0 0.0 1.0 1.0 1.0 +3 2 1.0 0 0.0 -1.0 -1.0 1.0 +4 2 1.0 0 0.0 1.0 -1.0 -1.0 +5 2 1.0 0 0.0 -1.0 1.0 -1.0 +6 3 0.0 -1 0.5 0.0 0.0 0.0 +7 3 0.0 -1 1.0 1.0 1.0 1.0 +8 3 0.0 -1 1.0 -1.0 -1.0 1.0 +9 3 0.0 -1 1.0 1.0 -1.0 -1.0 +10 3 0.0 -1 1.0 -1.0 1.0 -1.0 +11 3 0.0 1 0.5 0.0 0.0 0.0 +12 3 0.0 1 1.0 1.0 1.0 1.0 +13 3 0.0 1 1.0 -1.0 -1.0 1.0 +14 3 0.0 1 1.0 1.0 -1.0 -1.0 +15 3 0.0 1 1.0 -1.0 1.0 -1.0 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized new file mode 100644 index 0000000000000000000000000000000000000000..8c21a281a1ee8dc02819ab9ffc44246767633731 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized @@ -0,0 +1,31 @@ +Created by AJB + +14 atoms +3 atom types + +-5000.0 5000.0 xlo xhi +-5000.0 5000.0 ylo yhi +-5000.0 5000.0 zlo zhi + +Masses + +1 12.01070 # C nuclei mass +2 1.000794 # H nuclei mass +3 1.000000 # electron mass + +Atoms + +1 1 6.000000 0 0.0 0.000000 -0.000000 0.000000 +2 2 1.000000 0 0.0 1.247211 1.247211 1.247211 +3 2 1.000000 0 0.0 -1.247211 -1.247211 1.247211 +4 2 1.000000 0 0.0 1.247211 -1.247211 -1.247211 +5 2 1.000000 0 0.0 -1.247211 1.247211 -1.247211 +6 3 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 +7 3 0.000000 -1 1.486181 0.979221 0.979221 0.979221 +8 3 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 +9 3 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 +10 3 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 +11 3 0.000000 1 0.329128 -0.000000 0.000000 0.000000 +12 3 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 +13 3 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 +14 3 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics new file mode 100644 index 0000000000000000000000000000000000000000..2536fa8f4817aaff8fbc1d8b3dcdefa05f6df8c5 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics @@ -0,0 +1,41 @@ +variable sname index ch4 +log ${sname}.nve.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 100.0 +pair_coeff * * + +comm_modify vel yes + +# Minimize +min_style cg +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z +min_modify line quadratic dmax 0.1 +minimize 0 1.0e-6 1000 10000 + +# Dynamics + +compute effTemp all temp/eff + +thermo 1000 +thermo_style custom step pe temp press +thermo_modify temp effTemp + +velocity all create 300.0 4928459 dist gaussian rot yes mom yes + +timestep 0.005 +fix 1 all nve/eff + +# the custom dump includes the radii +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z +dump 3 all xyz 1000 ${sname}.nve.xyz + +run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min new file mode 100644 index 0000000000000000000000000000000000000000..69b7c15bd4f6065b445d3ed2740a7ad932647bdb --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min @@ -0,0 +1,32 @@ +variable sname index ch4 +log ${sname}.nve.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 100.0 +pair_coeff * * + +comm_modify vel yes + +compute effTemp all temp/eff + +compute energies all pair eff/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable ecoul equal c_energies[3] +variable erres equal c_energies[4] + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres + +min_style cg +compute 1 all property/atom spin eradius erforce +dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] +minimize 0 1e-6 2000 4000 + diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics new file mode 100644 index 0000000000000000000000000000000000000000..14f214296fb65c750e43a0012f913e8e48bc2671 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics @@ -0,0 +1,42 @@ +variable sname index ch4_ionized +log ${sname}.nvt.log + +units electron +newton on +boundary f f f + +atom_style electron + +read_data data.${sname} + +pair_style eff/cut 5000.0 0 0 +pair_coeff * * + +comm_modify vel yes + +# minimize +min_style cg +min_modify line quadratic +minimize 0 1.0e-6 10000 100000 + +# dynamics +compute effTemp all temp/eff + +thermo 100 +thermo_style custom step etotal pe ke temp press +thermo_modify temp effTemp + +# equilibrate +timestep 0.001 +fix 1 all nvt/eff temp 300.0 300.0 0.1 + +# the custom dump includes the radii +compute 1 all property/atom spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] +dump 2 all xyz 100 ${sname}.nvt.xyz + +run 1000000 + +fix 2 all nve/eff + +run 1000000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 new file mode 100644 index 0000000000000000000000000000000000000000..a82260876806b6184b4a59cb87c2d22822f22060 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 @@ -0,0 +1,49 @@ +# PREREQUISITES: +# system_ch4.data, system_ch4.in.init, system.in.settings +# Generate these files using: +# cd moltemplate_files/ +# moltemplate.sh -atomstyle electron system_ch4.lt + + +variable sname index ch4 +log ${sname}.nve.log + + +boundary f f f +include system_${sname}.in.init + + +read_data system_${sname}.data + + +include system_${sname}.in.settings + + + +# Minimize + +min_style cg +compute 1 all property/atom spin eradius +dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z +min_modify line quadratic dmax 0.1 +minimize 0 1.0e-6 1000 10000 + + +# Dynamics + +compute effTemp all temp/eff + +thermo 1000 +thermo_style custom step pe temp press +thermo_modify temp effTemp + +velocity all create 300.0 4928459 dist gaussian rot yes mom yes + +timestep 0.005 +fix 1 all nve/eff + +# the custom dump includes the radii +dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z +dump 3 all xyz 1000 ${sname}.nve.xyz + +run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized new file mode 100644 index 0000000000000000000000000000000000000000..73e93b1cd2a87f1d20159a2df6d6b1f3110b5cb7 --- /dev/null +++ b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized @@ -0,0 +1,62 @@ +# PREREQUISITES: +# system_ch4_ionized.data, system_ch4_ionized.in.init, system.in.settings +# Generate these files using: +# cd moltemplate_files/ +# moltemplate.sh -atomstyle electron system_ch4_ionized.lt + +# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command +# located in "orig_files/in.ch4_ionized.dynamics" (as well as the +# files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", +# which are both derived from it) causes LAMMPS to hang. +# Running LAMMPS on Andres' original eFF example has the same behavior. +# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. +# The "pair_style eff/cut 100" command works, so +# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). +# Please let me know if you solve this issue (jewett.aij -at- g mail ) + + +variable sname index ch4 +log ${sname}.nve.log + + +boundary f f f +include system_${sname}.in.init + + +read_data system_${sname}.data + + +include system_${sname}.in.settings + + + +# Minimize + +min_style cg +min_modify line quadratic +minimize 0 1.0e-6 10000 100000 + + + +# Dynamics + +compute effTemp all temp/eff + +thermo 100 +thermo_style custom step etotal pe ke temp press +thermo_modify temp effTemp + +# Equilibrate +timestep 0.001 +fix 1 all nvt/eff temp 300.0 300.0 0.1 + +# the custom dump includes the radii +compute 1 all property/atom spin eradius +dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] +dump 2 all xyz 100 ${sname}.nvt.xyz + +run 1000000 + +fix 2 all nve/eff + +run 1000000 diff --git a/tools/moltemplate/moltemplate/__init__.py b/tools/moltemplate/moltemplate/__init__.py index b9601769e1f1d1d62ac8e0c28facb6f1b9263047..ccd228a8c1dee865d244e181c86427e7aad3a2a1 100644 --- a/tools/moltemplate/moltemplate/__init__.py +++ b/tools/moltemplate/moltemplate/__init__.py @@ -1,11 +1,11 @@ from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ StackableCommand, PopCommand, PopRightCommand, PopLeftCommand, \ PushCommand, PushLeftCommand, PushRightCommand, ScopeCommand, \ - WriteVarBindingsFile, StaticObj, InstanceObj, \ + WriteVarBindingsFile, StaticObj, InstanceObj, ExtractFormattingCommands, \ BasicUI, ScopeBegin, ScopeEnd, WriteFileCommand, Render from .ttree_lex import TtreeShlex, split, LineLex, SplitQuotedString, \ EscCharStrToChar, SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, \ - HasWildCard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \ + HasWildcard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \ VarNPtr, VarBinding, SplitTemplate, SplitTemplateMulti, TableFromTemplate, \ ExtractCatName, DeleteLinesWithBadVars, TemplateLexer from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ diff --git a/tools/moltemplate/moltemplate/bonds_by_type.py b/tools/moltemplate/moltemplate/bonds_by_type.py index 6b36911f21d65d4dff6a222e9443370fdc6f3290..3df4a26582472c2af995fcb53b050de167e05a76 100755 --- a/tools/moltemplate/moltemplate/bonds_by_type.py +++ b/tools/moltemplate/moltemplate/bonds_by_type.py @@ -32,7 +32,7 @@ import sys try: from . import ttree_lex from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package import ttree_lex from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid diff --git a/tools/moltemplate/moltemplate/charge_by_bond.py b/tools/moltemplate/moltemplate/charge_by_bond.py index b8d7c756461d2d4229b871d7ee030e9390e92ab7..83acb83935b5467ffb725eb1703f833a72dd667f 100755 --- a/tools/moltemplate/moltemplate/charge_by_bond.py +++ b/tools/moltemplate/moltemplate/charge_by_bond.py @@ -1,11 +1,13 @@ #!/usr/bin/env python - # Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California +# Copyright (c) 2017, California Institute of Technology # All rights reserved. +g_program_name = __file__.split('/')[-1] # = 'charge_by_bond.py' +g_date_str = '2017-10-03' +g_version_str = '0.14.0' + import sys import re @@ -14,7 +16,7 @@ from collections import defaultdict try: from . import ttree_lex from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package import ttree_lex from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid @@ -23,6 +25,7 @@ except (SystemError, ValueError): def LookupChargePairs(chargebyatomid, # bond_ids, + # bond_types, # bond_pairs, lines_atoms, lines_bonds, @@ -137,7 +140,7 @@ def LookupChargePairs(chargebyatomid, # else: # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) - assert(len(bond_types) == 0) + #assert(len(bond_types) == 0) typepattern_to_chargepairs = [] warning_unassigned_chargepairs = None @@ -191,18 +194,20 @@ def LookupChargePairs(chargebyatomid, atomtype1 = atomids2types[atomid1] atomtype2 = atomids2types[atomid2] + found = False for typepattern, chargepair in typepattern_to_chargepairs: # use string comparisons to check if atom types match the pattern if ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern): # ("MatchesAll()" defined in "ttree_lex.py") chargebyatomid[atomid1] += chargepair[0] chargebyatomid[atomid2] += chargepair[1] + found = True elif ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern): chargebyatomid[atomid1] += chargepair[1] chargebyatomid[atomid2] += chargepair[0] - else: - if not warning_unassigned_chargepairs: - warning_unassigned_chargepairs = (atomid1, atomid2) + found = True + if (not found) and (not warning_unassigned_chargepairs): + warning_unassigned_chargepairs = (atomid1, atomid2) if warning_unassigned_chargepairs: sys.stderr.write('---------------------------------------------------------------------------\n' @@ -239,10 +244,6 @@ def main(): """ - g_program_name = __file__.split('/')[-1] # = 'charge_pairs_by_type.py' - g_date_str = '2016-12-22' - g_version_str = '0.13.0' - ####### Main Code Below: ####### sys.stderr.write(g_program_name + ' v' + g_version_str + ' ' + g_date_str + ' ') @@ -344,7 +345,7 @@ def main(): (' '.join(problem_args)) + '\n\n' ' (The actual problem may be earlier in the argument list.)\n') - bond_types = [] + #bond_types = [] fatoms = open(fname_atoms, 'r') lines_bonds = [] lines_bond_list = [] diff --git a/tools/moltemplate/moltemplate/dump2data.py b/tools/moltemplate/moltemplate/dump2data.py index 4c122d8ebad869c2a99e37280a43a0d62b3b7a46..249e6c9b2ef2d052027dcf72594b6e404fd4c405 100755 --- a/tools/moltemplate/moltemplate/dump2data.py +++ b/tools/moltemplate/moltemplate/dump2data.py @@ -22,8 +22,8 @@ A reference DATA file is needed (argument). # All rights reserved. g_program_name = 'dump2data.py' -g_date_str = '2017-7-27' -g_version_str = '0.53.0' +g_date_str = '2017-9-12' +g_version_str = '0.54.1' import sys from collections import defaultdict @@ -584,6 +584,7 @@ def WriteFrameToData(out_file, descr_str, misc_settings, data_settings, + dump_column_names, natoms, coords, coords_ixiyiz, @@ -677,13 +678,13 @@ def WriteFrameToData(out_file, # In principle, depending on the atom_style, # there could be multiple vectors per atom. for I in range(0, len(data_settings.ii_vects)): + i_vx = data_settings.ii_vects[I][0] + i_vy = data_settings.ii_vects[I][1] + i_vz = data_settings.ii_vects[I][2] if atomid in vects: vxvyvz = vects[atomid][I] assert((type(vxvyvz) is tuple) and (len(vxvyvz) == 3)) - i_vx = data_settings.ii_vects[I][0] - i_vy = data_settings.ii_vects[I][1] - i_vz = data_settings.ii_vects[I][2] if ((i_vx >= len(tokens)) or (i_vy >= len(tokens)) or (i_vz >= len(tokens))): @@ -697,8 +698,9 @@ def WriteFrameToData(out_file, tokens[i_vz] = vxvyvz[2] else: - if data_settings.column_names[ - i_vx] not in dump_column_names: + if (dump_column_names and + (data_settings.column_names[ + i_vx] not in dump_column_names)): raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"' + data_settings.column_names[i_vx] + '\"\n' ' However there are no columns with this name in your DUMP file\n' ' (or the column was not in the expected place).\n' @@ -1273,6 +1275,7 @@ def main(): descr_str, misc_settings, data_settings, + dump_column_names, frame_natoms, frame_coords, frame_coords_ixiyiz, diff --git a/tools/moltemplate/moltemplate/ettree.py b/tools/moltemplate/moltemplate/ettree.py index c8d90c7e42b7125964074a46441f9b33466b885b..20353a86ef5ab34ad8a1a92d7a098e3157aaf5ef 100755 --- a/tools/moltemplate/moltemplate/ettree.py +++ b/tools/moltemplate/moltemplate/ettree.py @@ -56,7 +56,7 @@ try: iEsptAtomCoords, iEsptAtomVects, iEsptAtomType, iEsptAtomID from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from ttree_lex import * @@ -482,7 +482,7 @@ def WriteFiles(files_content, suffix='', write_to_stdout=True): -def main() +def main(): """ This is is a "main module" wrapper for invoking ettree.py as a stand alone program. This program: @@ -495,8 +495,8 @@ def main() """ g_program_name = 'ettree.py' - g_date_str = '2016-12-22' - g_version_str = '0.36.0' + g_date_str = '2018-6-26' + g_version_str = '0.37.0' SimpleCounter.default_n0 = 0 # counters in Espresso begin at 0, not 1 diff --git a/tools/moltemplate/moltemplate/force_fields/README.txt b/tools/moltemplate/moltemplate/force_fields/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..d0650a0f7271e48a49a5a8ac9b34df1944531ae9 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/README.txt @@ -0,0 +1,13 @@ + +If moltemplate is unable to locate an .LT file that the user has requested +(ie. using the "import" command) in the current local directory, +moltemplate will search for that file here. + +This directory contains moltemplate files (.LT files) containing common +force fields (including parameters and rules for creating bonded interactions), +as well as definitions of molecules which are frequently used (for example +SPCE water). + +The scripts used to convert these force fields are located here as well, along +with the original files containing the force field parameters (when available). + diff --git a/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt b/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt deleted file mode 100644 index dd54c6b697121a2fa52cfa709cf7f36a4abd8067..0000000000000000000000000000000000000000 --- a/tools/moltemplate/moltemplate/force_fields/SDK_lipid+chol.lt +++ /dev/null @@ -1,423 +0,0 @@ -# Autogenerated by EMC 2 LT tool v0.2 on 2017-02-28 -# -# ./emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units -# -# Adapted from EMC by Pieter J. in 't Veld -# Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 - -SDK { - write_once("Data Masses") { - @atom:CM 42.080400 # CM - @atom:CMD2 26.037800 # CMD2 - @atom:CT 43.088300 # CT - @atom:CT2 29.061500 # CT2 - @atom:EST1 58.036600 # EST1 - @atom:EST2 58.036600 # EST2 - @atom:GL 41.072500 # GL - @atom:NC 87.164400 # NC - @atom:NH 44.076100 # NH - @atom:PH 94.971600 # PH - @atom:PHE 94.971600 # PHE - @atom:W 54.045600 # W - @atom:C2T 43.090000 # C2T - @atom:CM2 28.050000 # CM2 - @atom:CM2R 28.050000 # CM2R - @atom:CMDB 39.060000 # CMDB - @atom:CMB 40.060000 # CMB - @atom:CMR 41.070000 # CMR - @atom:CMR5 41.070000 # CMR5 - @atom:CTB 42.080000 # CTB - @atom:CTBA 27.050000 # CTBA - @atom:CTBB 27.050000 # CTBB - @atom:OAB 30.030000 # OAB - } # end of atom masses - - # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup ----- - replace{ @atom:CM @atom:CM_bCM_aCM_dCM_iCM} - replace{ @atom:CMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2} - replace{ @atom:CT @atom:CT_bCT_aCT_dCT_iCT} - replace{ @atom:CT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2} - replace{ @atom:EST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1} - replace{ @atom:EST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2} - replace{ @atom:GL @atom:GL_bGL_aGL_dGL_iGL} - replace{ @atom:NC @atom:NC_bNC_aNC_dNC_iNC} - replace{ @atom:NH @atom:NH_bNH_aNH_dNH_iNH} - replace{ @atom:PH @atom:PH_bPH_aPH_dPH_iPH} - replace{ @atom:PHE @atom:PHE_bPHE_aPHE_dPHE_iPHE} - replace{ @atom:W @atom:W_bW_aW_dW_iW} - replace{ @atom:C2T @atom:C2T_bC2T_aC2T_dC2T_iC2T} - replace{ @atom:CM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2} - replace{ @atom:CM2R @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R} - replace{ @atom:CMDB @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB} - replace{ @atom:CMB @atom:CMB_bCMB_aCMB_dCMB_iCMB} - replace{ @atom:CMR @atom:CMR_bCMR_aCMR_dCMR_iCMR} - replace{ @atom:CMR5 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5} - replace{ @atom:CTB @atom:CTB_bCTB_aCTB_dCTB_iCTB} - replace{ @atom:CTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA} - replace{ @atom:CTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB} - replace{ @atom:OAB @atom:OAB_bOAB_aOAB_dOAB_iOAB} - # END EQUIVALENCE - - write_once("In Settings") { - # ----- Non-Bonded interactions ----- - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.420000 4.506000 # CM-CM - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.312000 4.255500 # CM-CMD2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CM-CT - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.362000 4.363500 # CM-CT2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.403000 # CM-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.403000 # CM-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # CM-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.400000 5.128000 # CM-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.330000 4.553000 # CM-NH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.953000 # CM-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.953000 # CM-PHE - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:W_bW_aW_dW_iW lj12_4 0.340000 4.438500 # CM-W - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.232000 4.005000 # CMD2-CMD2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.330000 4.295000 # CMD2-CT - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.269000 4.113000 # CMD2-CT2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.440000 4.005000 # CMD2-EST1 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.440000 4.005000 # CMD2-EST2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.312000 4.255500 # CMD2-GL - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.350000 4.877500 # CMD2-NC - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.300000 4.302500 # CMD2-NH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.702500 # CMD2-PH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.702500 # CMD2-PHE - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:W_bW_aW_dW_iW lj12_4 0.270000 4.188000 # CMD2-W - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.469000 4.585000 # CT-CT - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.383000 4.403000 # CT-CT2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CT-EST1 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CT-EST2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CT-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CT-NC - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.340000 4.925000 # CT-NH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CT-PH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.320000 4.992500 # CT-PHE - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CT-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.312000 4.221000 # CT2-CT2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CT2-EST1 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CT2-EST2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.365000 # CT2-GL - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CT2-NC - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.320000 4.410500 # CT2-NH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CT2-PH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.280000 4.810500 # CT2-PHE - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CT2-W - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.495000 4.300000 # EST1-EST1 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST1-EST2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST1-GL - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST1-NC - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST1-NH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST1-PH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST1-PHE - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST1-W - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST2-EST2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST2-GL - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST2-NC - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST2-NH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST2-PH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST2-PHE - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST2-W - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # GL-GL - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.650000 4.620000 # GL-NC - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.750000 4.190000 # GL-NH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.750000 # GL-PH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.750000 # GL-PHE - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:W_bW_aW_dW_iW lj12_4 0.640000 4.438500 # GL-W - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.700000 5.750000 # NC-NC - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.880000 5.175000 # NC-NH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.150000 4.200000 # NC-PH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.150000 4.200000 # NC-PHE - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:W_bW_aW_dW_iW lj12_4 0.900000 4.610000 # NC-W - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:NH_bNH_aNH_dNH_iNH lj9_6 1.100000 4.600000 # NH-NH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.200000 3.800000 # NH-PH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.200000 3.800000 # NH-PHE - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:W_bW_aW_dW_iW lj12_4 0.800000 3.950000 # NH-W - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.400000 5.400000 # PH-PH - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 5.000000 # PH-PHE - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PH-W - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 4.600000 # PHE-PHE - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PHE-W - pair_coeff @atom:W_bW_aW_dW_iW @atom:W_bW_aW_dW_iW lj12_4 0.895000 4.371000 # W-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # C2T-NC - pair_coeff @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CMR5-CT - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.252000 4.767700 # C2T-CTBA - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.469000 4.585000 # CT-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.331000 4.771400 # C2T-CMR - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.383000 4.403000 # CT-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.252000 4.767700 # C2T-CTBB - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.383000 4.403000 # CT-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # C2T-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CT-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.254000 4.610100 # C2T-CM2R - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.383000 4.403000 # CT2-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.330000 4.295000 # C2T-CMD2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.312000 4.221000 # CT2-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.331000 4.771400 # C2T-CMR5 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.312000 4.221000 # CT2-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # C2T-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.415000 3.950500 # CT2-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:C2T_bC2T_aC2T_dC2T_iC2T lj9_6 0.400000 4.811500 # C2T-C2T - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.269000 5.015500 # CTB-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # C2T-OAB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CTB-EST1 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # C2T-PH - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CTB-EST2 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.354000 4.894100 # C2T-CMDB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CTB-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.297000 4.527200 # C2T-CT2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.464800 # CTB-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.291000 4.588000 # C2T-CM2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.464800 # CTB-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.391000 4.545500 # C2T-CM - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CTB-GL - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.409000 4.860100 # C2T-CT - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CTB-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.283000 4.910900 # C2T-CTB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CTB-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.310000 4.656400 # C2T-CMB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CTB-PH - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # C2T-EST1 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBA-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # C2T-EST2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBA-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.420000 4.506000 # CM-CMR - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBA-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.390000 4.434200 # CM-CM2R - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBA-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.420000 4.506000 # CM-CMR5 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBA-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.561000 4.093000 # CM-OAB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.461000 # CTBA-CTBA - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.362000 4.379000 # CM-CMDB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBA-CTBB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.336000 4.461900 # CM-CM2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBA-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.444000 4.545500 # CM-CTB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBA-OAB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.420000 4.506000 # CM-CMB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBB-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.362000 4.363500 # CM-CTBA - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBB-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.362000 4.363500 # CM-CTBB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBB-GL - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.248000 4.936800 # CM2-PH - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBB-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.413000 4.066900 # CM2-OAB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBB-EST2 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.237000 4.440300 # CM2-CM2R - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.248000 4.231300 # CM2-CMD2 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.333000 4.484600 # CM2-CMR5 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBB-CTBB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.228000 4.319900 # CM2-CT2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST1-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.265000 4.461000 # CM2-CM2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST2-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.267000 4.369700 # CM2-CMDB - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.669000 4.093000 # GL-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.301000 4.454600 # CM2-CT - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.637000 3.931900 # NC-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.353000 4.524600 # CM2-CTB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:W_bW_aW_dW_iW lj9_6 1.026000 4.025500 # OAB-W - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.333000 4.484600 # CM2-CMB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.928000 3.616600 # OAB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.306000 5.113800 # CM2-NC - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.580000 3.680000 # OAB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.366000 4.380500 # CM2-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.366000 4.380500 # CM2-EST2 - } # end of nonbonded parameters - - write_once("In Settings") { - # ----- Bonds ----- - bond_coeff @bond:CM-CM harmonic 6.160000 3.640000 - bond_coeff @bond:CM-CMD2 harmonic 8.000000 3.030000 - bond_coeff @bond:CM-CT harmonic 6.160000 3.650000 - bond_coeff @bond:CM-CT2 harmonic 9.000000 3.130000 - bond_coeff @bond:CM-EST1 harmonic 4.700000 3.550000 - bond_coeff @bond:CM-EST2 harmonic 5.100000 3.610000 - bond_coeff @bond:CM-PHE harmonic 12.000000 3.690000 - bond_coeff @bond:CM-SO4 harmonic 11.000000 3.630000 - bond_coeff @bond:CMD2-CT harmonic 8.000000 3.090000 - bond_coeff @bond:CMD2-CT2 harmonic 60.000000 2.540000 - bond_coeff @bond:CT-CT harmonic 6.955000 3.710000 - bond_coeff @bond:EST1-GL harmonic 30.000000 2.880000 - bond_coeff @bond:EST2-GL harmonic 8.400000 3.480000 - bond_coeff @bond:GL-PHE harmonic 8.900000 3.520000 - bond_coeff @bond:NC-PHE harmonic 4.800000 4.250000 - bond_coeff @bond:NH-PHE harmonic 9.400000 3.600000 - bond_coeff @bond:PHE1-PHE2 harmonic 2.500000 150.000000 - bond_coeff @bond:C2T-CM2 harmonic 55.000000 2.500000 - bond_coeff @bond:CM2-CTB harmonic 42.500000 2.900000 - bond_coeff @bond:CM2R-CTBA harmonic 45.000000 2.400000 - bond_coeff @bond:CM2R-OAB harmonic 50.000000 2.600000 - bond_coeff @bond:CMB-CMDB harmonic 75.000000 3.500000 - bond_coeff @bond:CMB-CMR5 harmonic 50.000000 3.000000 - bond_coeff @bond:CMB-CTBA harmonic 35.000000 3.400000 - bond_coeff @bond:CMB-CTBB harmonic 50.000000 3.000000 - bond_coeff @bond:CMDB-CTBA harmonic 40.000000 2.500000 - bond_coeff @bond:CMDB-OAB harmonic 55.000000 3.100000 - bond_coeff @bond:CMR5-CTBB harmonic 60.000000 2.300000 - bond_coeff @bond:CMR-CTBA harmonic 50.000000 3.000000 - bond_coeff @bond:CMR-CTBB harmonic 55.000000 2.500000 - bond_coeff @bond:CTB-CTBB harmonic 22.500000 3.400000 - bond_coeff @bond:CMR5-CTB harmonic 35.000000 3.100000 - } - - write_once("Data Bonds By Type") { - @bond:CM-CM @atom:*_bCM_a*_d*_i* @atom:*_bCM_a*_d*_i* - @bond:CM-CMD2 @atom:*_bCM_a*_d*_i* @atom:*_bCMD2_a*_d*_i* - @bond:CM-CT @atom:*_bCM_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CM-CT2 @atom:*_bCM_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CM-EST1 @atom:*_bCM_a*_d*_i* @atom:*_bEST1_a*_d*_i* - @bond:CM-EST2 @atom:*_bCM_a*_d*_i* @atom:*_bEST2_a*_d*_i* - @bond:CM-PHE @atom:*_bCM_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:CM-SO4 @atom:*_bCM_a*_d*_i* @atom:*_bSO4_a*_d*_i* - @bond:CMD2-CT @atom:*_bCMD2_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CMD2-CT2 @atom:*_bCMD2_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CT-CT @atom:*_bCT_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:EST1-GL @atom:*_bEST1_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:EST2-GL @atom:*_bEST2_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:GL-PHE @atom:*_bGL_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NC-PHE @atom:*_bNC_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NH-PHE @atom:*_bNH_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:PHE1-PHE2 @atom:*_bPHE1_a*_d*_i* @atom:*_bPHE2_a*_d*_i* - @bond:C2T-CM2 @atom:*_bC2T_a*_d*_i* @atom:*_bCM2_a*_d*_i* - @bond:CM2-CTB @atom:*_bCM2_a*_d*_i* @atom:*_bCTB_a*_d*_i* - @bond:CM2R-CTBA @atom:*_bCM2R_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CM2R-OAB @atom:*_bCM2R_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMB-CMDB @atom:*_bCMB_a*_d*_i* @atom:*_bCMDB_a*_d*_i* - @bond:CMB-CMR5 @atom:*_bCMB_a*_d*_i* @atom:*_bCMR5_a*_d*_i* - @bond:CMB-CTBA @atom:*_bCMB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMB-CTBB @atom:*_bCMB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMDB-CTBA @atom:*_bCMDB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMDB-OAB @atom:*_bCMDB_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMR5-CTBB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR-CTBA @atom:*_bCMR_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMR-CTBB @atom:*_bCMR_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CTB-CTBB @atom:*_bCTB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR5-CTB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTB_a*_d*_i* - } # end of bonds - - write_once("In Settings") { - # ----- Angles ----- - angle_coeff @angle:CM-CM-CM sdk 1.190000 173.000000 - angle_coeff @angle:CM-CM-CMD2 sdk 1.900000 161.000000 - angle_coeff @angle:CM-CM-CT sdk 1.190000 175.000000 - angle_coeff @angle:CM-CM-CT2 sdk 1.600000 172.000000 - angle_coeff @angle:CM-CM-EST1 sdk 1.000000 178.000000 - angle_coeff @angle:CM-CM-EST2 sdk 1.000000 178.000000 - angle_coeff @angle:CM-CM-PHE sdk 1.100000 178.000000 - angle_coeff @angle:CM-CMD2-CM sdk 6.000000 110.000000 - angle_coeff @angle:CM-EST1-GL sdk 0.800000 168.000000 - angle_coeff @angle:CM-EST2-GL sdk 0.800000 172.000000 - angle_coeff @angle:CM-PHE-NC sdk 3.300000 112.000000 - angle_coeff @angle:CT-CM-CT sdk 1.093000 175.500000 - angle_coeff @angle:CT-CM-CT2 sdk 1.600000 172.000000 - angle_coeff @angle:CT-CMD2-CT sdk 7.700000 116.000000 - angle_coeff @angle:CT2-CM-CT2 sdk 1.700000 173.000000 - angle_coeff @angle:CT2-CMD2-CT2 sdk 12.000000 110.000000 - angle_coeff @angle:EST1-GL-EST2 sdk 1.000000 95.000000 - angle_coeff @angle:EST1-GL-PHE sdk 1.400000 124.000000 - angle_coeff @angle:EST2-GL-PHE sdk 2.000000 138.000000 - angle_coeff @angle:GL-PHE-NC sdk 3.100000 112.000000 - angle_coeff @angle:GL-PHE-NH sdk 4.000000 102.000000 - angle_coeff @angle:C2T-CM2-CTB sdk 8.000000 160.000000 - angle_coeff @angle:CM2-CTB-CTBB sdk 4.000000 130.000000 - angle_coeff @angle:CM2R-CTBA-CMB harmonic 40.000000 112.500000 - angle_coeff @angle:CM2R-CTBA-CMDB harmonic 22.500000 75.900000 - angle_coeff @angle:CM2R-CTBA-CMR harmonic 35.000000 98.700000 - angle_coeff @angle:CM2R-OAB-CMDB harmonic 40.000000 63.900000 - angle_coeff @angle:CMB-CMDB-CTBA harmonic 45.000000 68.600000 - angle_coeff @angle:CMB-CMDB-OAB harmonic 65.000000 146.600000 - angle_coeff @angle:CMB-CMR5-CTBB harmonic 35.000000 67.800000 - angle_coeff @angle:CMB-CTBA-CMDB harmonic 25.000000 68.900000 - angle_coeff @angle:CMB-CTBA-CMR harmonic 75.000000 47.800000 - angle_coeff @angle:CMB-CTBB-CMR5 harmonic 25.000000 68.200000 - angle_coeff @angle:CMB-CTBB-CMR harmonic 50.000000 56.300000 - angle_coeff @angle:CMB-CTBB-CTB sdk 35.000000 120.700000 - angle_coeff @angle:CMDB-CMB-CMR5 harmonic 150.000000 175.600000 - angle_coeff @angle:CMDB-CMB-CTBA harmonic 62.500000 42.500000 - angle_coeff @angle:CMDB-CMB-CTBB harmonic 25.000000 134.200000 - angle_coeff @angle:CMDB-CTBA-CMR harmonic 50.000000 108.600000 - angle_coeff @angle:CMR5-CNB-CTBA harmonic 15.000000 135.800000 - angle_coeff @angle:CMR5-CMB-CTBB harmonic 45.000000 44.000000 - angle_coeff @angle:CMR5-CTBB-CTB harmonic 20.000000 62.700000 - angle_coeff @angle:CMR-CTBB-CMR5 harmonic 75.000000 107.000000 - angle_coeff @angle:CMR-CTBB-CTB sdk 37.500000 110.100000 - angle_coeff @angle:CTBA-CM2R-OAB harmonic 25.000000 107.400000 - angle_coeff @angle:CTBA-CMB-CTBB harmonic 20.000000 92.200000 - angle_coeff @angle:CTBA-CMDB-OAB harmonic 20.000000 91.800000 - angle_coeff @angle:CTBA-CMR-CTBB harmonic 15.000000 115.000000 - angle_coeff @angle:CMB-CMR5-CTB harmonic 88.000000 131.700000 - angle_coeff @angle:CTBB-CMR5-CTB harmonic 20.000000 77.400000 - angle_coeff @angle:CM2-CTB-CMR5 sdk 20.000000 118.000000 - angle_coeff @angle:CMR5-CTB-CTBB harmonic 62.500000 39.700000 - } - - write_once("Data Angles By Type") { - @angle:CM-CM-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-CM-CMD2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* - @angle:CM-CM-CT @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CM-CM-CT2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CM-CM-EST1 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* - @angle:CM-CM-EST2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:CM-CM-PHE @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:CM-CMD2-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-EST1-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-EST2-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-PHE-NC @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:CT-CM-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT-CM-CT2 @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT-CMD2-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT2-CM-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT2-CMD2-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:EST1-GL-EST2 @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:EST1-GL-PHE @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:EST2-GL-PHE @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:GL-PHE-NC @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:GL-PHE-NH @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNH_d*_i* - @angle:C2T-CM2-CTB @atom:*_b*_aC2T_d*_i* @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CTBB @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CM2R-CTBA-CMB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* - @angle:CM2R-CTBA-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CM2R-CTBA-CMR @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CM2R-OAB-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CMDB-CTBA @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMB-CMDB-OAB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CMB-CMR5-CTBB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CTBA-CMDB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CTBA-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CMR5 @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMB-CTBB-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMDB-CMB-CMR5 @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMDB-CMB-CTBA @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMDB-CMB-CTBB @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMDB-CTBA-CMR @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMR5-CNB-CTBA @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCNB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMR5-CMB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMR5-CTBB-CTB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMR-CTBB-CMR5 @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR-CTBB-CTB @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBA-CM2R-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMB-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CTBA-CMDB-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMR-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CMR5-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBB-CMR5-CTB @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CMR5 @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR5-CTB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - } # end of angles - - write_once("In Init") { - # Warning: This is a very generic "In Init" section, further - # modification prior to any simulation is extremely likely - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid sdk - pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 - special_bonds lj/coul 0.0 0.0 0.0 - } # end init -} # SDK diff --git a/tools/moltemplate/moltemplate/force_fields/__init__.py b/tools/moltemplate/moltemplate/force_fields/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..d228c3c18f479db2b55e8d5f19d0e4d01be6ed97 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt @@ -0,0 +1,30 @@ +This directoroy contains the COMPASS force field parameters in the original +MSI file format ("compass_published.frc" which is distributed with "msi2lmp"). +It can be converted into moltemplate format using the following command: + +msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt + +--- Credits: ---- + This is an incomplete version of the COMPASS force field based on available +public sources. Parameters for some common chemical groups are missing +(for example, the NH2 amine group). The commercial version of COMPASS is +much larger and presumably includes more up to date parameters and parameters +for a wider range of atom types and molecule types. (However files +containing those force field parameters are not publicly available.) + + This file has been graciously made available by Materials Design Inc. + + Here is a comment from "compass_published.frc": + + "This file created by Materials Design, Inc. (www.materialsdesign.com) +Please realize that we neither support this version, nor make any warranty +as to the correctness of the parameters. We have checked the numbers against +the literature, but of course there may still be errors, including errors of +interpretation. Also, the current version of COMPASS may well be different +that that originally published. + If you have comments or suggestions, feel free to email Paul Saxe +at psaxe (at) materialsdesign.com" + +(Note: This file predates moltemplate and was intended for use with other + software. Paul Saxe cannot be expected to answer questions related to + moltemplate.) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc b/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc new file mode 100644 index 0000000000000000000000000000000000000000..6c2e681b5cbdc992f77bf113c14fe7c319e5d66e --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc @@ -0,0 +1,1381 @@ +!BIOSYM forcefield 1 + +#version compass_published.frc 1.1 30-Jun-09 +#version compass_published.frc 1.0 01-Jun-09 + +#define compass + +!Ver Ref Function Label +!---- --- --------------------------------- ------ + 1.0 1 atom_types compass + 1.0 1 equivalence compass + 1.0 1 quartic_bond compass + 1.0 1 quartic_angle compass + 1.0 1 bond-bond compass + 1.0 1 bond-bond_1_3 compass + 1.0 1 bond-angle compass + 1.0 1 torsion_3 compass + 1.0 1 end_bond-torsion_3 compass + 1.0 1 middle_bond-torsion_3 compass + 1.0 1 angle-torsion_3 compass + 1.0 1 wilson_out_of_plane compass + 1.0 1 angle-angle compass + 1.0 1 angle-angle-torsion_1 compass + 1.0 1 nonbond(9-6) compass + 1.0 1 bond_increments compass + 1.0 1 templates compass + +#atom_types compass + +> Atom type definitions for any variant of compass +> Masses from CRC 1973/74 pages B-250. + +!Ver Ref Type Mass Element Comment +!---- --- ---- ---------- ------- ----------------------------------------- + 1.0 5 ar 39.94400 Ar argon + 1.0 1 c3a 12.01115 C aromatic carbon + 1.0 5 c1o 12.01115 C carbon in CO + 1.0 5 c2= 12.01115 C carbon in CO2 and CS2 + 1.0 7 c3' 12.01115 C carbonyl carbon [one polar substituent] + 1.0 1 c4 12.01115 C generic sp3 carbon + 1.0 8 c41o 12.01115 C carbon, sp3, in methanol + 1.0 8 c43o 12.01115 C carbon, sp3 in secondary alcohols + 1.0 1 c43 12.01115 C sp3 carbon with three heavy atoms attached + 1.0 1 c44 12.01115 C sp3 carbon with four heavy atoms attached + 1.0 3 c4o 12.01115 C alpha carbon + 1.0 9 c4z 12.01115 C carbon, sp3, bonded to -N3 + 1.0 1 h1 1.00797 H nonpolar hydrogen + 1.0 5 h1h 1.00797 H hydrogen in H2 + 1.0 3 h1o 1.00797 H strongly polar hydrogen, bonded to O,F + 1.0 5 he 4.00300 He helium + 1.0 5 kr 83.80000 Kr krypton + 1.0 5 n1n 14.00670 N nitrogen in N2 + 1.0 5 n1o 14.00670 N nitrogen in NO + 1.0 5 n1z 14.00670 N nitrogen, terminal atom in -N3 + 1.0 4 n2= 14.00670 N nitrogen + 1.0 5 n2o 14.00670 N nitrogen in NO2 + 1.0 9 n2t 14.00670 N nitrogen, central atom in -N3 + 1.0 9 n2z 14.00670 N nitrogen, first atom in -N3 + 1.0 7 n3m 14.00670 N sp3 nitrogen in amides without hydrogen + 1.0 6 n3o 14.00670 N nitrogen in nitro group + 1.0 5 ne 20.18300 Ne neon + 1.0 5 o1= 15.99940 O oxygen in NO2 and SO2 [and carbonyl] + 1.0 5 o1=* 15.99940 O oxygen in CO2 + 1.0 6 o12 15.99940 O oxygen in nitro group (-NO2) + 1.0 5 o1c 15.99940 O oxygen in CO + 1.0 5 o1n 15.99940 O oxygen in NO + 1.0 5 o1o 15.99940 O oxygen in O2 + 1.0 2 o2 15.99940 O generic oxygen with two bonds attached + 1.0 3 o2e 15.99940 O ether oxygen + 1.0 3 o2h 15.99940 O hydroxyl oxygen + 1.0 6 o2n 15.99940 O oxygen in nitrates + 1.0 7 o2s 15.99940 O ester oxygen + 1.0 2 o2z 15.99940 O oxygen, in siloxanes and zeolites + 1.0 4 p4= 30.97380 P phosphorous + 1.0 5 s1= 32.06400 S sulfur in CS2 + 1.0 5 s2= 32.06400 S sulfur in SO2 + 1.0 2 si4 28.08600 Si generic silicon with four bonds attached + 1.0 2 si4c 28.08600 Si a subset of si4, non-hydrogen atom attached [siloxanes] + 1.0 5 xe 131.30000 Xe xenon + + +#equivalence compass + +! Equivalences +! ----------------------------------------- +!Ver Ref Type NonB Bond Angle Torsion OOP +!---- --- ---- ---- ---- ----- ------- ---- + 1.0 5 ar ar ar ar ar ar + 1.0 5 c1o c1o c1o c1o c1o c1o + 1.0 5 c2= c2= c2= c2= c2= c2= + 1.0 1 c3a c3a c3a c3a c3a c3a + 1.0 7 c3' c3' c3' c3' c3' c3' + 1.0 1 c4 c4 c4 c4 c4 c4 + 1.0 8 c41o c41o c4 c4 c4 c4 + 1.0 8 c43o c43o c4 c4 c4 c4 + 1.0 1 c43 c43 c4 c4 c4 c4 + 1.0 1 c44 c44 c4 c4 c4 c4 + 1.0 3 c4o c4o c4 c4 c4 c4 + 1.0 9 c4z c4z c4 c4 c4 c4 + 1.0 1 h1 h1 h1 h1 h1 h1 + 1.0 5 h1h h1h h1h h1 h1 h1 + 1.0 3 h1o h1o h1 h1 h1 h1 + 1.0 5 he he he he he he + 1.0 5 kr kr kr kr kr kr + 1.0 5 n1n n1n n1n n1n n1n n1n + 1.0 5 n1o n1o n1o n1o n1o n1o + 1.0 9 n1z n1z n1t n1t n1t n1t + 1.0 4 n2= n2= n2= n2= n2= n2= + 1.0 5 n2o n2o n2o n2o n2o n2o + 1.0 9 n2t n2t n2t n2t n2t n2t + 1.0 9 n2z n2z n2z n2z n2z n2z + 1.0 7 n3m n3m n3m n3m n3m n3m + 1.0 6 n3o n3o n3o n3o n3o n3o + 1.0 5 ne ne ne ne ne ne + 1.0 5 o1= o1= o1= o1= o1= o1= + 1.0 5 o1=* o1=* o1= o1= o1= o1= + 1.0 6 o12 o12 o1= o1= o1= o1= + 1.0 5 o1c o1c o1c o1c o1c o1c + 1.0 5 o1n o1n o1n o1n o1n o1n + 1.0 5 o1o o1o o1o o1o o1o o1o + 1.0 2 o2 o2 o2 o2 o2 o2 + 1.0 3 o2h o2h o2h o2 o2 o2 + 1.0 3 o2e o2e o2e o2 o2 o2 + 1.0 6 o2n o2n o2n o2n o2 o2 + 1.0 7 o2s o2s o2e o2 o2 o2 + 1.0 2 o2z o2z o2z o2z o2z o2z + 1.0 4 p4= p4= p4= p4= p4= p4= + 1.0 5 s1= s1= s1= s1= s1= s1= + 1.0 5 s2= s2= s2= s2= s2= s2= + 1.0 2 si4 si4 si4 si4 si4 si4 + 1.0 2 si4c si4c si4 si4 si4 si4 + 1.0 5 xe xe xe xe xe xe + + +#quartic_bond compass + +> E = K2 * (R - R0)^2 + K3 * (R - R0)^3 + K4 * (R - R0)^4 + +!Ver Ref I J R0 K2 K3 K4 +!---- --- ---- ---- ------- -------- --------- -------- + 1.0 1 c3a c3a 1.4170 470.8361 -627.6179 1327.6345 + 1.0 1 c3a c4 1.5010 321.9021 -521.8208 572.1628 + 1.0 1 c3a h1 1.0982 372.8251 -803.4526 894.3173 + 1.0 1 c4 c4 1.5300 299.6700 -501.7700 679.8100 + 1.0 1 c4 h1 1.1010 345.0000 -691.8900 844.6000 + 1.0 2 o2z si4 1.6400 350.1232 -517.3424 673.7067 + 1.0 3 c3a o2 1.3768 428.8798 -738.2350 1114.9655 + 1.0 3 c3a o2e 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c3a o2h 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c4 o2e 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 c4 o2h 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 h1 o2h 0.9494 540.3633 -1311.8663 2132.4446 + 1.0 4 c3a n2= 1.4000 350.0000 0.0000 0.0000 + 1.0 4 c3a p4= 1.7890 197.7020 -332.2510 325.7160 + 1.0 4 c4 n2= 1.4740 337.0600 -147.3700 213.6330 + 1.0 4 c4 p4= 1.8000 218.1400 -329.5110 290.3490 + 1.0 4 cl1p p4= 2.0000 158.7770 -239.1290 210.0840 + 1.0 4 f1p p4= 1.5650 340.0000 -882.3840 1197.9190 + 1.0 4 h1 n2= 1.0310 540.1120 -1500.2952 2431.0080 + 1.0 4 h1 p4= 1.4300 285.2040 -575.6850 677.8460 + 1.0 4 n2= p4= 1.5980 393.0060 -751.4050 767.4310 + 1.0 4 n3 p4= 1.6780 329.0000 -713.7950 902.9190 + 1.0 4 o2 p4= 1.6000 333.0980 -726.6230 924.6200 + 1.0 5 h1h h1h 0.7412 414.2185 -805.6549 914.1296 + 1.0 5 n1n n1n 1.0977 1651.3730 -4069.3178 5984.9629 + 1.0 5 o1o o1o 1.2074 846.7150 -2247.1760 3478.9900 + 1.0 5 c1o o1c 1.1283 1368.7676 -3157.0007 4247.5298 + 1.0 5 n1o o1n 1.1506 1147.8362 -3167.7349 5099.5811 + 1.0 5 o1= s2= 1.4308 730.8387 -1531.7910 1859.7753 + 1.0 5 c2= o1= 1.1600 1161.3421 -2564.5706 3932.8735 + 1.0 5 n2o o1= 1.1930 620.0000 -1808.6018 3077.5918 + 1.0 5 c2= s1= 1.5540 559.0065 -1348.6633 1248.8604 + 1.0 6 c3a n3o 1.4300 313.8329 -568.6087 600.9597 + 1.0 6 c4 n3o 1.4740 301.6051 -535.7028 555.0420 + 1.0 6 c4 o2n 1.4350 400.3954 -835.1951 1313.0142 + 1.0 6 h1 n3o 1.0400 439.9346 -943.7307 1180.9318 + 1.0 6 n3o o1= 1.2100 765.0664 -2070.2830 2793.3218 + 1.0 6 n3o o2n 1.4020 300.0000 -1000.0000 2000.0000 + 1.0 7 c3' o2e 1.3750 368.7309 -832.4784 1274.0231 + 1.0 7 c3' c4 1.5140 312.3719 -465.8290 473.8300 + 1.0 7 c3' o1= 1.2160 823.7948 -1878.7939 2303.5310 + 1.0 7 c3' c3a 1.4890 339.3574 -655.7236 670.2362 + 1.0 7 c3' n3m 1.3850 359.1591 -558.4730 1146.3810 + 1.0 7 c3a n3m 1.3950 344.0452 -652.1208 1022.2242 + 1.0 9 n1t n1t 1.1354 1337.7450 -2675.4900 3121.4049 + 1.0 9 n2z n2t 1.2343 720.3345 -1542.6689 1799.7804 + 1.0 9 n2t n1t 1.1354 1198.7450 -2675.4900 3121.4049 + 1.0 9 n2z c4 1.4814 324.4578 -648.9156 757.0681 + 1.0 9 n2z h1 1.0221 440.1623 -960.3246 1120.3787 + 1.0 10 c3a si4 1.8634 233.2433 -276.8692 161.6659 + 1.0 10 c4 si4 1.8995 189.6536 -279.4210 307.5135 + 1.0 10 h1 si4 1.4783 202.7798 -305.3603 280.2685 + 1.0 10 si4 si4 2.3384 114.2164 -140.4212 80.7084 + 1.0 10 c4 n3m 1.4000 350.0000 0.0000 0.0000 + + +#quartic_angle compass + +> Delta = Theta - Theta0 +> E = K2 * Delta^2 + K3 * Delta^3 + K4 * Delta^4 + +!Ver Ref I J K Theta0 K2 K3 K4 +!---- --- ---- ---- ---- -------- ------- -------- -------- + 1.0 1 c3a c3a c3a 118.9000 61.0226 -34.9931 0.0000 + 1.0 1 c3a c3a c4 120.0500 44.7148 -22.7352 0.0000 + 1.0 1 c3a c3a h1 117.9400 35.1558 -12.4682 0.0000 + 1.0 1 c3a c4 c3a 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c3a c4 c4 108.4000 43.9594 -8.3924 -9.3379 + 1.0 1 c3a c4 h1 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c4 c4 c4 112.6700 39.5160 -7.4430 -9.5583 + 1.0 1 c4 c4 h1 110.7700 41.4530 -10.6040 5.1290 + 1.0 1 h1 c4 h1 107.6600 39.6410 -12.9210 -2.4318 + 1.0 2 h1 o2z si4 122.8000 23.7764 -19.8152 9.6331 + 1.0 2 si4 o2z si4 159.0000 8.5000 -13.4188 -4.1785 + 1.0 2 c3a si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 c4 si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 h1 si4 o2z 107.4000 57.6643 -10.6506 4.6274 + 1.0 2 o2z si4 o2z 110.7000 70.3069 -6.9375 0.0000 + 1.0 3 c3a c3a o2 123.4200 73.6781 -21.6787 0.0000 + 1.0 3 c4 c4 o2 111.2700 54.5381 -8.3642 -13.0838 + 1.0 3 h1 c4 o2 108.7280 58.5446 -10.8088 -12.4006 + 1.0 3 c3a o2 c4 102.9695 38.9739 -6.2595 -8.1710 + 1.0 3 c3a o2 h1 108.1900 53.1250 -8.5016 0.0000 + 1.0 3 c4 o2 c4 104.5000 35.7454 -10.0067 -6.2729 + 1.0 3 c4 o2 h1 105.8000 52.7061 -12.1090 -9.8681 + 1.0 4 c3a c3a n2= 120.0000 60.0000 0.0000 0.0000 + 1.0 4 c3a c3a p4= 120.0010 47.8410 -15.2290 -10.9070 + 1.0 4 c4 c4 n2= 117.3170 55.2420 0.0000 0.0000 + 1.0 4 h1 c4 n2= 107.4990 62.7310 0.0000 0.0000 + 1.0 4 h1 c4 p4= 110.8860 33.8300 -7.0430 -7.2460 + 1.0 4 c4 n2= h1 117.2000 37.2620 0.0000 0.0000 + 1.0 4 h1 n2= h1 110.9100 31.0910 0.0000 0.0000 + 1.0 4 h1 n2= p4= 120.0000 26.0680 -8.2980 -5.9430 + 1.0 4 p4= n2= p4= 135.0000 23.8680 -8.7360 0.0000 + 1.0 4 c4 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 h1 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 c4 o2 p4= 118.2830 35.0010 -10.3600 -7.8700 + 1.0 4 h1 o2 p4= 117.0000 26.0310 -5.8280 -5.6200 + 1.0 4 c3a p4= c3a 110.2310 56.1850 -17.3160 -12.7280 + 1.0 4 c3a p4= h1 108.2310 36.1850 -6.4880 -7.6460 + 1.0 4 c3a p4= n2= 109.6000 63.0620 -19.7400 -14.3290 + 1.0 4 c3a p4= n3 108.1650 70.9770 -11.5480 -15.1090 + 1.0 4 c3a p4= o2 107.3650 71.9770 -10.9430 -15.2900 + 1.0 4 c4 p4= c4 102.5000 48.2320 -5.7980 -9.9660 + 1.0 4 c4 p4= h1 102.9000 52.0710 -6.4680 -10.7730 + 1.0 4 c4 p4= n2= 119.3000 47.3660 -14.6410 -10.7360 + 1.0 4 h1 p4= h1 101.4080 39.6950 -5.1340 -8.2270 + 1.0 4 h1 p4= n2= 110.0330 45.9780 -14.0520 -10.3990 + 1.0 4 h1 p4= n3 103.9780 68.2570 -9.2210 -14.1740 + 1.0 4 h1 p4= o2 103.9780 73.2570 -9.8970 -15.2120 + 1.0 4 n2= p4= n2= 125.0000 90.5230 -20.8010 -19.6020 + 1.0 4 n2= p4= n3 123.2150 89.9230 -32.6120 -21.0960 + 1.0 4 n2= p4= o2 112.2150 99.9230 -32.0930 -22.8210 + 1.0 4 n3 p4= n3 107.1000 85.7690 -5.7790 -17.4890 + 1.0 4 n3 p4= o2 108.3000 86.7690 -5.1750 -17.6710 + 1.0 4 o2 p4= o2 107.5000 86.7690 -4.5700 -17.8520 + 1.0 5 o1= c2= o1= 180.0000 57.1000 0.0000 0.0000 + 1.0 5 s1= c2= s1= 180.0000 48.0000 0.0000 0.0000 + 1.0 5 o1= n2o o1= 134.1000 150.0000 -82.1013 -40.0005 + 1.0 5 o1= s2= o1= 119.3000 115.2627 -35.6278 -26.1261 + 1.0 6 c3a c3a n3o 118.8000 29.2436 -8.8495 -6.6020 + 1.0 6 h1 c4 n3o 107.0000 54.9318 -9.1333 -11.5434 + 1.0 6 h1 c4 o2n 108.7280 58.5446 -10.8088 -12.4006 + 1.0 6 c3a n3o o1= 117.7000 63.9404 -18.4524 -14.3129 + 1.0 6 c4 n3o o1= 117.5000 64.5228 -18.4582 -14.4215 + 1.0 6 h1 n3o o1= 115.7000 53.8034 -14.1991 -11.8708 + 1.0 6 o1= n3o o1= 128.0000 95.1035 -47.4240 -27.9164 + 1.0 6 c4 o2n n3o 108.5000 55.7454 -10.0067 -6.2729 + 1.0 6 c4 c4 o2n 105.0000 54.5381 -8.3642 -13.0838 + 1.0 6 o2n n3o o1= 112.8000 85.5228 -18.4582 -14.4215 + 1.0 7 c3' o2 c4 109.0000 38.9739 -6.2595 -8.1710 + 1.0 7 c3' c4 h1 107.8594 38.0833 -17.5074 0.0000 + 1.0 7 c3' n3m c3' 121.9556 76.3105 -26.3166 -17.6944 + 1.0 7 c3a c3a c3' 116.0640 71.2598 -15.8273 2.0506 + 1.0 7 c3a c3' n3m 108.4400 84.8377 -19.9640 2.7405 + 1.0 7 c3a c3' o1= 125.5320 72.3167 -16.0650 2.0818 + 1.0 7 c3a c3a n3m 120.7640 73.2738 -27.4033 13.3920 + 1.0 7 c3a n3m c3' 120.0700 47.1131 -32.5592 13.1257 + 1.0 7 o1= c3' o2 118.9855 98.6813 -22.2485 10.3673 + 1.0 7 o1= c3' c4 119.3000 65.1016 -17.9766 0.0000 + 1.0 7 o2 c3' c4 100.3182 88.8631 -3.8323 -7.9802 + 1.0 7 n3m c3' o1= 121.5420 92.5720 -34.4800 -11.1871 + 1.0 9 n2z n2t n1t 171.6211 47.7899 0.0000 0.0000 + 1.0 9 n2t n2z h1 110.0345 55.7635 0.6618 0.0022 + 1.0 9 n2t n2z c4 113.5017 82.6294 0.9845 0.0033 + 1.0 9 n2z c4 h1 107.9744 52.7803 0.6615 0.0023 + 1.0 9 n2z c4 c4 110.9900 77.9387 0.9499 0.0033 + 1.0 10 c3a c3a si4 120.0000 30.4689 -23.5439 0.0000 + 1.0 10 c4 c4 si4 112.6700 39.5160 -7.4430 0.0000 + 1.0 10 h1 c4 si4 112.0355 28.7721 -13.9523 0.0000 + 1.0 10 c3a si4 h1 109.5932 41.9497 -42.3639 48.1442 + 1.0 10 c4 si4 c4 113.1855 36.2069 -20.3939 20.0172 + 1.0 10 c4 si4 h1 112.0977 36.4832 -12.8094 0.0000 + 1.0 10 h1 si4 h1 108.6051 32.5415 -8.3164 0.0000 + 1.0 10 c4 si4 si4 113.0000 19.4692 -34.3471 0.0000 + 1.0 10 h1 si4 si4 112.0893 22.5062 -11.5926 0.0000 + 1.0 10 si4 si4 si4 114.2676 24.9501 -19.5949 0.0000 + +#bond-bond compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K K(b,b') +!---- --- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a 68.2856 + 1.0 1 c3a c3a c4 12.0676 + 1.0 1 c3a c3a h1 1.0795 + 1.0 1 c3a c4 h1 2.9168 + 1.0 1 c4 c4 h1 3.3872 + 1.0 1 h1 c4 h1 5.3316 + 1.1 2 h1 c4 si4 6.3820 + 1.0 2 h1 o2z si4 6.3820 + 1.0 2 si4 o2z si4 41.1143 + 1.0 2 c4 si4 o2z 5.4896 + 1.0 2 h1 si4 o2z 11.6183 + 1.0 2 o2z si4 o2z 41.1143 + 1.0 3 c3a c3a o2 48.4754 + 1.0 3 h1 c3a o2 4.5800 + 1.0 3 c4 c4 o2 11.4318 + 1.0 3 h1 c4 o2 23.1979 + 1.0 3 o2 c4 o2 8.2983 + 1.0 3 c3a o2 h1 20.6577 + 1.0 3 c4 o2 c4 -7.1131 + 1.0 3 c4 o2 h1 -9.6879 + 1.0 4 c4 c4 n2= 22.7100 + 1.0 4 h1 c4 n2= 5.6640 + 1.0 4 h1 c4 p4= 1.0500 + 1.0 4 c4 n2= h1 12.5630 + 1.0 4 h1 n2= h1 1.4570 + 1.0 4 h1 n2= p4= -18.2870 + 1.0 4 p4= n2= p4= 20.0000 + 1.0 4 c4 p4= c4 6.2460 + 1.0 4 c4 p4= h1 3.8820 + 1.0 4 c4 p4= n2= 1.0720 + 1.0 4 h1 p4= h1 20.0000 + 1.0 4 h1 p4= n2= 12.5700 + 1.0 4 n2= p4= n2= 20.0000 + 1.0 5 o1= c2= o1= 275.4350 + 1.0 5 s1= c2= s1= 100.7369 + 1.0 5 o1= n2o o1= 20.0000 + 1.0 5 o1= s2= o1= 20.0000 + 1.0 6 c3a c3a n3o 21.0495 + 1.0 6 c4 c4 o2n 11.4318 + 1.0 6 h1 c4 n3o 3.3770 + 1.0 6 h1 c4 o2n 23.1979 + 1.0 6 c3a n3o o1= 93.7948 + 1.0 6 o2n n3o o1= 80.0000 + 1.0 6 c4 n3o o1= 48.1403 + 1.0 6 h1 n3o o1= 14.8226 + 1.0 6 o1= n3o o1= 265.7106 + 1.0 7 c3' o2 c3a 69.5999 + 1.0 7 c3' c4 h1 2.2522 + 1.0 7 c3' n3m c3' 25.9530 + 1.0 7 c3a c4 o2 0.0000 + 1.0 7 c3a o2 c3a 0.0000 + 1.0 7 c3' c3a c3a 37.8749 + 1.0 7 c3a c3' n3m 0.0000 + 1.0 7 c3a c3' o1= 116.9445 + 1.0 7 c3a c3a n3m 37.8749 + 1.0 7 c3a n3m c3' 0.0000 + 1.0 7 o1= c3' o2 210.1813 + 1.0 7 c4 c3' o1= 77.5201 + 1.0 7 c4 c3' o2 19.1069 + 1.0 7 n3m c3' o1= 138.4954 + 1.0 9 h1 n2z n2t 14.9026 + 1.0 9 n2z n2t n1t 204.9909 + 1.0 9 n2t n2z c4 84.2075 + 1.0 9 n2z c4 h1 18.4621 + 1.0 9 n2z c4 c4 36.9309 + 1.0 10 h1 c4 si4 1.6561 + 1.0 10 c3a c3a si4 21.3938 + 1.0 10 c3a si4 h1 3.9264 + 1.0 10 c4 si4 c4 3.7419 + 1.0 10 c4 si4 h1 3.9340 + 1.0 10 c4 si4 si4 2.3030 + 1.0 10 h1 si4 h1 4.6408 + 1.0 10 h1 si4 si4 3.5172 + 1.0 10 si4 si4 si4 6.0704 + + +#bond-bond_1_3 compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K L K(b,b') +!--- --- ----- ----- ----- ----- -------- + 1.0 1 c3a c3a c3a c3a 53.0000 + 1.0 1 c3a c3a c3a c4 2.5085 + 1.0 1 c3a c3a c3a h1 -6.2741 + 1.0 1 c4 c3a c3a h1 0.8743 + 1.0 1 h1 c3a c3a h1 -1.7077 + 1.0 1 c3a c3a c4 h1 -3.4826 + 1.0 3 c3a c3a c3a o2 -2.2436 + 1.0 3 h1 c3a c3a o2 -2.0517 + 1.0 3 c3a c3a o2 h1 1.1590 + + +#bond-angle compass + +> E = K * (R - R0) * (Theta - Theta0) + +!Ver Ref I J K K(b,theta) K(b',theta) +!---- --- ---- ---- ---- ---------- ----------- + 1.0 1 c3a c3a c3a 28.8708 + 1.0 1 c3a c3a c4 31.0771 47.0579 + 1.0 1 c3a c3a h1 20.0033 24.2183 + 1.0 1 c3a c4 h1 26.4608 11.7717 + 1.0 1 c4 c4 c4 8.0160 + 1.0 1 c4 c4 h1 20.7540 11.4210 + 1.0 1 h1 c4 h1 18.1030 + 1.0 2 h1 o2z si4 18.0902 31.0726 + 1.0 2 si4 o2z si4 28.6686 + 1.0 2 c4 si4 o2z 6.4278 20.5669 + 1.0 2 h1 si4 o2z 6.4278 20.5669 + 1.0 2 o2z si4 o2z 23.4380 + 1.0 3 c3a c3a o2 58.4790 107.6806 + 1.0 3 c4 c4 o2 2.6868 20.4033 + 1.0 3 h1 c4 o2 4.6189 55.3270 + 1.0 3 c3a o2 h1 53.8614 23.9224 + 1.0 3 c4 o2 c4 -2.8112 + 1.0 3 c4 o2 h1 28.5800 18.9277 + 1.0 4 c4 c4 n2= 19.2440 59.4220 + 1.0 4 h1 c4 n2= 6.4070 46.3730 + 1.0 4 h1 c4 p4= 19.8120 16.9400 + 1.0 4 c4 n2= h1 18.4860 7.8370 + 1.0 4 h1 n2= h1 8.4900 + 1.0 4 h1 n2= p4= 40.0630 90.7910 + 1.0 4 c4 p4= c4 12.8050 + 1.0 4 c4 p4= h1 11.1260 -19.4700 + 1.0 4 c4 p4= n2= -7.1280 26.3530 + 1.0 4 h1 p4= n2= -24.3830 72.9250 + 1.0 5 o1= n2o o1= -50.0000 + 1.0 5 o1= s2= o1= 45.0585 + 1.0 6 c3a c3a n3o 30.5211 59.8025 + 1.0 6 c4 c4 o2n 2.6868 20.4033 + 1.0 6 h1 c4 n3o 12.2491 30.5314 + 1.0 6 h1 c4 o2n 4.6189 55.3270 + 1.0 6 c3a n3o o1= 40.3757 92.1955 + 1.0 6 c4 n3o o1= 27.2141 93.9927 + 1.0 6 h1 n3o o1= -8.6275 58.6036 + 1.0 6 o1= n3o o1= 95.6936 + 1.0 7 c3' o2 c4 21.5366 -16.6748 + 1.0 7 c3' c4 h1 15.5988 14.6287 + 1.0 7 c3' n3m c3' 20.0533 + 1.0 7 c3' c3a c3a 23.6977 45.8865 + 1.0 7 c3a c3a n3m 35.8865 53.6977 + 1.0 7 c3a c3' o1= 72.8758 76.1093 + 1.0 7 o1= c3' o2 79.4497 57.0987 + 1.0 7 c4 c3' o1= 31.8455 46.6613 + 1.0 7 c4 c3' o2 1.3435 4.6978 + 1.0 7 n3m c3' o1= 62.7124 52.4045 + 1.0 9 h1 n2z n2t 37.4419 141.1218 + 1.0 9 n2z n2t n1t 25.5611 1.2222 + 1.0 9 n2t n2z c4 195.9722 88.2679 + 1.0 9 n2z c4 h1 61.9652 3.3182 + 1.0 9 n2z c4 c4 67.8888 34.8803 + 1.0 10 c3a c3a si4 14.5831 23.7679 + 1.0 10 h1 c4 si4 16.6908 18.2764 + 1.0 10 c3a si4 h1 22.5947 8.7811 + 1.0 10 c4 si4 c4 18.5805 + 1.0 10 c4 si4 h1 13.3961 7.4104 + 1.0 10 c4 si4 si4 16.9455 11.4377 + 1.0 10 h1 si4 h1 9.3467 + 1.0 10 h1 si4 si4 5.6630 2.0706 + 1.0 10 si4 si4 si4 8.9899 + + +#torsion_3 compass + +> E = SUM(n=1,3) { V(n) * [ 1 - cos(n*Phi - Phi0(n)) ] } + +!Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 +!---- --- ---- ---- ---- ---- ------- ------ ------- ------ ------- ------ + 1.0 1 c3a c3a c3a c3a 8.3667 0.0 1.2000 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a c4 0.0000 0.0 4.4072 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a h1 0.0000 0.0 3.9661 0.0 0.0000 0.0 + 1.0 1 c4 c3a c3a h1 0.0000 0.0 1.5590 0.0 0.0000 0.0 + 1.0 1 h1 c3a c3a h1 0.0000 0.0 2.3500 0.0 0.0000 0.0 + 1.0 1 c3a c3a c4 c3a -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 c4 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 h1 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c4 c4 h1 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 + 1.0 1 c4 c4 c4 c4 0.0000 0.0 0.0514 0.0 -0.1430 0.0 + 1.0 1 c4 c4 c4 h1 0.0000 0.0 0.0316 0.0 -0.1681 0.0 + 1.0 1 h1 c4 c4 h1 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 + 1.0 1 * c3a c3a * 0.0000 0.0 4.5000 0.0 0.0000 0.0 + 1.0 1 * c4 c4 * 0.0000 0.0 0.0000 0.0 -0.1530 0.0 + 1.0 2 h1 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 o2z 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 si4 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 o2z -0.2250 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 * o2z si4 * 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 3 c3a c3a c3a o2 0.0000 0.0 4.8498 0.0 0.0000 0.0 + 1.0 3 h1 c3a c3a o2 0.0000 0.0 1.7234 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 c4 0.0000 0.0 1.5000 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 h1 -0.6900 0.0 0.5097 0.0 0.0095 0.0 + 1.0 3 c4 c4 c4 o2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 + 1.0 3 h1 c4 c4 o2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 + 1.0 3 o2 c4 c4 o2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 + 1.0 3 c4 c4 o2 c4 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 + 1.0 3 c4 c4 o2 h1 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 + 1.0 3 h1 c4 o2 c3a 0.9513 0.0 0.1155 0.0 0.0720 0.0 + 1.0 3 h1 c4 o2 c4 0.5302 0.0 0.0000 0.0 -0.3966 0.0 + 1.0 3 h1 c4 o2 h1 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 + 1.0 4 c3a c3a c3a p4= 0.0000 0.0 5.4770 0.0 0.0000 0.0 + 1.0 4 h1 c3a c3a p4= 0.0000 0.0 2.2700 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= h1 -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= n2= -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c4 c4 c4 n2= 0.0970 0.0 0.0720 0.0 -0.2580 0.0 + 1.0 4 h1 c4 c4 n2= -0.1510 0.0 0.0100 0.0 -0.1860 0.0 + 1.0 4 c4 c4 n2= h1 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 + 1.0 4 h1 c4 n2= h1 1.2660 0.0 -0.7740 0.0 0.0380 0.0 + 1.0 4 h1 c4 p4= c4 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= h1 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= n2= 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 n2= p4= c3a 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= c4 0.0000 0.0 0.0000 0.0 -0.3690 0.0 + 1.0 4 h1 n2= p4= h1 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= o2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 p4= n2= p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 p4= n2= p4= n2= 1.8000 0.0 0.5000 0.0 2.0000 0.0 + 1.0 4 h1 n3 p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= n2= 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= o2 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= h1 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= n2= 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= o2 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * o2 p4= * 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * c3a n2= * 0.0000 0.0 1.0000 0.0 0.0000 0.0 + 1.0 4 * c3a p4= * -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 * c4 n2= * 0.0000 0.0 0.0000 0.0 -0.0200 0.0 + 1.0 4 * c4 p4= * 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 * n2= p4= * 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 * n3 p4= * 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 6 c3a c3a c3a n3o 0.0000 0.0 7.2124 0.0 0.0000 0.0 + 1.0 6 h1 c3a c3a n3o 0.0000 0.0 2.9126 0.0 0.0000 0.0 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0 1.1600 0.0 0.0000 0.0 + 1.0 6 c4 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 h1 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 c4 c4 o2 n3o 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 + 1.0 6 o1= n3o o2 c4 0.0000 0.0 2.0000 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 0.0000 0.0 4.6282 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a h1 0.0000 0.0 2.1670 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3a c3a 0.0000 0.0 0.6500 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3' o1 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 + 1.0 7 c3' o2 c4 c4 0.1302 0.0 -0.3250 0.0 0.1134 0.0 + 1.0 7 c3' o2 c4 h1 0.9513 0.0 0.1155 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3' o1= 0.0000 0.0 0.7800 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3a n3m 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 7 c3a n3m c3' o1= 0.0000 0.0 2.0521 0.0 0.0000 0.0 + 1.0 7 c4 o2 c3' c4 -2.5594 0.0 2.2013 0.0 0.0325 0.0 + 1.0 7 c4 o2 c3' o1= 0.8905 0.0 3.2644 0.0 0.2646 0.0 + 1.0 7 o1= c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 o2 c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 n3m c3a c3a h1 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 9 h1 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.2637 0.0 + 1.0 9 c4 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.1823 0.0 + 1.0 9 n2t n2z c4 h1 0.0000 0.0 0.0000 0.0 -0.2181 0.0 + 1.0 9 n2t n2z c4 c4 0.0000 0.0 0.0000 0.0 -0.2021 0.0 + 1.0 9 n2z c4 c4 h1 0.0000 0.0 0.0000 0.0 -0.2259 0.0 + 1.0 10 c3a c3a c3a si4 0.0000 0.0 4.3270 0.0 0.0000 0.0 + 1.0 10 h1 c3a c3a si4 0.0000 0.0 1.5093 0.0 0.0000 0.0 + 1.0 10 c3a c3a si4 * 0.0000 0.0 0.0000 0.0 -0.0231 0.0 + 1.0 10 c4 c4 si4 si4 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * c4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * si4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + + +#end_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a -0.1185 6.3204 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 -0.6890 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -0.0732 0.0000 0.0000 + 1.0 1 c4 c4 c4 h1 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 + 1.0 1 h1 c4 c4 h1 0.2130 0.3120 0.0777 + 1.0 3 c3a c3a c3a o2 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 + 1.0 3 c3a c3a o2 h1 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 + 1.0 3 c4 c4 c4 o2 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 + 1.0 3 h1 c4 c4 o2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 + 1.0 3 o2 c4 c4 o2 1.0165 0.7553 -0.4609 + 1.0 3 c4 c4 o2 c4 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 + 1.0 3 c4 c4 o2 h1 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 + 1.0 3 h1 c4 o2 c4 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 + 1.0 3 h1 c4 o2 h1 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 + 1.0 7 o1= c3' n3m c3' -0.7019 0.8305 -0.6874 0.1726 -0.4823 0.2666 + 1.0 7 c4 c4 o2 c3' -1.2164 -0.1715 -0.0964 0.2560 0.8133 -0.0728 + 1.0 7 h1 c4 o2 c3' 0.9589 0.9190 -0.6015 0.2282 2.2998 -0.4473 + 1.0 7 c4 c3' o2 c4 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 + 1.0 7 o1= c3' o2 c4 -4.2421 10.1102 1.6824 0.0882 -2.4309 -0.7426 + 1.0 7 o1= c3' c4 h1 0.0536 0.0354 0.3853 2.9036 0.5307 0.1439 + 1.0 7 o2 c3' c4 h1 0.4160 -0.1140 0.7099 0.7800 1.3339 0.3268 + + +#middle_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +!Ver Ref I J K L F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- -------- ------- ------- + 1.0 1 c3a c3a c3a c3a 27.5989 -2.3120 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 9.1792 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -1.1521 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 3.9421 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 4.8228 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -5.5679 1.4083 0.3010 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -17.7870 -7.1877 0.0000 + 1.0 1 c4 c4 c4 h1 -14.8790 -3.6581 -0.3138 + 1.0 1 h1 c4 c4 h1 -14.2610 -0.5322 -0.4864 + 1.0 3 c3a c3a c3a o2 0.0000 4.8255 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 5.5432 0.0000 + 1.0 3 c3a c3a o2 h1 1.1580 3.2697 3.5132 + 1.0 3 c4 c4 c4 o2 -21.8842 -7.6764 -0.6868 + 1.0 3 h1 c4 c4 o2 -16.7975 -1.2296 -0.2750 + 1.0 3 o2 c4 c4 o2 -17.2585 -3.6157 -0.8364 + 1.0 3 c4 c4 o2 c4 -5.9288 -2.7007 -0.3175 + 1.0 3 c4 c4 o2 h1 1.2472 0.0000 0.7485 + 1.0 3 h1 c4 o2 c4 -6.8007 -4.6546 -1.4101 + 1.0 3 h1 c4 o2 h1 0.0000 0.9241 -0.5889 + 1.0 4 c4 c4 c4 n2= 0.0000 0.0000 0.0000 + 1.0 4 h1 c4 c4 n2= -3.5150 -2.2980 -1.2770 + 1.0 4 c4 c4 n2= h1 -2.3800 2.5290 -0.7300 + 1.0 4 h1 c4 n2= h1 -0.4140 -2.8620 0.0070 + 1.0 4 p4= n2= p4= n2= 0.0000 0.0000 0.0000 + 1.0 7 c3' c3a c3a c3a 0.0000 3.8762 0.0000 + 1.0 7 o1= c3' n3m c3' -0.1118 -1.1990 0.6784 + 1.0 7 c4 c4 o2 c3' 9.9416 2.6421 2.2333 + 1.0 7 h1 c4 o2 c3' 7.7147 4.2557 -1.0118 + 1.0 7 o1= c3' c3a c3a 0.0000 2.4002 0.0000 + 1.0 7 c3a c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 7 c4 c3' o2 c4 1.3445 3.5515 -4.9202 + 1.0 7 o1= c3' o2 c4 0.4552 7.3091 0.2842 + 1.0 7 o1= c3' c4 h1 0.0000 0.0000 -1.0000 + 1.0 7 o2 c3' c4 h1 -13.7686 -2.5959 1.1934 + 1.0 7 h1 c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 10 c3a c3a c3a si4 0.0000 11.1576 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 6.2168 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.3146 + 1.0 10 h1 c4 si4 h1 0.0000 0.0000 -0.5906 + 1.0 10 h1 c4 si4 si4 0.0000 0.0000 -0.1909 + 1.0 10 c4 si4 si4 h1 0.0000 0.0000 -0.6941 + 1.0 10 h1 si4 si4 h1 0.0000 0.0000 -0.6302 + + +#angle-torsion_3 compass + +> E = (Theta - Theta0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a 1.9767 1.0239 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 2.4501 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 0.3886 -0.3139 0.1389 + 1.0 1 c4 c4 c4 h1 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 + 1.0 1 h1 c4 c4 h1 -0.8085 0.5569 -0.2466 + 1.0 3 c3a c3a c3a o2 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 + 1.0 3 c3a c3a o2 h1 -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 + 1.0 3 c4 c4 c4 o2 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 + 1.0 3 h1 c4 c4 o2 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 + 1.0 3 o2 c4 c4 o2 0.5511 0.9737 -0.6673 + 1.0 3 c4 c4 o2 c4 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 + 1.0 3 c4 c4 o2 h1 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 + 1.0 3 h1 c4 o2 c4 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 + 1.0 3 h1 c4 o2 h1 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 + 1.0 4 c4 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 h1 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 c4 c4 n2= h1 -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 + 1.0 4 h1 c4 n2= h1 -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 + 1.0 6 c3a c3a c3a n3o 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 + 1.0 6 h1 c3a c3a n3o 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 + 1.0 6 h1 c4 n3o o1= 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 + 1.0 6 o1= n3o o2 c4 -3.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 7 o1= c3' n3m c3' -1.5747 2.3997 -0.2851 -0.3038 -0.0548 -0.3188 + 1.0 7 c4 c4 o2 c3' -0.4620 1.4492 -0.6765 -0.0890 -0.9159 0.7229 + 1.0 7 h1 c4 o2 c3' -0.4990 2.8061 -0.0401 -0.3142 -0.8699 0.0971 + 1.0 7 c4 c3' o2 c4 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 + 1.0 7 o1= c3' o2 c4 5.9732 2.7261 1.9052 2.3573 1.0059 -0.0327 + 1.0 7 o1= c3' c4 h1 -2.0667 0.7308 -0.2083 14.4728 0.3339 0.0800 + 1.0 7 o2 c3' c4 h1 -0.0241 1.4427 0.1212 13.2959 0.8005 -0.0071 + 1.0 10 c3a c3a c3a si4 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 + 1.0 10 h1 c4 si4 c4 0.0000 0.0000 0.3382 0.0000 0.0000 0.4272 + + +#wilson_out_of_plane compass + +> E = K * (Chi - Chi0)^2 + +!Ver Ref I J K L K Chi0 +!---- --- ---- ---- ---- ---- ------- ---- + 1.0 1 c3a c3a c3a c3a 7.1794 0.0 + 1.0 1 c3a c3a c3a c4 7.8153 0.0 + 1.0 1 c3a c3a c3a h1 4.8912 0.0 + 1.0 3 c3a c3a c3a o2 13.0421 0.0 + 1.0 4 c3a c3a c3a n2= 8.0000 0.0 + 1.0 4 c3a c3a c3a p4= 6.7090 0.0 + 1.0 6 c3a c3a c3a n3o 0.9194 0.0 + 1.0 6 c3a n3o o1= o1= 36.2612 0.0 + 1.0 6 c4 n3o o1= o1= 44.3062 0.0 + 1.0 6 h1 n3o o1= o1= 38.5581 0.0 + 1.0 6 o1= n3o o1= o2 45.0000 0.0 + 1.0 7 c3' c3' n3m c3a 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 17.0526 0.0 + 1.0 7 c3' n3m c3' c3a 0.0000 0.0 + 1.0 7 c3a c3a n3m c3a 17.0526 0.0 +!1.0 7 c3a c3a c3a n3m 17.0526 0.0 + 1.0 7 c3a c3' n3m o1= 30.0000 0.0 +!1.0 7 c3a c3a c3' c3a 17.0526 0.0 +!1.0 7 c3a c3' o1= n3m 30.0000 0.0 + 1.0 7 c3a o1= c3' n3m 30.0000 0.0 + 1.0 7 c4 c3' o2 o1= 46.9264 0.0 + 1.0 10 c3a c3a si4 c3a 5.3654 0.0 + + +#angle-angle compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') + +! J' I' K' +!Ver Ref I J K K +!---- --- ---- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 + 1.0 1 c3a c3a h1 c3a 0.0000 + 1.0 1 c4 c4 c3a h1 2.0403 + 1.0 1 h1 c4 c3a h1 3.0118 + 1.0 1 c3a c4 c4 h1 -1.8202 + 1.0 1 c4 c4 c4 c4 -0.1729 + 1.0 1 c4 c4 c4 h1 -1.3199 + 1.0 1 h1 c4 c4 h1 -0.4825 + 1.0 1 c3a c4 h1 c4 1.0827 + 1.0 1 c3a c4 h1 h1 2.3794 + 1.0 1 c4 c4 h1 c4 0.1184 + 1.0 1 c4 c4 h1 h1 0.2738 + 1.0 1 h1 c4 h1 h1 -0.3157 + 1.0 3 c3a c3a c3a o2 0.0000 + 1.0 3 c3a c3a o2 c3a 0.0000 + 1.0 3 c4 c4 c4 o2 -0.8330 + 1.0 3 h1 c4 c4 o2 2.5926 + 1.0 3 c4 c4 h1 o2 3.9177 + 1.0 3 h1 c4 h1 o2 2.4259 + 1.0 3 c4 c4 o2 c4 -3.5744 + 1.0 3 c4 c4 o2 h1 0.1689 + 1.0 3 h1 c4 o2 h1 2.1283 + 1.0 4 h1 c4 c4 n2= 1.0910 + 1.0 4 c4 c4 h1 n2= 2.7530 + 1.0 4 h1 c4 h1 n2= 1.7680 + 1.0 4 c4 c4 n2= h1 -1.3060 + 1.0 4 h1 c4 n2= h1 -2.9470 + 1.0 7 h1 c4 c3' o2 4.7955 + 1.0 7 c3' c4 h1 h1 -1.7653 + 1.0 11 h1 c4 c3' h1 0.0 + 1.0 10 h1 c4 h1 si4 0.0000 + 1.0 10 h1 c4 si4 h1 2.2050 + 1.0 10 c4 si4 c4 h1 3.3827 + 1.0 10 c4 si4 c4 si4 1.3465 + 1.0 10 h1 si4 c4 h1 4.6809 + 1.0 10 si4 si4 c4 si4 -5.6849 + 1.0 10 c4 si4 h1 c4 2.7963 + 1.0 10 c4 si4 h1 h1 4.4559 + 1.0 10 c4 si4 h1 si4 3.4758 + 1.0 10 h1 si4 h1 h1 2.0665 + 1.0 10 si4 si4 h1 si4 3.4924 + 1.0 10 c4 si4 si4 c4 2.0805 + 1.0 10 c4 si4 si4 h1 -2.9623 + 1.0 10 c4 si4 si4 si4 4.5272 + 1.0 10 h1 si4 si4 h1 1.6082 + 1.0 10 si4 si4 si4 h1 4.1996 + + +#angle-angle-torsion_1 compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi) + +!Ver Ref I J K L K(Ang,Ang,Tor) +!---- --- ---- ---- ---- ---- -------------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a c4 -14.4097 + 1.0 1 c3a c3a c3a h1 -4.8141 + 1.0 1 c4 c3a c3a h1 4.4444 + 1.0 1 h1 c3a c3a h1 0.3598 + 1.0 1 c3a c3a c4 h1 -5.8888 + 1.0 1 c4 c4 c4 c4 -22.0450 + 1.0 1 c4 c4 c4 h1 -16.1640 + 1.0 1 h1 c4 c4 h1 -12.5640 + 1.0 3 c3a c3a c3a o2 -21.0247 + 1.0 3 h1 c3a c3a o2 4.2296 + 1.0 3 c3a c3a o2 h1 -4.6072 + 1.0 3 c4 c4 c4 o2 -29.0420 + 1.0 3 h1 c4 c4 o2 -20.2006 + 1.0 3 o2 c4 c4 o2 -14.0484 + 1.0 3 c4 c4 o2 c4 -19.0059 + 1.0 3 c4 c4 o2 h1 -12.1038 + 1.0 3 h1 c4 o2 c4 -16.4438 + 1.0 3 h1 c4 o2 h1 -10.5093 + 1.0 4 c4 c4 c4 n2= 0.0000 + 1.0 4 h1 c4 c4 n2= -27.5060 + 1.0 4 c4 c4 n2= h1 -8.8980 + 1.0 4 h1 c4 n2= h1 -9.6280 + 1.0 4 h1 c4 p4= c4 -25.5460 + 1.0 4 h1 c4 p4= h1 -16.0180 + 1.0 4 h1 c4 p4= n2= -19.9340 + 1.0 4 h1 n2= p4= c4 -11.1020 + 1.0 4 h1 n2= p4= h1 -3.7880 + 1.0 6 c3a c3a c3a n3o -34.9681 + 1.0 6 h1 c3a c3a n3o 2.1508 + 1.0 6 c3a c3a n3o o1= -18.0436 + 1.0 6 h1 c4 n3o o1= -16.2615 + 1.0 7 o1= c3' n3m c3' -3.3556 + 1.0 7 c4 c4 o2 c3' -15.7082 + 1.0 7 h1 c4 o2 c3' -13.1500 + 1.0 7 c4 c3' o2 c4 -12.2070 + 1.0 7 o1= c3' o2 c4 -32.9368 + 1.0 7 o1= c3' c4 h1 -23.1923 + 1.0 7 o2 c3' c4 h1 -13.9734 + 1.0 10 c4 si4 c4 h1 -17.5802 + 1.0 10 h1 si4 c4 h1 -12.9341 + 1.0 10 h1 c4 si4 si4 -13.3679 + 1.0 10 c4 si4 si4 h1 -16.9141 + 1.0 10 h1 si4 si4 h1 -10.8232 + 1.0 10 h1 si4 si4 si4 -12.2900 + + +#nonbond(9-6) compass + +> E = eps(ij) [2(r(ij)*/r(ij))**9 - 3(r(ij)*/r(ij))**6] +> where r(ij) = [(r(i)**6 + r(j)**6))/2]**(1/6) +> +> eps(ij) = 2 sqrt(eps(i) * eps(j)) * +> r(i)^3 * r(j)^3/[r(i)^6 + r(j)^6] + +@combination sixth-power +@type r-eps + +!Ver Ref I r eps +!---- --- ---- --------- --------- + 1.0 1 c3a 3.9150 0.0680 + 1.0 1 c4 3.8540 0.0620 + 1.0 1 c43 3.8540 0.0400 + 1.0 1 c44 3.8540 0.0200 + 1.0 1 h1 2.8780 0.0230 + 1.0 2 o2z 3.3000 0.0800 + 1.0 2 si4 4.4050 0.1980 + 1.0 2 si4c 4.2900 0.1310 + 1.0 3 c4o 3.8150 0.0680 + 1.0 3 h1o 1.0870 0.0080 + 1.0 3 o2 3.3000 0.0800 + 1.0 3 o2e 3.3000 0.1200 + 1.0 3 o2h 3.5800 0.0960 + 1.0 4 n2= 3.8300 0.0960 + 1.0 4 p4= 4.2950 0.0650 + 1.0 5 he 2.9000 0.0050 + 1.0 5 ne 3.2000 0.0550 + 1.0 5 ar 3.8800 0.2000 + 1.0 5 kr 4.3000 0.2800 + 1.0 5 xe 4.2600 0.3900 + 1.0 5 h1h 1.4210 0.0216 + 1.0 5 n1n 3.8008 0.0598 + 1.0 5 c1o 4.0120 0.0530 + 1.0 5 o1o 3.4758 0.0780 + 1.0 5 o1c 3.6020 0.0850 + 1.0 5 n1o 3.4600 0.1280 + 1.0 5 o1n 3.3000 0.1560 + 1.0 5 c2= 3.9150 0.0680 + 1.0 5 s2= 4.0470 0.1250 + 1.0 5 n2o 3.5290 0.3330 + 1.0 5 o1= 3.4300 0.1920 + 1.0 5 o1=* 3.3600 0.0670 + 1.0 5 s1= 4.0070 0.3130 + 1.0 6 n3o 3.7600 0.0480 + 1.0 6 o12 3.4000 0.0480 + 1.0 6 o2n 3.6500 0.2000 + 1.0 7 c3' 3.9000 0.0640 + 1.0 7 n3m 3.7200 0.1500 + 1.0 7 o2s 3.3000 0.0960 + 1.1 8 c4o 3.8700 0.0748 + 1.1 8 c41o 3.8700 0.1080 + 1.1 8 c43o 3.6700 0.0498 + 1.0 9 c4z 3.6500 0.0800 + 1.0 9 n1z 3.5200 0.0850 + 1.0 9 n2t 3.3000 0.0500 + 1.0 9 n2z 3.4000 0.1200 + + +#bond_increments compass + +!Ver Ref I J DeltaIJ DeltaJI +!---- --- ---- ---- ------- ------- + 1.0 1 c3a c3a 0.0000 0.0000 + 1.0 1 c3a c4 0.0000 0.0000 + 1.0 1 c3a h1 -0.1268 0.1268 + 1.0 1 c4 c4 0.0000 0.0000 + 1.0 1 c4 h1 -0.0530 0.0530 + 1.0 2 o2z si4 -0.2225 0.2225 + 1.0 3 c3a o2e 0.0420 -0.0420 + 1.0 3 c3a o2h 0.0420 -0.0420 + 1.0 3 c4 o2e 0.1600 -0.1600 + 1.0 3 c4 o2h 0.1600 -0.1600 + 1.0 3 h1 o2 0.4200 -0.4200 + 1.0 3 h1 o2h 0.4200 -0.4200 + 1.0 4 c3a n2= 0.1990 -0.1990 + 1.0 4 c3a p4= -0.0600 0.0600 + 1.0 4 c4 n2= 0.3450 -0.3450 + 1.0 4 c4 p4= -0.0500 0.0500 + 1.0 4 cl1p p4= -0.1200 0.1200 + 1.0 4 f1p p4= -0.1800 0.1800 + 1.0 4 h1 n2= 0.3280 -0.3280 + 1.0 4 h1 p4= -0.0500 0.0500 + 1.0 4 n2= n2= 0.0000 0.0000 + 1.0 4 n2= n3 0.0250 -0.0250 + 1.0 4 n2= o2 -0.0430 0.0430 + 1.0 4 n2= p4= -0.3500 0.3500 + 1.0 4 n3 p4= -0.1200 0.1200 + 1.0 4 o2 p4= -0.1400 0.1400 + 1.0 5 c1o o1c -0.0203 0.0203 + 1.0 5 c2= o1= 0.4000 -0.4000 + 1.0 5 c2= s1= 0.0258 -0.0258 + 1.0 5 n2o o1= 0.0730 -0.0730 + 1.0 5 h1h h1h 0.0000 0.0000 + 1.0 5 n1n n1n 0.0000 0.0000 + 1.0 5 n1o o1n 0.0288 -0.0288 + 1.0 5 o1= s2= -0.2351 0.2351 + 1.0 5 o1o o1o 0.0000 0.0000 + 1.0 6 c3a n3o 0.2390 -0.2390 + 1.0 6 c4 n3o 0.2100 -0.2100 + 1.0 6 c4 o2n 0.3170 -0.3170 + 1.0 6 h1 n3o 0.1880 -0.1880 + 1.0 6 n3o o1= 0.4280 -0.4280 + 1.0 6 n3o o2n 0.0010 -0.0010 + 1.0 7 c3' o2e 0.1120 -0.1120 + 1.0 7 c3' c4 0.0000 0.0000 + 1.0 7 c3' o1= 0.4500 -0.4500 + 1.0 7 c3' c3a 0.0350 -0.0350 + 1.0 7 c3' n3m 0.0000 0.0000 + 1.0 7 c3a n3m 0.0950 -0.0950 + 1.1 8 h1 o2h 0.4100 -0.4100 + 1.0 9 n2z c4 -0.3110 0.3110 + 1.0 9 n2z h1 -0.3350 0.3350 + 1.0 9 n2t n1t 0.3860 -0.3860 + 1.0 9 n2t n2z 0.2470 -0.2470 + 1.0 10 c3a si4 -0.1170 0.1170 + 1.0 10 c4 si4 -0.1350 0.1350 + 1.0 10 h1 si4 -0.1260 0.1260 + +#templates compass + +type: ? + ! anything + template: (>*) +end_type + +type: ar + ! Argon atom + template: (>Ar) +end_type + +type:c1o + ! Carbon in CO + template: [>C[~O]] +end_type + +type:c2= + ! Carbon in =C= (e.g. CO2, CS2) + template: [>C[~*][~*]] +end_type + +type:c3' + ! Carbonyl carbon [one polar substituent such as O,N] + ! e.g. amide, acid and ester + template: (>C (~O) (~*) (~*)) + atom_test:1 + hybridization:sp2 + end_test + atom_test:3 + allowed_elements: C, H + end_test + atom_test:4 + allowed_elements: O, N + end_test +end_type + +type:c3a + ! SP2 aromatic carbon + template:(>C(~*)(~*)(~*)) + atom_test:1 + hybridization: SP2 + aromaticity:AROMATIC + end_test +end_type + +type:c3a + ! Transferred from pcff - may not be required. + ! This is used for aromatic carbons that fail the aromaticity test because + ! the current ring checker is too lame to figure on a ring with more than + ! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict + ! with the above 'c3a' definition. This can be removed when the ring checker + ! is made more robust. + template: [>C(-*)(:*)(:*)] + atom_test:1 + hybridization:SP2 + aromaticity:NON_AROMATIC + end_test +end_type + +type:c4 + ! generic SP3 carbon + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:c41o + ! Carbon, sp3, in methanol (and dimethyl ether?) + template: [>C(-O(-*))(-H)(-H)(-H)] + atom_test:1 + hybridization:SP3 + end_test + atom_test:3 + allowed_elements:C,H +end_type + +type: c43 + ! sp3 carbon with 1 h and 3 heavy atoms + template: (>C(-H)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type:c43o + ! Carbon, sp3, in secondary alcohols + template: [>C(-O(-H))(-H)(-C)(-C)] + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c44 + ! sp3 carbon with four heavy atoms attached + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:2 + disallowed_elements:H + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type: c4o + ! alpha carbon (e.g. alpha to oxygen in ethers and alcohols) + template: (>C(-O)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c4z + ! Carbon, sp3, bonded to -N3 (azides) + template: (>C(-N(~N(~N)))(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:h1 + ! nonpolar hydrogen + template: (>H (-*) ) + atom_test:2 + allowed_elements:C,Si + end_test +end_type + +type:h1h + ! Hydrogen in H2 + template: [>H[-H]] +end_type + +type:h1o + ! strongly polar hydrogen (bonded to fluorine, nitrogen, Oxygen - h* in pcff) + template: (>H(-*)) + atom_test:2 + allowed_elements:O,N,F + end_test +end_type + +type: he + ! Helium atom + template: (>He) +end_type + +type: kr + ! Krypton atom + template: (>Kr) +end_type + +type:n1n + ! Nitrogen in N2 + template: [>N[~N]] +end_type + +type:n1o + ! Nitrogen in NO + template: [>N[~O]] +end_type + +type:n1z + ! Nitrogen, terminal atom in -N3 + template: [>N[~N[~N(~*)]]] +end_type + +type:n2= + ! Nitrogen (in phosphazenes, or generic???) + template: [>N(~*)(~*)] +end_type + +type:n2o + ! Nitrogen in NO2 + template: [>N[~O][~O]] +end_type + +type:n2t + ! Nitrogen, central atom in -N3 + template: [>N[~N][~N(~*)]] +end_type + +type:n2z + ! Nitrogen, first atom in -N3 + template: (>N[~N[~N]](~*)) +end_type + +type: n3m + ! sp3 nitrogen in amides without hydrogen + template: (>N(-C[=O])(-C)(-C)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: n3o + ! Nitrogen in nitro group + template: (>N[~O][~O](~O(~C))) +end_type + +type: ne + ! Neon atom + template: (>Ne) +end_type + +type:o1= + ! Oxygen in NO2 and SO2 [and carbonyl] + template: (>O(~*)) + atom_test:2 + allowed_elements:N,S,C + end_test +end_type + +type:o1=* + ! Oxygen in CO2 + template: [>O[~C[~O]]] +end_type + +type:o12 + ! Oxygen in nitro group -NO2 + template: [>O[~N[~O](~*)]] +end_type + +type:o1c + ! Oxygen in CO + template: [>O[~C]] +end_type + +type:o1n + ! Oxygen in NO + template: [>O[~N]] +end_type + +type:o1o + ! Oxygen in O2 + template: [>O[~O]] +end_type + +type:o2 + ! Generic oxygen with two bonds attached + template: [>O(~*)(~*)] +end_type + +type:o2e + ! Ether oxygen + template: [>O(-C)(-C)] + atom_test: 1 + aromaticity:NON_AROMATIC + end_test +end_type + +type:o2h + ! Hydroxyl oxygen + template: (>O[-H](~*)) +end_type + +type:o2n + ! Oxygen in nitrates + template: (>O[~N[~O][~O]](~C)) +end_type + +type:o2s + ! Ester oxygen + template: (>O[~C[~O](~*)](~C)) +end_type + +type: o2z + ! Oxygen in siloxanes and zeolites + template: (>O(-Si)(-*) ) + atom_test: 3 + allowed_elements: Si, H + end_test +end_type + +type: p4= + ! Phosphorous [in phosphazenes] + template: (>P(~*)(~*)(~*)(~*)) +end_type + +type:s1= + ! Sulfur in CS2 + template: [>S[~C[~S]]] +end_type + +type:s2= + ! Sulfur in SO2 + template: [>S[~O][~O]] +end_type + +type: si4 + ! Generic silicon with four bonds attached + template: (>Si(-*)(-*)(-*)(-*)) +end_type + +type: si4c + ! A subset of si4, non-hydrogen atom attached [siloxanes??] + template: (>Si(-O)(-*)(-*)(-*)) + atom_test: 3 + allowed_elements: O, C + end_test + atom_test: 4 + allowed_elements: O, C + end_test + atom_test: 5 + allowed_elements: O, C + end_test +end_type + +type: xe + ! Xenon atom + template: (>Xe) +end_type + +precedence: +(? + (ar) + (c1o) + (c2=) + (c3a) (c3') + (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) + (h1) (h1h) (h1o) + (he) + (kr) + (n1n) (n1o) (n1z) + (n2= (n2o) (n2t) (n2z) ) + (n3m) (n3o) + (ne) + (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) + (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) + (p4=) + (s1=) + (s2=) + (si4 (si4c) ) + (xe) +) +end_precedence + + + +#reference 1 +@Author tester +@Date 01-Jun-09 +Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) + +This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that +we neither support this version, nor make any warranty as to the correctness of the parameters. +We have checked the numbers against the literature, but of course there may still be errors, +including errors of interpretation. Also, the current version of COMPASS may well be different +that that originally published. + +If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com + +#reference 2 +@Author tester +@Date 27-Jun-09 +Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) + +#reference 3 +@Author tester +@Date 27-Jun-09 +Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) + +#reference 4 +@Author tester +@Date 30-Jun-09 +Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) + +#reference 5 +@Author tester +@Date 28-Jun-09 +Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) + +#reference 6 +@Author tester +@Date 29-Jun-09 +Parameters for nitrate esters from JPC B104, 2477-89 (2000) + +#reference 7 +@Author tester +@Date 30-Jun-09 +Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) + +#reference 8 +@Author tester +@Date 30-Jun-09 +Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) + +#reference 9 +@Author tester +@Date 30-Jun-09 +Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) + +#reference 10 +@Author tester +@Date 02-Jul-09 +Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_published.lt b/tools/moltemplate/moltemplate/force_fields/compass_published.lt new file mode 100644 index 0000000000000000000000000000000000000000..3ec7595f28baf46ebc9c330415e035b6c277934b --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/compass_published.lt @@ -0,0 +1,4148 @@ +# This file was generated automatically using: +# msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt + +# This is an incomplete version of the COMPASS force field based on available +# public sources. Parameters for common atoms and many groups are missing +# (for example, sp2 carbons and the NH2 amine group). The commercial version +# of COMPASS is much larger and presumably includes more up to date +# parameters and parameters for a wider range of atom types and molecule types. +# (However files containing those force field parameters have not been publicly +# disclosed.) We would like to thank Materials Design Inc. for collecting +# these force field parameters and making them publicly available. + +# USAGE: You can create molecules using this force-field this way: +# +# MyMolecule inherits COMPASS { +# # atom-id mol-id atom-type charge X Y Z +# write('Data Atoms') { +# $atom:C1 $mol @atom:c4 0.00 -0.6695 0.000000 0.000000 +# $atom:H11 $mol @atom:h1 0.00 -1.234217 -0.854458 0.000000 +# : : : : : : +# } +# } +# +# You can omit the atom charge in your molecule definition. +# (Partial charges will be assigned later according to the force field rules.) +# Responsibility for choosing the atom types (eg "@atom:c4", "@atom:h1") falls +# on the user. You must select the type of each atom in the molecule carefully +# by looking at the description in the "Data Masses" section of this file +# (see below), and looking for a reasonable match. If your simulation is +# non-neutral, or moltemplate complains that you have missing bond, angle, or +# dihedral types, this means at least one of your atom types is incorrect. + + + +COMPASS { + + + # AtomType Mass # "Description" (version, reference) + + write_once("Data Masses") { + @atom:ar 39.944 # Ar, "argon" (ver=1.0, ref=5) + @atom:c3a 12.01115 # C, "aromatic carbon" (ver=1.0, ref=1) + @atom:c1o 12.01115 # C, "carbon in CO" (ver=1.0, ref=5) + @atom:c2= 12.01115 # C, "carbon in CO2 and CS2" (ver=1.0, ref=5) + @atom:c3prime 12.01115 # C, "carbonyl carbon [one polar substituent]" (ver=1.0, ref=7) + @atom:c4 12.01115 # C, "generic sp3 carbon" (ver=1.0, ref=1) + @atom:c41o 12.01115 # C, "carbon, sp3, in methanol" (ver=1.0, ref=8) + @atom:c43o 12.01115 # C, "carbon, sp3 in secondary alcohols" (ver=1.0, ref=8) + @atom:c43 12.01115 # C, "sp3 carbon with three heavy atoms attached" (ver=1.0, ref=1) + @atom:c44 12.01115 # C, "sp3 carbon with four heavy atoms attached" (ver=1.0, ref=1) + @atom:c4o 12.01115 # C, "alpha carbon" (ver=1.0, ref=3) + @atom:c4z 12.01115 # C, "carbon, sp3, bonded to -N3" (ver=1.0, ref=9) + @atom:h1 1.00797 # H, "nonpolar hydrogen" (ver=1.0, ref=1) + @atom:h1h 1.00797 # H, "hydrogen in H2" (ver=1.0, ref=5) + @atom:h1o 1.00797 # H, "strongly polar hydrogen, bonded to O,F" (ver=1.0, ref=3) + @atom:he 4.003 # He, "helium" (ver=1.0, ref=5) + @atom:kr 83.8 # Kr, "krypton" (ver=1.0, ref=5) + @atom:n1n 14.0067 # N, "nitrogen in N2" (ver=1.0, ref=5) + @atom:n1o 14.0067 # N, "nitrogen in NO" (ver=1.0, ref=5) + @atom:n1z 14.0067 # N, "nitrogen, terminal atom in -N3" (ver=1.0, ref=5) + @atom:n2= 14.0067 # N, "nitrogen" (ver=1.0, ref=4) + @atom:n2o 14.0067 # N, "nitrogen in NO2" (ver=1.0, ref=5) + @atom:n2t 14.0067 # N, "nitrogen, central atom in -N3" (ver=1.0, ref=9) + @atom:n2z 14.0067 # N, "nitrogen, first atom in -N3" (ver=1.0, ref=9) + @atom:n3m 14.0067 # N, "sp3 nitrogen in amides without hydrogen" (ver=1.0, ref=7) + @atom:n3o 14.0067 # N, "nitrogen in nitro group" (ver=1.0, ref=6) + @atom:ne 20.183 # Ne, "neon" (ver=1.0, ref=5) + @atom:o1= 15.9994 # O, "oxygen in NO2 and SO2 [and carbonyl]" (ver=1.0, ref=5) + @atom:o1=star 15.9994 # O, "oxygen in CO2" (ver=1.0, ref=5) + @atom:o12 15.9994 # O, "oxygen in nitro group (-NO2)" (ver=1.0, ref=6) + @atom:o1c 15.9994 # O, "oxygen in CO" (ver=1.0, ref=5) + @atom:o1n 15.9994 # O, "oxygen in NO" (ver=1.0, ref=5) + @atom:o1o 15.9994 # O, "oxygen in O2" (ver=1.0, ref=5) + @atom:o2 15.9994 # O, "generic oxygen with two bonds attached" (ver=1.0, ref=2) + @atom:o2e 15.9994 # O, "ether oxygen" (ver=1.0, ref=3) + @atom:o2h 15.9994 # O, "hydroxyl oxygen" (ver=1.0, ref=3) + @atom:o2n 15.9994 # O, "oxygen in nitrates" (ver=1.0, ref=6) + @atom:o2s 15.9994 # O, "ester oxygen" (ver=1.0, ref=7) + @atom:o2z 15.9994 # O, "oxygen, in siloxanes and zeolites" (ver=1.0, ref=2) + @atom:p4= 30.9738 # P, "phosphorous" (ver=1.0, ref=4) + @atom:s1= 32.064 # S, "sulfur in CS2" (ver=1.0, ref=5) + @atom:s2= 32.064 # S, "sulfur in SO2" (ver=1.0, ref=5) + @atom:si4 28.086 # Si, "generic silicon with four bonds attached" (ver=1.0, ref=2) + @atom:si4c 28.086 # Si, "a subset of si4, non-hydrogen atom attached [siloxanes]" (ver=1.0, ref=2) + @atom:xe 131.3 # Xe, "xenon" (ver=1.0, ref=5) + } #(end of atom masses) + + + # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- + # Each type of atom has a separate ID used for looking up bond parameters + # and a separate ID for looking up 3-body angle interaction parameters + # and a separate ID for looking up 4-body dihedral interaction parameters + # and a separate ID for looking up 4-body improper interaction parameters + # The complete @atom type name includes ALL of these ID numbers. There's + # no need to force the end-user to type the complete name of each atom. + # The "replace" command used below informs moltemplate that the short + # @atom names we have been using abovee are equivalent to the complete + # @atom names used below: + + replace{ @atom:ar @atom:ar,par,bar,aar,dar,iar } + replace{ @atom:c3a @atom:c3a,pc3a,bc3a,ac3a,dc3a,ic3a } + replace{ @atom:c1o @atom:c1o,pc1o,bc1o,ac1o,dc1o,ic1o } + replace{ @atom:c2= @atom:c2=,pc2=,bc2=,ac2=,dc2=,ic2= } + replace{ @atom:c3prime @atom:c3prime,pc3prime,bc3prime,ac3prime,dc3prime,ic3prime } + replace{ @atom:c4 @atom:c4,pc4,bc4,ac4,dc4,ic4 } + replace{ @atom:c41o @atom:c41o,pc41o,bc4,ac4,dc4,ic4 } + replace{ @atom:c43o @atom:c43o,pc43o,bc4,ac4,dc4,ic4 } + replace{ @atom:c43 @atom:c43,pc43,bc4,ac4,dc4,ic4 } + replace{ @atom:c44 @atom:c44,pc44,bc4,ac4,dc4,ic4 } + replace{ @atom:c4o @atom:c4o,pc4o,bc4,ac4,dc4,ic4 } + replace{ @atom:c4z @atom:c4z,pc4z,bc4,ac4,dc4,ic4 } + replace{ @atom:h1 @atom:h1,ph1,bh1,ah1,dh1,ih1 } + replace{ @atom:h1h @atom:h1h,ph1h,bh1h,ah1,dh1,ih1 } + replace{ @atom:h1o @atom:h1o,ph1o,bh1,ah1,dh1,ih1 } + replace{ @atom:he @atom:he,phe,bhe,ahe,dhe,ihe } + replace{ @atom:kr @atom:kr,pkr,bkr,akr,dkr,ikr } + replace{ @atom:n1n @atom:n1n,pn1n,bn1n,an1n,dn1n,in1n } + replace{ @atom:n1o @atom:n1o,pn1o,bn1o,an1o,dn1o,in1o } + replace{ @atom:n1z @atom:n1z,pn1z,bn1t,an1t,dn1t,in1t } + replace{ @atom:n2= @atom:n2=,pn2=,bn2=,an2=,dn2=,in2= } + replace{ @atom:n2o @atom:n2o,pn2o,bn2o,an2o,dn2o,in2o } + replace{ @atom:n2t @atom:n2t,pn2t,bn2t,an2t,dn2t,in2t } + replace{ @atom:n2z @atom:n2z,pn2z,bn2z,an2z,dn2z,in2z } + replace{ @atom:n3m @atom:n3m,pn3m,bn3m,an3m,dn3m,in3m } + replace{ @atom:n3o @atom:n3o,pn3o,bn3o,an3o,dn3o,in3o } + replace{ @atom:ne @atom:ne,pne,bne,ane,dne,ine } + replace{ @atom:o1= @atom:o1=,po1=,bo1=,ao1=,do1=,io1= } + replace{ @atom:o1=star @atom:o1=star,po1=star,bo1=,ao1=,do1=,io1= } + replace{ @atom:o12 @atom:o12,po12,bo1=,ao1=,do1=,io1= } + replace{ @atom:o1c @atom:o1c,po1c,bo1c,ao1c,do1c,io1c } + replace{ @atom:o1n @atom:o1n,po1n,bo1n,ao1n,do1n,io1n } + replace{ @atom:o1o @atom:o1o,po1o,bo1o,ao1o,do1o,io1o } + replace{ @atom:o2 @atom:o2,po2,bo2,ao2,do2,io2 } + replace{ @atom:o2e @atom:o2e,po2e,bo2e,ao2,do2,io2 } + replace{ @atom:o2h @atom:o2h,po2h,bo2h,ao2,do2,io2 } + replace{ @atom:o2n @atom:o2n,po2n,bo2n,ao2n,do2,io2 } + replace{ @atom:o2s @atom:o2s,po2s,bo2e,ao2,do2,io2 } + replace{ @atom:o2z @atom:o2z,po2z,bo2z,ao2z,do2z,io2z } + replace{ @atom:p4= @atom:p4=,pp4=,bp4=,ap4=,dp4=,ip4= } + replace{ @atom:s1= @atom:s1=,ps1=,bs1=,as1=,ds1=,is1= } + replace{ @atom:s2= @atom:s2=,ps2=,bs2=,as2=,ds2=,is2= } + replace{ @atom:si4 @atom:si4,psi4,bsi4,asi4,dsi4,isi4 } + replace{ @atom:si4c @atom:si4c,psi4c,bsi4,asi4,dsi4,isi4 } + replace{ @atom:xe @atom:xe,pxe,bxe,axe,dxe,ixe } + + + + + # --------------- Non-Bonded Interactions: --------------------- + # Syntax: + # pair_coeff AtomType1 AtomType2 pair_style_name parameters... + + write_once("In Settings") { + pair_coeff @atom:*,pc3a,b*,a*,d*,i* @atom:*,pc3a,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc4,b*,a*,d*,i* @atom:*,pc4,b*,a*,d*,i* lj/class2/coul/long 0.0620 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc43,b*,a*,d*,i* @atom:*,pc43,b*,a*,d*,i* lj/class2/coul/long 0.0400 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,pc44,b*,a*,d*,i* @atom:*,pc44,b*,a*,d*,i* lj/class2/coul/long 0.0200 3.8540 # (ver=1.0, ref=1) + pair_coeff @atom:*,ph1,b*,a*,d*,i* @atom:*,ph1,b*,a*,d*,i* lj/class2/coul/long 0.0230 2.8780 # (ver=1.0, ref=1) + pair_coeff @atom:*,po2z,b*,a*,d*,i* @atom:*,po2z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=2) + pair_coeff @atom:*,psi4,b*,a*,d*,i* @atom:*,psi4,b*,a*,d*,i* lj/class2/coul/long 0.1980 4.4050 # (ver=1.0, ref=2) + pair_coeff @atom:*,psi4c,b*,a*,d*,i* @atom:*,psi4c,b*,a*,d*,i* lj/class2/coul/long 0.1310 4.2900 # (ver=1.0, ref=2) + pair_coeff @atom:*,pc4o,b*,a*,d*,i* @atom:*,pc4o,b*,a*,d*,i* lj/class2/coul/long 0.0748 3.8700 # (ver=1.1, ref=8) + pair_coeff @atom:*,ph1o,b*,a*,d*,i* @atom:*,ph1o,b*,a*,d*,i* lj/class2/coul/long 0.0080 1.0870 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2,b*,a*,d*,i* @atom:*,po2,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2e,b*,a*,d*,i* @atom:*,po2e,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.3000 # (ver=1.0, ref=3) + pair_coeff @atom:*,po2h,b*,a*,d*,i* @atom:*,po2h,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.5800 # (ver=1.0, ref=3) + pair_coeff @atom:*,pn2=,b*,a*,d*,i* @atom:*,pn2=,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.8300 # (ver=1.0, ref=4) + pair_coeff @atom:*,pp4=,b*,a*,d*,i* @atom:*,pp4=,b*,a*,d*,i* lj/class2/coul/long 0.0650 4.2950 # (ver=1.0, ref=4) + pair_coeff @atom:*,phe,b*,a*,d*,i* @atom:*,phe,b*,a*,d*,i* lj/class2/coul/long 0.0050 2.9000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pne,b*,a*,d*,i* @atom:*,pne,b*,a*,d*,i* lj/class2/coul/long 0.0550 3.2000 # (ver=1.0, ref=5) + pair_coeff @atom:*,par,b*,a*,d*,i* @atom:*,par,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.8800 # (ver=1.0, ref=5) + pair_coeff @atom:*,pkr,b*,a*,d*,i* @atom:*,pkr,b*,a*,d*,i* lj/class2/coul/long 0.2800 4.3000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pxe,b*,a*,d*,i* @atom:*,pxe,b*,a*,d*,i* lj/class2/coul/long 0.3900 4.2600 # (ver=1.0, ref=5) + pair_coeff @atom:*,ph1h,b*,a*,d*,i* @atom:*,ph1h,b*,a*,d*,i* lj/class2/coul/long 0.0216 1.4210 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn1n,b*,a*,d*,i* @atom:*,pn1n,b*,a*,d*,i* lj/class2/coul/long 0.0598 3.8008 # (ver=1.0, ref=5) + pair_coeff @atom:*,pc1o,b*,a*,d*,i* @atom:*,pc1o,b*,a*,d*,i* lj/class2/coul/long 0.0530 4.0120 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1o,b*,a*,d*,i* @atom:*,po1o,b*,a*,d*,i* lj/class2/coul/long 0.0780 3.4758 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1c,b*,a*,d*,i* @atom:*,po1c,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.6020 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn1o,b*,a*,d*,i* @atom:*,pn1o,b*,a*,d*,i* lj/class2/coul/long 0.1280 3.4600 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1n,b*,a*,d*,i* @atom:*,po1n,b*,a*,d*,i* lj/class2/coul/long 0.1560 3.3000 # (ver=1.0, ref=5) + pair_coeff @atom:*,pc2=,b*,a*,d*,i* @atom:*,pc2=,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=5) + pair_coeff @atom:*,ps2=,b*,a*,d*,i* @atom:*,ps2=,b*,a*,d*,i* lj/class2/coul/long 0.1250 4.0470 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn2o,b*,a*,d*,i* @atom:*,pn2o,b*,a*,d*,i* lj/class2/coul/long 0.3330 3.5290 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1=,b*,a*,d*,i* @atom:*,po1=,b*,a*,d*,i* lj/class2/coul/long 0.1920 3.4300 # (ver=1.0, ref=5) + pair_coeff @atom:*,po1=star,b*,a*,d*,i* @atom:*,po1=star,b*,a*,d*,i* lj/class2/coul/long 0.0670 3.3600 # (ver=1.0, ref=5) + pair_coeff @atom:*,ps1=,b*,a*,d*,i* @atom:*,ps1=,b*,a*,d*,i* lj/class2/coul/long 0.3130 4.0070 # (ver=1.0, ref=5) + pair_coeff @atom:*,pn3o,b*,a*,d*,i* @atom:*,pn3o,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.7600 # (ver=1.0, ref=6) + pair_coeff @atom:*,po12,b*,a*,d*,i* @atom:*,po12,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.4000 # (ver=1.0, ref=6) + pair_coeff @atom:*,po2n,b*,a*,d*,i* @atom:*,po2n,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.6500 # (ver=1.0, ref=6) + pair_coeff @atom:*,pc3prime,b*,a*,d*,i* @atom:*,pc3prime,b*,a*,d*,i* lj/class2/coul/long 0.0640 3.9000 # (ver=1.0, ref=7) + pair_coeff @atom:*,pn3m,b*,a*,d*,i* @atom:*,pn3m,b*,a*,d*,i* lj/class2/coul/long 0.1500 3.7200 # (ver=1.0, ref=7) + pair_coeff @atom:*,po2s,b*,a*,d*,i* @atom:*,po2s,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.3000 # (ver=1.0, ref=7) + pair_coeff @atom:*,pc41o,b*,a*,d*,i* @atom:*,pc41o,b*,a*,d*,i* lj/class2/coul/long 0.1080 3.8700 # (ver=1.1, ref=8) + pair_coeff @atom:*,pc43o,b*,a*,d*,i* @atom:*,pc43o,b*,a*,d*,i* lj/class2/coul/long 0.0498 3.6700 # (ver=1.1, ref=8) + pair_coeff @atom:*,pc4z,b*,a*,d*,i* @atom:*,pc4z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.6500 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn1z,b*,a*,d*,i* @atom:*,pn1z,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.5200 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn2t,b*,a*,d*,i* @atom:*,pn2t,b*,a*,d*,i* lj/class2/coul/long 0.0500 3.3000 # (ver=1.0, ref=9) + pair_coeff @atom:*,pn2z,b*,a*,d*,i* @atom:*,pn2z,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.4000 # (ver=1.0, ref=9) + } #(end of pair_coeffs) + + + + # ---------- Charge By Bond (a.k.a. "bond equivalences") ---------- + + + + write_once("Data Charge By Bond") { + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1260 0.1260 # (ver=1.0, ref=10) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1350 0.1350 # (ver=1.0, ref=10) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1170 0.1170 # (ver=1.0, ref=10) + @atom:*,p*,bn2t,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.2470 -0.2470 # (ver=1.0, ref=9) + @atom:*,p*,bn1t,a*,d*,i* @atom:*,p*,bn2t,a*,d*,i* -0.3860 0.3860 # (ver=1.0, ref=9) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3350 -0.3350 # (ver=1.0, ref=9) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3110 -0.3110 # (ver=1.0, ref=9) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0950 -0.0950 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3prime,a*,d*,i* -0.0350 0.0350 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4500 -0.4500 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) + @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1120 -0.1120 # (ver=1.0, ref=7) + @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.0010 -0.0010 # (ver=1.0, ref=6) + @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4280 -0.4280 # (ver=1.0, ref=6) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.1880 -0.1880 # (ver=1.0, ref=6) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.3170 -0.3170 # (ver=1.0, ref=6) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2100 -0.2100 # (ver=1.0, ref=6) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2390 -0.2390 # (ver=1.0, ref=6) + @atom:*,p*,bo1o,a*,d*,i* @atom:*,p*,bo1o,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bo1=,a*,d*,i* @atom:*,p*,bs2=,a*,d*,i* -0.2351 0.2351 # (ver=1.0, ref=5) + @atom:*,p*,bn1o,a*,d*,i* @atom:*,p*,bo1n,a*,d*,i* 0.0288 -0.0288 # (ver=1.0, ref=5) + @atom:*,p*,bn1n,a*,d*,i* @atom:*,p*,bn1n,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bh1h,a*,d*,i* @atom:*,p*,bh1h,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) + @atom:*,p*,bn2o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.0730 -0.0730 # (ver=1.0, ref=5) + @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bs1=,a*,d*,i* 0.0258 -0.0258 # (ver=1.0, ref=5) + @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4000 -0.4000 # (ver=1.0, ref=5) + @atom:*,p*,bc1o,a*,d*,i* @atom:*,p*,bo1c,a*,d*,i* -0.0203 0.0203 # (ver=1.0, ref=5) + @atom:*,p*,bo2,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1400 0.1400 # (ver=1.0, ref=4) + @atom:*,p*,bn3,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.3500 0.3500 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* -0.0430 0.0430 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn3,a*,d*,i* 0.0250 -0.0250 # (ver=1.0, ref=4) + @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3280 -0.3280 # (ver=1.0, ref=4) + @atom:*,p*,bf1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1800 0.1800 # (ver=1.0, ref=4) + @atom:*,p*,bcl1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3450 -0.3450 # (ver=1.0, ref=4) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0600 0.0600 # (ver=1.0, ref=4) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.1990 -0.1990 # (ver=1.0, ref=4) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* 0.4200 -0.4200 # (ver=1.0, ref=3) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) + @atom:*,p*,bo2z,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.2225 0.2225 # (ver=1.0, ref=2) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.0530 0.0530 # (ver=1.0, ref=1) + @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.1268 0.1268 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3a,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) + @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.4100 -0.4100 # (ver=1.1, ref=8) + } #(end of Charge by Bond (bond equivalences)) + + + + + + # --------------- Bond Interactions: --------------------- + + + # -- Rules for generating (2-body) "bond" interactions: -- + # BondType AtomType1 AtomType2 + + write_once("Data Bonds By Type") { + @bond:c4,n3m @atom:*,bc4,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:si4,si4 @atom:*,bsi4,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:h1,si4 @atom:*,bh1,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c4,si4 @atom:*,bc4,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c3a,si4 @atom:*,bc3a,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:h1,n2z @atom:*,bh1,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:c4,n2z @atom:*,bc4,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:n1t,n2t @atom:*,bn1t,a*,d*,i* @atom:*,bn2t,a*,d*,i* + @bond:n2t,n2z @atom:*,bn2t,a*,d*,i* @atom:*,bn2z,a*,d*,i* + @bond:n1t,n1t @atom:*,bn1t,a*,d*,i* @atom:*,bn1t,a*,d*,i* + @bond:c3a,n3m @atom:*,bc3a,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:c3prime,n3m @atom:*,bc3prime,a*,d*,i* @atom:*,bn3m,a*,d*,i* + @bond:c3a,c3prime @atom:*,bc3a,a*,d*,i* @atom:*,bc3prime,a*,d*,i* + @bond:c3prime,o1= @atom:*,bc3prime,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:c3prime,c4 @atom:*,bc3prime,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3prime,o2e @atom:*,bc3prime,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:n3o,o2n @atom:*,bn3o,a*,d*,i* @atom:*,bo2n,a*,d*,i* + @bond:n3o,o1= @atom:*,bn3o,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:h1,n3o @atom:*,bh1,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c4,o2n @atom:*,bc4,a*,d*,i* @atom:*,bo2n,a*,d*,i* + @bond:c4,n3o @atom:*,bc4,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c3a,n3o @atom:*,bc3a,a*,d*,i* @atom:*,bn3o,a*,d*,i* + @bond:c2=,s1= @atom:*,bc2=,a*,d*,i* @atom:*,bs1=,a*,d*,i* + @bond:n2o,o1= @atom:*,bn2o,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:c2=,o1= @atom:*,bc2=,a*,d*,i* @atom:*,bo1=,a*,d*,i* + @bond:o1=,s2= @atom:*,bo1=,a*,d*,i* @atom:*,bs2=,a*,d*,i* + @bond:n1o,o1n @atom:*,bn1o,a*,d*,i* @atom:*,bo1n,a*,d*,i* + @bond:c1o,o1c @atom:*,bc1o,a*,d*,i* @atom:*,bo1c,a*,d*,i* + @bond:o1o,o1o @atom:*,bo1o,a*,d*,i* @atom:*,bo1o,a*,d*,i* + @bond:n1n,n1n @atom:*,bn1n,a*,d*,i* @atom:*,bn1n,a*,d*,i* + @bond:h1h,h1h @atom:*,bh1h,a*,d*,i* @atom:*,bh1h,a*,d*,i* + @bond:o2,p4= @atom:*,bo2,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:n3,p4= @atom:*,bn3,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:n2=,p4= @atom:*,bn2=,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:h1,p4= @atom:*,bh1,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:h1,n2= @atom:*,bh1,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:f1p,p4= @atom:*,bf1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:cl1p,p4= @atom:*,bcl1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c4,p4= @atom:*,bc4,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c4,n2= @atom:*,bc4,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:c3a,p4= @atom:*,bc3a,a*,d*,i* @atom:*,bp4=,a*,d*,i* + @bond:c3a,n2= @atom:*,bc3a,a*,d*,i* @atom:*,bn2=,a*,d*,i* + @bond:h1,o2h @atom:*,bh1,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c4,o2h @atom:*,bc4,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c4,o2e @atom:*,bc4,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:c3a,o2h @atom:*,bc3a,a*,d*,i* @atom:*,bo2h,a*,d*,i* + @bond:c3a,o2e @atom:*,bc3a,a*,d*,i* @atom:*,bo2e,a*,d*,i* + @bond:c3a,o2 @atom:*,bc3a,a*,d*,i* @atom:*,bo2,a*,d*,i* + @bond:o2z,si4 @atom:*,bo2z,a*,d*,i* @atom:*,bsi4,a*,d*,i* + @bond:c4,h1 @atom:*,bc4,a*,d*,i* @atom:*,bh1,a*,d*,i* + @bond:c4,c4 @atom:*,bc4,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3a,h1 @atom:*,bc3a,a*,d*,i* @atom:*,bh1,a*,d*,i* + @bond:c3a,c4 @atom:*,bc3a,a*,d*,i* @atom:*,bc4,a*,d*,i* + @bond:c3a,c3a @atom:*,bc3a,a*,d*,i* @atom:*,bc3a,a*,d*,i* + } # end of "Data Bonds By Type" section + + + + # ------------ Bond Parameters: ---------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/bond_class2.html + + # Syntax: + # bond_coeff BondTypeName BondStyle parameters... + + + write_once("In Settings") { + bond_coeff @bond:c4,n3m class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=10) + bond_coeff @bond:si4,si4 class2 2.3384 114.2164 -140.4212 80.7084 # (ver=1.0, ref=10) + bond_coeff @bond:h1,si4 class2 1.4783 202.7798 -305.3603 280.2685 # (ver=1.0, ref=10) + bond_coeff @bond:c4,si4 class2 1.8995 189.6536 -279.4210 307.5135 # (ver=1.0, ref=10) + bond_coeff @bond:c3a,si4 class2 1.8634 233.2433 -276.8692 161.6659 # (ver=1.0, ref=10) + bond_coeff @bond:h1,n2z class2 1.0221 440.1623 -960.3246 1120.3787 # (ver=1.0, ref=9) + bond_coeff @bond:c4,n2z class2 1.4814 324.4578 -648.9156 757.0681 # (ver=1.0, ref=9) + bond_coeff @bond:n1t,n2t class2 1.1354 1198.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) + bond_coeff @bond:n2t,n2z class2 1.2343 720.3345 -1542.6689 1799.7804 # (ver=1.0, ref=9) + bond_coeff @bond:n1t,n1t class2 1.1354 1337.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) + bond_coeff @bond:c3a,n3m class2 1.3950 344.0452 -652.1208 1022.2242 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,n3m class2 1.3850 359.1591 -558.4730 1146.3810 # (ver=1.0, ref=7) + bond_coeff @bond:c3a,c3prime class2 1.4890 339.3574 -655.7236 670.2362 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,o1= class2 1.2160 823.7948 -1878.7939 2303.5310 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,c4 class2 1.5140 312.3719 -465.8290 473.8300 # (ver=1.0, ref=7) + bond_coeff @bond:c3prime,o2e class2 1.3750 368.7309 -832.4784 1274.0231 # (ver=1.0, ref=7) + bond_coeff @bond:n3o,o2n class2 1.4020 300.0000 -1000.0000 2000.0000 # (ver=1.0, ref=6) + bond_coeff @bond:n3o,o1= class2 1.2100 765.0664 -2070.2830 2793.3218 # (ver=1.0, ref=6) + bond_coeff @bond:h1,n3o class2 1.0400 439.9346 -943.7307 1180.9318 # (ver=1.0, ref=6) + bond_coeff @bond:c4,o2n class2 1.4350 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=6) + bond_coeff @bond:c4,n3o class2 1.4740 301.6051 -535.7028 555.0420 # (ver=1.0, ref=6) + bond_coeff @bond:c3a,n3o class2 1.4300 313.8329 -568.6087 600.9597 # (ver=1.0, ref=6) + bond_coeff @bond:c2=,s1= class2 1.5540 559.0065 -1348.6633 1248.8604 # (ver=1.0, ref=5) + bond_coeff @bond:n2o,o1= class2 1.1930 620.0000 -1808.6018 3077.5918 # (ver=1.0, ref=5) + bond_coeff @bond:c2=,o1= class2 1.1600 1161.3421 -2564.5706 3932.8735 # (ver=1.0, ref=5) + bond_coeff @bond:o1=,s2= class2 1.4308 730.8387 -1531.7910 1859.7753 # (ver=1.0, ref=5) + bond_coeff @bond:n1o,o1n class2 1.1506 1147.8362 -3167.7349 5099.5811 # (ver=1.0, ref=5) + bond_coeff @bond:c1o,o1c class2 1.1283 1368.7676 -3157.0007 4247.5298 # (ver=1.0, ref=5) + bond_coeff @bond:o1o,o1o class2 1.2074 846.7150 -2247.1760 3478.9900 # (ver=1.0, ref=5) + bond_coeff @bond:n1n,n1n class2 1.0977 1651.3730 -4069.3178 5984.9629 # (ver=1.0, ref=5) + bond_coeff @bond:h1h,h1h class2 0.7412 414.2185 -805.6549 914.1296 # (ver=1.0, ref=5) + bond_coeff @bond:o2,p4= class2 1.6000 333.0980 -726.6230 924.6200 # (ver=1.0, ref=4) + bond_coeff @bond:n3,p4= class2 1.6780 329.0000 -713.7950 902.9190 # (ver=1.0, ref=4) + bond_coeff @bond:n2=,p4= class2 1.5980 393.0060 -751.4050 767.4310 # (ver=1.0, ref=4) + bond_coeff @bond:h1,p4= class2 1.4300 285.2040 -575.6850 677.8460 # (ver=1.0, ref=4) + bond_coeff @bond:h1,n2= class2 1.0310 540.1120 -1500.2952 2431.0080 # (ver=1.0, ref=4) + bond_coeff @bond:f1p,p4= class2 1.5650 340.0000 -882.3840 1197.9190 # (ver=1.0, ref=4) + bond_coeff @bond:cl1p,p4= class2 2.0000 158.7770 -239.1290 210.0840 # (ver=1.0, ref=4) + bond_coeff @bond:c4,p4= class2 1.8000 218.1400 -329.5110 290.3490 # (ver=1.0, ref=4) + bond_coeff @bond:c4,n2= class2 1.4740 337.0600 -147.3700 213.6330 # (ver=1.0, ref=4) + bond_coeff @bond:c3a,p4= class2 1.7890 197.7020 -332.2510 325.7160 # (ver=1.0, ref=4) + bond_coeff @bond:c3a,n2= class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=4) + bond_coeff @bond:h1,o2h class2 0.9494 540.3633 -1311.8663 2132.4446 # (ver=1.0, ref=3) + bond_coeff @bond:c4,o2h class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) + bond_coeff @bond:c4,o2e class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2h class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2e class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:c3a,o2 class2 1.3768 428.8798 -738.2350 1114.9655 # (ver=1.0, ref=3) + bond_coeff @bond:o2z,si4 class2 1.6400 350.1232 -517.3424 673.7067 # (ver=1.0, ref=2) + bond_coeff @bond:c4,h1 class2 1.1010 345.0000 -691.8900 844.6000 # (ver=1.0, ref=1) + bond_coeff @bond:c4,c4 class2 1.5300 299.6700 -501.7700 679.8100 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,h1 class2 1.0982 372.8251 -803.4526 894.3173 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,c4 class2 1.5010 321.9021 -521.8208 572.1628 # (ver=1.0, ref=1) + bond_coeff @bond:c3a,c3a class2 1.4170 470.8361 -627.6179 1327.6345 # (ver=1.0, ref=1) + } # end of bond_coeff commands + + + # --------------- Angle Interactions: --------------------- + + + # -- Rules for generating (3-body) "angle" interactions: -- + # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2] + + write_once("Data Angles By Type") { + @angle:c3a,o2,c3a,c3a,o2h,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,o2,c3a,c3a,o2e,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,o2,c3a,c3a,o2,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,c4,o2,c3a,c4,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c3a,c4,o2,c3a,c4,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,o2,c3prime,c3a,o2e,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:o2,c4,o2,o2h,c4,o2h @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:o2,c4,o2,o2h,c4,o2e @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:o2,c4,o2,o2e,c4,o2h @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:o2,c4,o2,o2e,c4,o2e @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:h1,c3a,o2,h1,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,si4,si4,h1,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,si4,si4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,si4,h1,h1,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,si4,h1,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,si4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,si4,h1,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:h1,c4,si4,h1,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,c4,si4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c3a,c3a,si4,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:c4,c4,n2z,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:h1,c4,n2z,h1,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:c4,n2z,n2t,c4,n2z,n2t @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* + @angle:h1,n2z,n2t,h1,n2z,n2t @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* + @angle:n1t,n2t,n2z,n1t,n2t,n2z @atom:*,p*,bn1t,an1t,d*,i* @atom:*,p*,bn2t,an2t,d*,i* @atom:*,p*,bn2z,an2z,d*,i* + @angle:n3m,c3prime,o1=,n3m,c3prime,o1= @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c4,c3prime,o2,c4,c3prime,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c4,c3prime,o1=,c4,c3prime,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o1=,c3prime,o2,o1=,c3prime,o2e @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,n3m,c3prime,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3a,c3a,n3m,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* + @angle:c3a,c3prime,o1=,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c3a,c3prime,n3m,c3a,c3prime,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* + @angle:c3a,c3a,c3prime,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* + @angle:c3prime,c4,h1,c3prime,c4,h1 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3prime,o2,c4,c3prime,o2e,c4 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:o1=,n3o,o2n,o1=,n3o,o2n @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:c4,c4,o2n,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:c4,o2n,n3o,c4,o2n,n3o @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:o1=,n3o,o1=,o1=,n3o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:h1,n3o,o1=,h1,n3o,o1= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c4,n3o,o1=,c4,n3o,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:c3a,n3o,o1=,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:h1,c4,o2n,h1,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* + @angle:h1,c4,n3o,h1,c4,n3o @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:c3a,c3a,n3o,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* + @angle:o1=,s2=,o1=,o1=,s2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bs2=,as2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o1=,n2o,o1=,o1=,n2o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn2o,an2o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:s1=,c2=,s1=,s1=,c2=,s1= @atom:*,p*,bs1=,as1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bs1=,as1=,d*,i* + @angle:o1=,c2=,o1=,o1=,c2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* + @angle:o2,p4=,o2,o2,p4=,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:n2=,p4=,o2,n2=,p4=,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:n2=,p4=,n2=,n2=,p4=,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:h1,p4=,o2,h1,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:h1,p4=,n2=,h1,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:h1,p4=,h1,h1,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,p4=,n2=,c4,p4=,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,p4=,h1,c4,p4=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,p4=,c4,c4,p4=,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,p4=,o2,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:c3a,p4=,n2=,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c3a,p4=,h1,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,p4=,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:p4=,n2=,p4=,p4=,n2=,p4= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,n2=,p4=,h1,n2=,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,n2=,h1,h1,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,n2=,h1,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:h1,c4,p4=,h1,c4,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:h1,c4,n2=,h1,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,c4,n2=,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c3a,c3a,p4=,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* + @angle:c3a,c3a,n2=,c3a,c3a,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn2=,an2=,d*,i* + @angle:c4,o2,h1,c4,o2h,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,o2,c4,c4,o2h,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c4,o2,c4,c4,o2e,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,o2,h1,c3a,o2h,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,o2,c4,c3a,o2h,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,o2,c4,c3a,o2e,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:h1,c4,o2,h1,c4,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:h1,c4,o2,h1,c4,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c4,c4,o2,c4,c4,o2h @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c4,c4,o2,c4,c4,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* + @angle:c3a,c3a,o2,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* + @angle:o2z,si4,o2z,o2z,si4,o2z @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:h1,si4,o2z,h1,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:c4,si4,o2z,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:c3a,si4,o2z,c3a,si4,o2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* + @angle:si4,o2z,si4,si4,o2z,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* + @angle:h1,c4,h1,h1,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,c4,h1,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c4,h1,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,c4,c4,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c4,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:c3a,c3a,h1,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bh1,ah1,d*,i* + @angle:c3a,c3a,c4,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* + @angle:c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* + @angle:n3,p4=,o2,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,ao2,d*,i* + @angle:n3,p4=,n3,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:n2=,p4=,n3,X,X,X @atom:*,p*,b*,an2=,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:h1,p4=,n3,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:c3a,p4=,n3,X,X,X @atom:*,p*,b*,ac3a,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* + @angle:h1,o2,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:c4,o2,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:h1,n3,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:c4,n3,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* + @angle:h1,o2z,si4,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2z,d*,i* @atom:*,p*,b*,asi4,d*,i* + } # end of "Data Angles By Type" section + + + + # ------- Angle Force Field Parameters: ------- # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/angle_class2.html + + # Syntax: + # angle_coeff AngleTypeName AngleStyle parameters... + + + write_once("In Settings") { + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 bb 69.5999 1.3768 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 ba 0.0 0.0 1.3768 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 114.2676 24.9501 -19.5949 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 bb 6.0704 2.3384 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 ba 8.9899 8.9899 2.3384 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 112.0893 22.5062 -11.5926 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 bb 3.5172 1.4783 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 ba 5.6630 2.0706 1.4783 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 113.0000 19.4692 -34.3471 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 bb 2.3030 1.8995 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 ba 16.9455 11.4377 1.8995 2.3384 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 108.6051 32.5415 -8.3164 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 bb 4.6408 1.4783 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 ba 9.3467 9.3467 1.4783 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 112.0977 36.4832 -12.8094 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 bb 3.9340 1.8995 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 ba 13.3961 7.4104 1.8995 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 113.1855 36.2069 -20.3939 20.0172 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 bb 3.7419 1.8995 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 ba 18.5805 18.5805 1.8995 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 109.5932 41.9497 -42.3639 48.1442 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 bb 3.9264 1.8634 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 ba 22.5947 8.7811 1.8634 1.4783 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 112.0355 28.7721 -13.9523 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 bb 1.6561 1.1010 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 ba 16.6908 18.2764 1.1010 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 112.6700 39.5160 -7.4430 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 bb 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 ba 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 120.0000 30.4689 -23.5439 0.0000 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 bb 21.3938 1.4170 1.8634 # (ver=1.0, ref=10) + angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 ba 14.5831 23.7679 1.4170 1.8634 # (ver=1.0, ref=10) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 110.9900 77.9387 0.9499 0.0033 # (ver=1.0, ref=9) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 bb 36.9309 1.5300 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 ba 34.8803 67.8888 1.5300 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 107.9744 52.7803 0.6615 0.0023 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 bb 18.4621 1.1010 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 ba 3.3182 61.9652 1.1010 1.4814 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 113.5017 82.6294 0.9845 0.0033 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 bb 84.2075 1.4814 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 ba 88.2679 195.9722 1.4814 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 110.0345 55.7635 0.6618 0.0022 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 bb 14.9026 1.0221 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 ba 37.4419 141.1218 1.0221 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 171.6211 47.7899 0.0000 0.0000 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 bb 204.9909 1.1354 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 ba 1.2222 25.5611 1.1354 1.2343 # (ver=1.0, ref=9) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 121.5420 92.5720 -34.4800 -11.1871 # (ver=1.0, ref=7) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 bb 138.4954 1.3850 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 ba 62.7124 52.4045 1.3850 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 100.3182 88.8631 -3.8323 -7.9802 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 bb 19.1069 1.5140 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 ba 1.3435 4.6978 1.5140 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 119.3000 65.1016 -17.9766 0.0000 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 bb 77.5201 1.5140 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 ba 31.8455 46.6613 1.5140 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 118.9855 98.6813 -22.2485 10.3673 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 bb 210.1813 1.2160 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 ba 79.4497 57.0987 1.2160 1.3750 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 120.0700 47.1131 -32.5592 13.1257 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 bb 0.0000 1.3950 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 ba 0.0 0.0 1.3950 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 120.7640 73.2738 -27.4033 13.3920 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 bb 37.8749 1.4170 1.3950 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 ba 35.8865 53.6977 1.4170 1.3950 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 125.5320 72.3167 -16.0650 2.0818 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 bb 116.9445 1.4890 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 ba 72.8758 76.1093 1.4890 1.2160 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 108.4400 84.8377 -19.9640 2.7405 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 bb 0.0000 1.4890 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 ba 0.0 0.0 1.4890 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 116.0640 71.2598 -15.8273 2.0506 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 bb 37.8749 1.4170 1.4890 # (ver=1.0, ref=7) + angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 ba 45.8865 23.6977 1.4170 1.4890 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 121.9556 76.3105 -26.3166 -17.6944 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 bb 25.9530 1.3850 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 ba 20.0533 20.0533 1.3850 1.3850 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 107.8594 38.0833 -17.5074 0.0000 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 bb 2.2522 1.5140 1.1010 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 ba 15.5988 14.6287 1.5140 1.1010 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 109.0000 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 bb 0.0 1.3750 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 ba 21.5366 -16.6748 1.3750 1.4200 # (ver=1.0, ref=7) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 112.8000 85.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 bb 80.0000 1.2100 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 ba 0.0 0.0 1.2100 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 105.0000 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 bb 11.4318 1.5300 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 ba 2.6868 20.4033 1.5300 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 108.5000 55.7454 -10.0067 -6.2729 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 bb 0.0 1.4350 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 ba 0.0 0.0 1.4350 1.4020 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 128.0000 95.1035 -47.4240 -27.9164 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 bb 265.7106 1.2100 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 ba 95.6936 95.6936 1.2100 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 115.7000 53.8034 -14.1991 -11.8708 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 bb 14.8226 1.0400 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 ba -8.6275 58.6036 1.0400 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 117.5000 64.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 bb 48.1403 1.4740 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 ba 27.2141 93.9927 1.4740 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 117.7000 63.9404 -18.4524 -14.3129 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 bb 93.7948 1.4300 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 ba 40.3757 92.1955 1.4300 1.2100 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 bb 23.1979 1.1010 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 ba 4.6189 55.3270 1.1010 1.4350 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 107.0000 54.9318 -9.1333 -11.5434 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 bb 3.3770 1.1010 1.4740 # (ver=1.0, ref=6) + angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 ba 12.2491 30.5314 1.1010 1.4740 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 118.8000 29.2436 -8.8495 -6.6020 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 bb 21.0495 1.4170 1.4300 # (ver=1.0, ref=6) + angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 ba 30.5211 59.8025 1.4170 1.4300 # (ver=1.0, ref=6) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 119.3000 115.2627 -35.6278 -26.1261 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 bb 20.0000 1.4308 1.4308 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 ba 45.0585 45.0585 1.4308 1.4308 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 134.1000 150.0000 -82.1013 -40.0005 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 bb 20.0000 1.1930 1.1930 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 ba -50.0000 -50.0000 1.1930 1.1930 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 180.0000 48.0000 0.0000 0.0000 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 bb 100.7369 1.5540 1.5540 # (ver=1.0, ref=5) + angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 ba 0.0 0.0 1.5540 1.5540 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 180.0000 57.1000 0.0000 0.0000 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 bb 275.4350 1.1600 1.1600 # (ver=1.0, ref=5) + angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 ba 0.0 0.0 1.1600 1.1600 # (ver=1.0, ref=5) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 107.5000 86.7690 -4.5700 -17.8520 # (ver=1.0, ref=4) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 bb 0.0 1.6000 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 ba 0.0 0.0 1.6000 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 112.2150 99.9230 -32.0930 -22.8210 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 bb 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 ba 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 125.0000 90.5230 -20.8010 -19.6020 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 103.9780 73.2570 -9.8970 -15.2120 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 bb 0.0 1.4300 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 ba 0.0 0.0 1.4300 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 110.0330 45.9780 -14.0520 -10.3990 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 bb 12.5700 1.4300 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 ba -24.3830 72.9250 1.4300 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 101.4080 39.6950 -5.1340 -8.2270 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 bb 20.0000 1.4300 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 ba 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 119.3000 47.3660 -14.6410 -10.7360 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 bb 1.0720 1.8000 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 ba -7.1280 26.3530 1.8000 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 102.9000 52.0710 -6.4680 -10.7730 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 bb 3.8820 1.8000 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 ba 11.1260 -19.4700 1.8000 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 102.5000 48.2320 -5.7980 -9.9660 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 bb 6.2460 1.8000 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 ba 12.8050 12.8050 1.8000 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 107.3650 71.9770 -10.9430 -15.2900 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 bb 0.0 1.7890 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 ba 0.0 0.0 1.7890 1.6000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 109.6000 63.0620 -19.7400 -14.3290 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 bb 0.0 1.7890 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 ba 0.0 0.0 1.7890 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 108.2310 36.1850 -6.4880 -7.6460 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 bb 0.0 1.7890 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 ba 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 110.2310 56.1850 -17.3160 -12.7280 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 bb 0.0 1.7890 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 ba 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 135.0000 23.8680 -8.7360 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 120.0000 26.0680 -8.2980 -5.9430 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 bb -18.2870 1.0310 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 ba 40.0630 90.7910 1.0310 1.5980 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 110.9100 31.0910 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 bb 1.4570 1.0310 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 ba 8.4900 8.4900 1.0310 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 117.2000 37.2620 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 bb 12.5630 1.4740 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 ba 18.4860 7.8370 1.4740 1.0310 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 110.8860 33.8300 -7.0430 -7.2460 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 bb 1.0500 1.1010 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 ba 19.8120 16.9400 1.1010 1.8000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 107.4990 62.7310 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 bb 5.6640 1.1010 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 ba 6.4070 46.3730 1.1010 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 117.3170 55.2420 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 bb 22.7100 1.5300 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 ba 19.2440 59.4220 1.5300 1.4740 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 120.0010 47.8410 -15.2290 -10.9070 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 bb 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 ba 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 120.0000 60.0000 0.0000 0.0000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 bb 0.0 1.4170 1.4000 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 ba 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 105.8000 52.7061 -12.1090 -9.8681 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 bb -9.6879 1.4200 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 ba 28.5800 18.9277 1.4200 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 108.1900 53.1250 -8.5016 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 bb 20.6577 1.3768 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 ba 53.8614 23.9224 1.3768 0.9494 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 110.7000 70.3069 -6.9375 0.0000 # (ver=1.0, ref=2) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 ba 23.4380 23.4380 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 107.4000 57.6643 -10.6506 4.6274 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 bb 11.6183 1.4783 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 ba 6.4278 20.5669 1.4783 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 bb 5.4896 1.8995 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 ba 6.4278 20.5669 1.8995 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 bb 0.0 1.8634 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 ba 0.0 0.0 1.8634 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 159.0000 8.5000 -13.4188 -4.1785 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 ba 28.6686 28.6686 1.6400 1.6400 # (ver=1.0, ref=2) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 107.6600 39.6410 -12.9210 -2.4318 # (ver=1.0, ref=1) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 bb 5.3316 1.1010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 ba 18.1030 18.1030 1.1010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 110.7700 41.4530 -10.6040 5.1290 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 bb 3.3872 1.5300 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 ba 20.7540 11.4210 1.5300 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 112.6700 39.5160 -7.4430 -9.5583 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 bb 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 ba 8.0160 8.0160 1.5300 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 bb 2.9168 1.5010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 ba 26.4608 11.7717 1.5010 1.1010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 108.4000 43.9594 -8.3924 -9.3379 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 bb 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 ba 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 bb 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 ba 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 117.9400 35.1558 -12.4682 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 bb 1.0795 1.4170 1.0982 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 ba 20.0033 24.2183 1.4170 1.0982 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 120.0500 44.7148 -22.7352 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 bb 12.0676 1.4170 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 ba 31.0771 47.0579 1.4170 1.5010 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 118.9000 61.0226 -34.9931 0.0000 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 bb 68.2856 1.4170 1.4170 # (ver=1.0, ref=1) + angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 ba 28.8708 28.8708 1.4170 1.4170 # (ver=1.0, ref=1) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 108.3000 86.7690 -5.1750 -17.6710 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,o2,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 107.1000 85.7690 -5.7790 -17.4890 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n3,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 123.2150 89.9230 -32.6120 -21.0960 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:n2=,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 103.9780 68.2570 -9.2210 -14.1740 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 108.1650 70.9770 -11.5480 -15.1090 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c3a,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 117.0000 26.0310 -5.8280 -5.6200 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 118.2830 35.0010 -10.3600 -7.8700 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:c4,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 122.8000 23.7764 -19.8152 9.6331 # (ver=1.0, ref=2) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=2) + angle_coeff @angle:h1,o2z,si4,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + } # end of angle_coeff commands + + + # --------------- Dihedral Interactions: --------------------- + + + # -- Rules for generating (4-body) "dihedral" interactions: -- + # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] + + + write_once("Data Dihedrals By Type") { + @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* + @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* + @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* + @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* + @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* + @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* + @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* + @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* + @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* + @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* + @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,do2,i* + @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* + @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* + @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* + @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* + @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2e,ao2,d*,i* 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@atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* + @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* + @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* 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@atom:*,p*,bc3a,ac3a,d*,i* + @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + 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@atom:*,p*,bo2e,ao2,do2,i* + @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,do2,i* + @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* + @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* + @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* + @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,dn3m,i* @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,do1,i* + @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dn3o,i* @atom:*,p*,b*,a*,do1=,i* + @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dc3a,i* @atom:*,p*,b*,a*,dn2=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* + @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* + @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* + @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* + @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* + @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* + @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,dh1,i* + @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dh1,i* + } # end of "Data Dihedrals By Type" section + + + + # ------- Dihedral Force Field Parameters: ------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/dihedral_class2.html + + # Syntax: + # dihedral_coeff DihedralTypeName DihedralStyle parameters... + + + write_once("In Settings") { + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat -12.2900 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0977 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 aat -12.9341 112.0977 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 bb13 0.0 1.4783 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 at 0.4272 0.0000 0.0000 0.3382 0.0000 0.0000 113.1855 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 aat -17.5802 113.1855 112.0355 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6302 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat -10.8232 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6941 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat -16.9141 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0000 0.0000 -0.1909 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat -13.3679 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0000 0.0000 -0.5906 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 mbt 0.0000 0.0000 -0.3146 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 at 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 120.0000 109.5932 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 aat 0.0 120.0000 109.5932 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 bb13 0.0 1.4170 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 mbt 1.3445 3.5515 -4.9202 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 ebt 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 1.5140 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 at 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 100.3182 109.0000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 aat -12.2070 100.3182 109.0000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 bb13 0.0 1.5140 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 mbt -0.1118 -1.1990 0.6784 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 ebt 0.1726 -0.4823 0.2666 -0.7019 0.8305 -0.6874 1.3850 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 at -0.3188 -0.0548 -0.3038 -0.2851 2.3997 -1.5747 121.9556 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 aat -3.3556 121.9556 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 bb13 0.0 1.3850 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 aat 0.0 114.2676 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 bb13 0.0 2.3384 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 aat 0.0 114.2676 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 bb13 0.0 2.3384 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 aat 0.0 114.2676 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 bb13 0.0 2.3384 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat 0.0 112.0893 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat 0.0 112.0893 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 aat 0.0 112.0893 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 bb13 0.0 1.4783 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 aat 0.0 113.0000 114.2676 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 bb13 0.0 1.8995 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat 0.0 113.0000 112.0893 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 aat 0.0 113.0000 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat 0.0 112.0355 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 aat 0.0 112.0355 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 bb13 0.0 1.1010 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 aat 0.0 112.0355 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 aat 0.0 112.6700 114.9060 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 bb13 0.0 1.5300 1.6400 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 aat 0.0 112.6700 112.0977 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 bb13 0.0 1.5300 1.4783 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 aat 0.0 112.6700 113.1855 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 aat 0.0 114.9060 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 bb13 0.0 1.6400 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.5932 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 aat 0.0 109.5932 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 bb13 0.0 1.4783 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 1.5093 0.0 0.0000 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0000 6.2168 0.0000 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 117.9400 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.3270 0.0 0.0000 0.0 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0000 11.1576 0.0000 1.4170 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 118.9000 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=10) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.2259 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2021 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 aat 0.0 110.9900 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 bb13 0.0 1.5300 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2181 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.9744 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 aat 0.0 107.9744 113.5017 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 bb13 0.0 1.1010 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.1823 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.5017 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 aat 0.0 113.5017 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 bb13 0.0 1.4814 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.2637 0.0 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0221 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0345 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 aat 0.0 110.0345 171.6211 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 bb13 0.0 1.0221 1.1354 # (ver=1.0, ref=9) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 mbt -13.7686 -2.5959 1.1934 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 ebt 0.7800 1.3339 0.3268 0.4160 -0.1140 0.7099 1.1010 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 at -0.0071 0.8005 13.2959 0.1212 1.4427 -0.0241 107.8594 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 aat -13.9734 107.8594 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 bb13 0.0 1.1010 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 mbt 0.0000 0.0000 -1.0000 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 ebt 2.9036 0.5307 0.1439 0.0536 0.0354 0.3853 1.1010 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 at 0.0800 0.3339 14.4728 -0.2083 0.7308 -2.0667 107.8594 119.3000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 aat -23.1923 107.8594 119.3000 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 bb13 0.0 1.1010 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 0.8905 0.0 3.2644 0.0 0.2646 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 mbt 0.4552 7.3091 0.2842 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 ebt 0.0882 -2.4309 -0.7426 -4.2421 10.1102 1.6824 1.4200 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 at -0.0327 1.0059 2.3573 1.9052 2.7261 5.9732 109.0000 118.9855 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 aat -32.9368 109.0000 118.9855 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 bb13 0.0 1.4200 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 -2.5594 0.0 2.2013 0.0 0.0325 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 mbt 0.0 0.0 0.0 1.3750 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.0000 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 aat 0.0 109.0000 100.3182 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 bb13 0.0 1.4200 1.5140 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 0.0000 0.0 2.0521 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 mbt 0.0 0.0 0.0 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0700 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 aat 0.0 120.0700 121.5420 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 bb13 0.0 1.3950 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 0.0000 0.0 0.7800 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 mbt 0.0000 2.4002 0.0000 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 125.5320 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 aat 0.0 116.0640 125.5320 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 bb13 0.0 1.4170 1.2160 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 mbt 7.7147 4.2557 -1.0118 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 ebt 0.2282 2.2998 -0.4473 0.9589 0.9190 -0.6015 1.3750 1.1010 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 at 0.0971 -0.8699 -0.3142 -0.0401 2.8061 -0.4990 109.0000 108.7280 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 aat -13.1500 109.0000 108.7280 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 bb13 0.0 1.3750 1.1010 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 0.1302 0.0 -0.3250 0.0 0.1134 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 mbt 9.9416 2.6421 2.2333 1.4200 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 ebt 0.2560 0.8133 -0.0728 -1.2164 -0.1715 -0.0964 1.3750 1.5300 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 at 0.7229 -0.9159 -0.0890 -0.6765 1.4492 -0.4620 109.0000 111.2700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 aat -15.7082 109.0000 111.2700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 bb13 0.0 1.3750 1.5300 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 0.0000 0.0 0.6500 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 mbt 0.0 0.0 0.0 1.3950 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 aat 0.0 120.7640 120.0700 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 bb13 0.0 1.4170 1.3850 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 2.1670 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.6282 0.0 0.0000 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0000 3.8762 0.0000 1.4170 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 0.0000 0.0 2.0000 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 -3.0000 108.5000 112.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 aat 0.0 108.5000 112.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 bb13 0.0 1.4350 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 mbt 0.0 0.0 0.0 1.4350 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 aat 0.0 105.0000 108.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 bb13 0.0 1.5300 1.4020 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 at 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 107.0000 117.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 aat -16.2615 107.0000 117.5000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 bb13 0.0 1.1010 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 0.0000 0.0 1.1600 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 118.8000 117.7000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 aat -18.0436 118.8000 117.7000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 bb13 0.0 1.4170 1.2100 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 2.9126 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 117.9400 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 2.1508 117.9400 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 7.2124 0.0 0.0000 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 118.9000 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat -34.9681 118.9000 118.8000 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 aat 0.0 135.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 bb13 0.0 1.5980 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 aat 0.0 135.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 aat 0.0 135.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 bb13 0.0 1.5980 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 aat 0.0 135.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 bb13 0.0 1.5980 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 aat 0.0 135.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 bb13 0.0 1.5980 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 aat 0.0 120.0000 125.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 bb13 0.0 1.0310 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 aat 0.0 120.0000 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 bb13 0.0 1.0310 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 aat 0.0 120.0000 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 bb13 0.0 1.0310 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.5000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 aat 0.0 110.8860 102.5000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 bb13 0.0 1.1010 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat 0.0 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat 0.0 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 107.3650 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 aat 0.0 120.0010 107.3650 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 bb13 0.0 1.4170 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 110.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 aat 0.0 120.0010 110.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 1.8000 0.0 0.5000 0.0 2.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 mbt 0.0000 0.0000 0.0000 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 125.0000 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 aat 0.0 125.0000 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0330 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 aat 0.0 110.0330 135.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 bb13 0.0 1.4300 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat -3.7880 120.0000 110.0330 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3690 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 119.3000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 aat -11.1020 119.3000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 bb13 0.0 1.8000 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.6000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 aat 0.0 109.6000 120.0000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 bb13 0.0 1.7890 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat -19.9340 110.8860 119.3000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat -16.0180 110.8860 102.9000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.1010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.5000 110.8860 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 aat -25.5460 102.5000 110.8860 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 bb13 0.0 1.8000 1.1010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 1.2660 0.0 -0.7740 0.0 0.0380 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt -0.4140 -2.8620 0.0070 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat -9.6280 107.4990 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt -2.3800 2.5290 -0.7300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat -8.8980 117.3170 117.2000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 -0.1510 0.0 0.0100 0.0 -0.1860 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt -3.5150 -2.2980 -1.2770 1.5300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 110.7700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat -27.5060 110.7700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0970 0.0 0.0720 0.0 -0.2580 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 112.6700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0000 112.6700 117.3170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 2.2700 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 5.4770 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 mbt 0.0000 0.9241 -0.5889 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 ebt -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 at -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 aat -10.5093 108.7280 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 bb13 0.0 1.1010 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 mbt 1.2472 0.0000 0.7485 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 ebt -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 at -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 aat -12.1038 111.2700 105.8000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 bb13 0.0 1.5300 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat -14.0484 105.0000 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat -20.2006 110.7700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat -29.0420 112.6700 105.0000 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 110.7000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 aat 0.0 159.0000 110.7000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4783 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 107.4000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 aat 0.0 159.0000 107.4000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 bb13 0.0 1.6400 1.4783 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8995 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 bb13 0.0 1.6400 1.8995 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8634 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 bb13 0.0 1.6400 1.8634 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 -0.2250 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 aat 0.0 110.7000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 aat 0.0 107.4000 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 bb13 0.0 1.4783 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 aat 0.0 114.9060 159.0000 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 bb13 0.0 1.8995 1.6400 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 bb13 0.0 1.8995 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 bb13 0.0 1.8995 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 bb13 0.0 1.8995 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 bb13 0.0 1.8995 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 bb13 0.0 1.8995 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 bb13 0.0 1.4350 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat 0.0 105.0000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 aat 0.0 105.0000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 bb13 0.0 1.4350 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 aat 0.0 105.0000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 bb13 0.0 1.4350 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 aat 0.0 105.0000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 bb13 0.0 1.4350 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 bb13 0.0 1.4350 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 aat 0.0 105.0000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 bb13 0.0 1.4350 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 bb13 0.0 1.4814 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 aat 0.0 110.9900 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 bb13 0.0 1.4814 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 aat 0.0 110.9900 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 bb13 0.0 1.4814 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 aat 0.0 110.9900 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 bb13 0.0 1.4814 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 aat 0.0 110.9900 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 bb13 0.0 1.4814 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 bb13 0.0 1.4814 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 aat 0.0 110.9900 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 bb13 0.0 1.4814 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 bb13 0.0 1.4740 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 aat 0.0 117.3170 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 bb13 0.0 1.4740 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 aat 0.0 117.3170 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 bb13 0.0 1.4740 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 aat 0.0 117.3170 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 bb13 0.0 1.4740 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 aat 0.0 117.3170 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 bb13 0.0 1.4740 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 bb13 0.0 1.4740 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 aat 0.0 117.3170 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 bb13 0.0 1.4740 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat 0.0 110.7700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat 0.0 110.7700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat 0.0 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 bb13 0.0 1.1010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 aat 0.0 110.7700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 bb13 0.0 1.1010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 bb13 0.0 1.5300 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 bb13 0.0 1.5300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 bb13 0.0 1.5010 1.8995 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 aat 0.0 108.4000 105.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 bb13 0.0 1.5010 1.4350 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 aat 0.0 108.4000 110.9900 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 bb13 0.0 1.5010 1.4814 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 aat 0.0 108.4000 117.3170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 bb13 0.0 1.5010 1.4740 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 bb13 0.0 1.5010 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 aat 0.0 108.4000 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 bb13 0.0 1.8634 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 bb13 0.0 1.8634 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 bb13 0.0 1.8634 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 bb13 0.0 1.8634 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 bb13 0.0 1.8634 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 bb13 0.0 1.8634 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 bb13 0.0 1.8634 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 bb13 0.0 1.8634 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 bb13 0.0 1.8634 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 bb13 0.0 1.7890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 aat 0.0 120.0010 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 bb13 0.0 1.7890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 aat 0.0 120.0010 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 bb13 0.0 1.7890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 aat 0.0 120.0010 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 bb13 0.0 1.7890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 bb13 0.0 1.7890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 aat 0.0 120.0010 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 bb13 0.0 1.7890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 aat 0.0 120.0010 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 bb13 0.0 1.7890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 aat 0.0 120.0010 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 bb13 0.0 1.7890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 aat 0.0 120.0010 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 bb13 0.0 1.7890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 bb13 0.0 1.4300 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 aat 0.0 118.8000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 bb13 0.0 1.4300 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 aat 0.0 118.8000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 bb13 0.0 1.4300 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 aat 0.0 118.8000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 bb13 0.0 1.4300 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 bb13 0.0 1.4300 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 aat 0.0 118.8000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 bb13 0.0 1.4300 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 aat 0.0 118.8000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 bb13 0.0 1.4300 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 aat 0.0 118.8000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 bb13 0.0 1.4300 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 aat 0.0 118.8000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 bb13 0.0 1.4300 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 bb13 0.0 1.3950 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 aat 0.0 120.7640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 bb13 0.0 1.3950 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 aat 0.0 120.7640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 bb13 0.0 1.3950 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 aat 0.0 120.7640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 bb13 0.0 1.3950 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 bb13 0.0 1.3950 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 aat 0.0 120.7640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 bb13 0.0 1.3950 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 aat 0.0 120.7640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 bb13 0.0 1.3950 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 aat 0.0 120.7640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 bb13 0.0 1.3950 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 aat 0.0 120.7640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 bb13 0.0 1.3950 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 bb13 0.0 1.4000 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 bb13 0.0 1.4000 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 bb13 0.0 1.4000 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 bb13 0.0 1.4000 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 bb13 0.0 1.4000 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 bb13 0.0 1.4000 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 bb13 0.0 1.4000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 bb13 0.0 1.4000 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 bb13 0.0 1.4000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 0.0 117.9400 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 bb13 0.0 1.0982 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.0 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 0.0 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 aat 0.0 117.9400 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 bb13 0.0 1.0982 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 aat 0.0 117.9400 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 bb13 0.0 1.0982 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 aat 0.0 117.9400 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 bb13 0.0 1.0982 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 bb13 0.0 1.5010 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 aat 0.0 120.0500 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 bb13 0.0 1.5010 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 aat 0.0 120.0500 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 bb13 0.0 1.5010 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 aat 0.0 120.0500 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 bb13 0.0 1.5010 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 bb13 0.0 1.5010 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 0.0 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.0 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 aat 0.0 120.0500 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 aat 0.0 120.0500 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 bb13 0.0 1.5010 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 aat 0.0 120.0500 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 bb13 0.0 1.5010 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 bb13 0.0 1.4890 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 aat 0.0 116.0640 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 bb13 0.0 1.4890 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 aat 0.0 116.0640 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 bb13 0.0 1.4890 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 aat 0.0 116.0640 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 bb13 0.0 1.4890 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 bb13 0.0 1.4890 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 aat 0.0 116.0640 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 bb13 0.0 1.4890 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 aat 0.0 116.0640 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 bb13 0.0 1.4890 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 aat 0.0 116.0640 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 bb13 0.0 1.4890 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat 0.0 118.9000 118.8000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 bb13 0.0 1.4170 1.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat 0.0 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 0.0 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat 0.0 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 0.0 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt -14.2610 -0.5322 -0.4864 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 at -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat -12.5640 110.7700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0316 0.0 -0.1681 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt -14.8790 -3.6581 -0.3138 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 at -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat -16.1640 112.6700 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0514 0.0 -0.1430 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt -17.7870 -7.1877 0.0000 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat -22.0450 112.6700 112.6700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 mbt 0.0000 0.0000 0.0000 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 aat 0.0 120.0500 108.4000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 bb13 0.0 1.4170 1.5300 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 mbt 0.0 0.0 0.0 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 aat 0.0 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 -0.6900 0.0 0.5097 0.0 0.0095 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 mbt 1.1580 3.2697 3.5132 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 ebt 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 1.4170 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 at -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 123.4200 108.1900 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 aat -4.6072 123.4200 108.1900 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 bb13 1.1590 1.4170 0.9494 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 mbt -5.5679 1.4083 0.3010 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 ebt -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 1.4170 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 at 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 aat -5.8888 120.0500 111.0000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 bb13 -3.4826 1.4170 1.1010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 2.3500 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0000 4.8228 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.3598 117.9400 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 -1.7077 1.0982 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 1.5590 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0000 3.9421 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 4.4444 120.0500 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.8743 1.5010 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 3.9661 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0000 -1.1521 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat -4.8141 118.9000 117.9400 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 -6.2741 1.4170 1.0982 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.4072 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0000 9.1792 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat -14.4097 118.9000 120.0500 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 2.5085 1.4170 1.5010 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 8.3667 0.0 1.2000 0.0 0.0000 0.0 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 27.5989 -2.3120 0.0000 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 53.0000 1.4170 1.4170 # (ver=1.0, ref=1) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=7) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=6) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 1.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) + dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) + } # end of dihedral_coeff commands + + + # --------------- Improper Interactions: --------------------- + + + # -- Rules for generating (4-body) "improper" interactions: -- + # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] + + write_once("Data Impropers By Type (cenJsortIKL)") { + @improper:c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 + @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c4,h1,o2,c4,c4,h1,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,c4,h1,n2=,h1,c4,h1,n2= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= + @improper:h1,c4,h1,si4,h1,c4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,c4,h1,h1,h1,c4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,si4,c4,si4,c4,si4,c4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,c4,h1,h1,c4,c4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,h1,h1,h1,si4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,si4,h1,si4,c4,si4,h1,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c4,c4,c4,o2,c4,c4,c4,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,c4,h1,o2,h1,c4,h1,o2 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 + @improper:c4,c4,h1,n2=,c4,c4,h1,n2= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= + @improper:c4,si4,h1,h1,c4,si4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 + @improper:h1,si4,h1,si4,h1,si4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an2=,d*,in2= + @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac3prime,d*,ic3prime + @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,asi4,d*,isi4 + @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ap4=,d*,ip4= + @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime + @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m + @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o + @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2n,d*,io2 + @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ao2,d*,io2 + @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ah1,d*,ih1 + @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2,d*,io2 + @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= + @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 + @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a + @improper:c3a,c3prime,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m + @improper:c3a,o1=,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,io1= @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m + } # end of "Data Impropers By Type" section + + + + # ------- Improper Force Field Parameters: ------- + # For an explanation of these parameters, visit: + # http://lammps.sandia.gov/doc/improper_class2.html + +# Syntax: + # improper_coeff ImproperTypeName ImproperStyle parameters... + + + write_once("In Settings") { + improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 aa -0.1729 -0.1729 -0.1729 112.6700 112.6700 112.6700 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 aa 2.3794 3.0118 2.3794 111.0000 111.0000 107.6600 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 aa 3.9177 2.5926 0.1689 110.7700 111.2700 108.7280 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) + improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 aa 1.7680 1.7680 -2.9470 107.6600 107.4990 107.4990 # (ver=1.0, ref=4) + improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 aa 0.0000 0.0000 2.2050 107.6600 112.0355 112.0355 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 aa 3.3827 3.3827 2.7963 113.1855 112.0977 112.0977 # (ver=1.0, ref=10) + improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 aa -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 aa -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700 # (ver=1.0, ref=1) + improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 aa 1.3465 1.3465 2.0805 113.1855 113.0000 113.0000 # (ver=1.0, ref=10) + improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 aa 0.2738 -0.4825 0.2738 110.7700 110.7700 107.6600 # (ver=1.0, ref=7) + improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 aa 2.0665 2.0665 2.0665 108.6051 108.6051 108.6051 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 aa 4.1996 3.4924 4.1996 112.0893 112.0893 114.2676 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 aa 4.5272 -5.6849 4.5272 113.0000 113.0000 114.2676 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aa -1.8202 2.0403 1.0827 108.4000 111.0000 110.7700 # (ver=1.0, ref=1) + improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 aa -1.7653 0.0 -1.7653 107.8594 107.8594 107.6600 # (ver=1.0, ref=7) + improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 aa 3.4758 0.0 -2.9623 112.0977 113.0000 112.0893 # (ver=1.0, ref=10) + improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 aa -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) + improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 aa 2.4259 2.4259 2.1283 107.6600 108.7280 108.7280 # (ver=1.0, ref=3) + improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 aa 2.7530 1.0910 -1.3060 110.7700 117.3170 107.4990 # (ver=1.0, ref=4) + improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 aa 4.4559 4.6809 4.4559 112.0977 112.0977 108.6051 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 aa 0.0 0.0 1.6082 108.6051 112.0893 112.0893 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 30.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 aa 0.0 0.0 0.0 108.4400 125.5320 121.5420 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 8.0000 -0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 0.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 aa 0.0 0.0 0.0 120.0700 120.0700 121.9556 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 5.3654 0.0 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=10) + improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 6.7090 -0.0 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aa 0.0 0.0 0.0 118.9000 120.0010 120.0010 # (ver=1.0, ref=4) + improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 17.0526 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aa 0.0 0.0 0.0 118.9000 116.0640 116.0640 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 17.0526 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aa 0.0 0.0 0.0 118.9000 120.7640 120.7640 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.9194 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aa 0.0 0.0 0.0 118.9000 118.8000 118.8000 # (ver=1.0, ref=6) + improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 45.0000 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 aa 0.0 0.0 0.0 128.0000 112.8000 112.8000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 13.0421 -0.0 # (ver=1.0, ref=3) + improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aa 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200 # (ver=1.0, ref=3) + improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 38.5581 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 115.7000 115.7000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 4.8912 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aa 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400 # (ver=1.0, ref=1) + improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 46.9264 0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 aa 0.0 0.0 0.0 119.3000 100.3182 118.9855 # (ver=1.0, ref=7) + improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 44.3062 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.5000 117.5000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 36.2612 -0.0 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.7000 117.7000 128.0000 # (ver=1.0, ref=6) + improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 7.8153 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aa 0.0 0.0 0.0 118.9000 120.0500 120.0500 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 7.1794 -0.0 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aa 0.0000 0.0000 0.0000 118.9000 118.9000 118.9000 # (ver=1.0, ref=1) + improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 0.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 30.0000 -0.0 # (ver=1.0, ref=7) + improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) + } # end of improper_coeff commands + + + + + + + # -------------------- Select LAMMPS style(s) ------------------ + + + # LAMMPS supports many different kinds of bonded and non-bonded + # interactions which can be selected at run time. Eventually + # we must inform LAMMPS which of them we will need. We specify + # this in the "In Init" section: + + write_once("In Init") { + units real + atom_style full + bond_style hybrid class2 + # http://lammps.sandia.gov/doc/bond_class2.html + + angle_style hybrid class2 + # http://lammps.sandia.gov/doc/angle_class2.html + + dihedral_style hybrid class2 + # http://lammps.sandia.gov/doc/dihedral_class2.html + + improper_style hybrid class2 + # http://lammps.sandia.gov/doc/improper_class2.html + + pair_style hybrid lj/class2/coul/long 10.0 + # http://lammps.sandia.gov/doc/pair_class2.html + + pair_modify mix sixthpower tail yes + special_bonds lj/coul 0.0 0.0 1.0 dihedral yes + kspace_style pppm 0.0001 + } #end of init parameters + +} # COMPASS + +# +# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED: +# special_bonds lj/coul 0.0 0.0 1.0 dihedral yes +# (See http://lammps.sandia.gov/doc/special_bonds.html for details) + + + + +# ---- templates from the original .frc file used for atom type selection: --- +# +# type: ? +# template: (>*) +# end_type +# +# type: ar +# template: (>Ar) +# end_type +# +# type:c1o +# template: [>C[~O]] +# end_type +# +# type:c2= +# template: [>C[~*][~*]] +# end_type +# +# type:c3' +# template: (>C (~O) (~*) (~*)) +# atom_test:1 +# hybridization:sp2 +# end_test +# atom_test:3 +# allowed_elements: C, H +# end_test +# atom_test:4 +# allowed_elements: O, N +# end_test +# end_type +# +# type:c3a +# template:(>C(~*)(~*)(~*)) +# atom_test:1 +# hybridization: SP2 +# aromaticity:AROMATIC +# end_test +# end_type +# +# type:c3a +# template: [>C(-*)(:*)(:*)] +# atom_test:1 +# hybridization:SP2 +# aromaticity:NON_AROMATIC +# end_test +# end_type +# +# type:c4 +# template: (>C(-*)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type:c41o +# template: [>C(-O(-*))(-H)(-H)(-H)] +# atom_test:1 +# hybridization:SP3 +# end_test +# atom_test:3 +# allowed_elements:C,H +# end_type +# +# type: c43 +# template: (>C(-H)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# atom_test:3 +# disallowed_elements:H +# atom_test:4 +# disallowed_elements:H +# atom_test:5 +# disallowed_elements:H +# end_test +# end_type +# +# type:c43o +# template: [>C(-O(-H))(-H)(-C)(-C)] +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: c44 +# template: (>C(-*)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# atom_test:2 +# disallowed_elements:H +# atom_test:3 +# disallowed_elements:H +# atom_test:4 +# disallowed_elements:H +# atom_test:5 +# disallowed_elements:H +# end_test +# end_type +# +# type: c4o +# template: (>C(-O)(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: c4z +# template: (>C(-N(~N(~N)))(-*)(-*)(-*)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type:h1 +# template: (>H (-*) ) +# atom_test:2 +# allowed_elements:C,Si +# end_test +# end_type +# +# type:h1h +# template: [>H[-H]] +# end_type +# +# type:h1o +# template: (>H(-*)) +# atom_test:2 +# allowed_elements:O,N,F +# end_test +# end_type +# +# type: he +# template: (>He) +# end_type +# +# type: kr +# template: (>Kr) +# end_type +# +# type:n1n +# template: [>N[~N]] +# end_type +# +# type:n1o +# template: [>N[~O]] +# end_type +# +# type:n1z +# template: [>N[~N[~N(~*)]]] +# end_type +# +# type:n2= +# template: [>N(~*)(~*)] +# end_type +# +# type:n2o +# template: [>N[~O][~O]] +# end_type +# +# type:n2t +# template: [>N[~N][~N(~*)]] +# end_type +# +# type:n2z +# template: (>N[~N[~N]](~*)) +# end_type +# +# type: n3m +# template: (>N(-C[=O])(-C)(-C)) +# atom_test:1 +# hybridization:SP3 +# end_test +# end_type +# +# type: n3o +# template: (>N[~O][~O](~O(~C))) +# end_type +# +# type: ne +# template: (>Ne) +# end_type +# +# type:o1= +# template: (>O(~*)) +# atom_test:2 +# allowed_elements:N,S,C +# end_test +# end_type +# +# type:o1=* +# template: [>O[~C[~O]]] +# end_type +# +# type:o12 +# template: [>O[~N[~O](~*)]] +# end_type +# +# type:o1c +# template: [>O[~C]] +# end_type +# +# type:o1n +# template: [>O[~N]] +# end_type +# +# type:o1o +# template: [>O[~O]] +# end_type +# +# type:o2 +# template: [>O(~*)(~*)] +# end_type +# +# type:o2e +# template: [>O(-C)(-C)] +# atom_test: 1 +# aromaticity:NON_AROMATIC +# end_test +# end_type +# +# type:o2h +# template: (>O[-H](~*)) +# end_type +# +# type:o2n +# template: (>O[~N[~O][~O]](~C)) +# end_type +# +# type:o2s +# template: (>O[~C[~O](~*)](~C)) +# end_type +# +# type: o2z +# template: (>O(-Si)(-*) ) +# atom_test: 3 +# allowed_elements: Si, H +# end_test +# end_type +# +# type: p4= +# template: (>P(~*)(~*)(~*)(~*)) +# end_type +# +# type:s1= +# template: [>S[~C[~S]]] +# end_type +# +# type:s2= +# template: [>S[~O][~O]] +# end_type +# +# type: si4 +# template: (>Si(-*)(-*)(-*)(-*)) +# end_type +# +# type: si4c +# template: (>Si(-O)(-*)(-*)(-*)) +# atom_test: 3 +# allowed_elements: O, C +# end_test +# atom_test: 4 +# allowed_elements: O, C +# end_test +# atom_test: 5 +# allowed_elements: O, C +# end_test +# end_type +# +# type: xe +# template: (>Xe) +# end_type +# +# precedence: +# (? +# (ar) +# (c1o) +# (c2=) +# (c3a) (c3') +# (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) +# (h1) (h1h) (h1o) +# (he) +# (kr) +# (n1n) (n1o) (n1z) +# (n2= (n2o) (n2t) (n2z) ) +# (n3m) (n3o) +# (ne) +# (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) +# (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) +# (p4=) +# (s1=) +# (s2=) +# (si4 (si4c) ) +# (xe) +# ) +# end_precedence +# +# +# + + + + +# ---- references from the original .frc file: ---- + +# reference 1 +# @Author tester +# @Date 01-Jun-09 +# Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) +# This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that +# we neither support this version, nor make any warranty as to the correctness of the parameters. +# We have checked the numbers against the literature, but of course there may still be errors, +# including errors of interpretation. Also, the current version of COMPASS may well be different +# that that originally published. +# If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com + +# reference 2 +# @Author tester +# @Date 27-Jun-09 +# Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) + +# reference 3 +# @Author tester +# @Date 27-Jun-09 +# Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) + +# reference 4 +# @Author tester +# @Date 30-Jun-09 +# Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) + +# reference 5 +# @Author tester +# @Date 28-Jun-09 +# Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) + +# reference 6 +# @Author tester +# @Date 29-Jun-09 +# Parameters for nitrate esters from JPC B104, 2477-89 (2000) + +# reference 7 +# @Author tester +# @Date 30-Jun-09 +# Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) + +# reference 8 +# @Author tester +# @Date 30-Jun-09 +# Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) + +# reference 9 +# @Author tester +# @Date 30-Jun-09 +# Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) + +# reference 10 +# @Author tester +# @Date 02-Jul-09 +# Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) + + + + + +# ---- additional warnings: ---- +# WARNING: Undefined bond length (r0) in angle: h1 o2z si4 +# WARNING: Undefined bond length (r0) in angle: c4 n3 p4= +# WARNING: Undefined bond length (r0) in angle: h1 n3 p4= +# WARNING: Undefined bond length (r0) in angle: c4 o2 p4= +# WARNING: Undefined bond length (r0) in angle: h1 o2 p4= +# WARNING: Undefined bond length (r0) in angle: c3a p4= n3 +# WARNING: Undefined bond length (r0) in angle: h1 p4= n3 +# WARNING: Undefined bond length (r0) in angle: n2= p4= n3 +# WARNING: Undefined bond length (r0) in angle: n3 p4= n3 +# WARNING: Undefined bond length (r0) in angle: n3 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 si4 o2z h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 o2z +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= n2= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= h1 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= n2= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= o2 +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X o2 p4= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X c3a n2= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X n3 p4= X +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 c4 n3o o1= +# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c3prime n3m c3prime o1 +# WARNING: Undefined rest angle (theta0) in improper: c3a o1= c3prime n3m +# WARNING: Undefined rest angle (theta0) in improper: c3a c3prime c3prime n3m diff --git a/tools/moltemplate/moltemplate/force_fields/amber/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/amber/README.txt rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh index 07442dbee7982b2df79235d543e8591583eb7298..98a77f3b05515d8fca2a695b496057c26d2f699d 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm2lt.sh +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh @@ -61,6 +61,8 @@ echo "$MOLTEMPLATE_USAGE_MSG" echo "####################################################################" echo "# Moltemplate can not assign atom charge. You must assign atomic" echo "# charges yourself. (Moltemplate is only a simple text manipulation tool.)" +echo "# You can do this afterwards using commands like \"set atom 70 charge -0.212\"" +echo "# For details, see http://lammps.sandia.gov/doc/set.html)" echo "####################################################################" echo "" echo "" diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py similarity index 91% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py index dd465841b5cf16f0c49014a603d097bf85b67910..447857675eff46731e9bcdd08780090072b59e49 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_angle_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_angle_to_lt.py @@ -22,7 +22,11 @@ for i in range(0, len(lines_gaff)): keq = tokens[0] req = tokens[1] comments=' '.join(tokens[2:]) - sys.stdout.write(' angle_coeff '+angletype+' '+angle_style_name+' '+keq+' '+req+' # '+comments+'\n') + sys.stdout.write(' angle_coeff '+angletype+' '+angle_style_name+' '+keq+' '+req) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of angle_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py similarity index 90% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py index bacc49b7d51dc74e0cf912f290d462aded2b21bc..abfde23dab181e147ac2a17a3b2cb110fe7e0edb 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_bond_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py @@ -21,7 +21,11 @@ for i in range(0, len(lines_gaff)): keq = tokens[0] req = tokens[1] comments=' '.join(tokens[2:]) - sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req+' # '+comments+'\n') + sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of bond_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py similarity index 97% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py index 8729e3fe166d87c90efc997304602f3d7ff3c5b5..f4f8e3a645a59fb494e350c07e12d25b898a73b4 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_dihedral_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py @@ -29,7 +29,9 @@ for i in range(0, len(lines_gaff)): # ...I THINK (?). (Very confusing. See documentation below...) dn = float(tokens[2]) n = int(float(tokens[3])) - comments=' # '+(' '.join(tokens[4:])) + comments=' '.join(tokens[4:]) + if len(comments.strip()) > 0: + comments = ' # ' + comments in_dihedral_coeffs.append([dihedraltype, Kn, n, dn, comments]) #print(Kn, n, dn) diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py similarity index 94% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py index 8cc7828f89d9d3640440b6fb4055fe09f05935d0..ebf48d4f1892cad4b59a2ea02a1edf2fd5b66a89 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_improper_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py @@ -31,11 +31,13 @@ for i in range(0, len(lines_gaff)): dn = float(tokens[1]) n = int(float(tokens[2])) comments=' '.join(tokens[3:]) + if len(comments.strip()) > 0: + comments = ' # ' + comments if (dn < 0.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+' # '+comments+'\n') + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+comments+'\n') elif (179.999 < abs(dn) < 180.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+' # '+comments+'\n') + sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+comments+'\n') else: sys.stderr.write('Error: Illegal bondImproper parameters:\n' ' As of 2013-8-03, LAMMPS doens hot have an improper style\n' diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_mass_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_mass_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py diff --git a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py similarity index 93% rename from tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py index 61e7672589d640eaee481f568d1ef1414e47632b..f24a92b78fc2f3030e337df04b6997c17be9bbda 100755 --- a/tools/moltemplate/moltemplate/force_fields/amber/amberparm_pair_to_lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py @@ -51,7 +51,11 @@ for i in range(0, len(lines_gaff)): sig=str(float(tokens[1])*2.0*pow(2.0, (-1.0/6.0))) eps=tokens[2] comments=' '.join(tokens[3:]) - sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n') + sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig) + if len(comments.strip()) > 0: + sys.stdout.write(' # '+comments) + sys.stdout.write('\n') + sys.stdout.write(' } # (end of pair_coeffs)\n') sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..f110af62ca6f24f82e460d2c739df6e49116d822 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt @@ -0,0 +1,18 @@ +This directory contains a tool "emcprm2lt.py" which +converts ".PRM" files containing lists of force-field parameters +in EMC format into MOLTEMPLATE files in ".LT" format. +(Several force fields including MARTINI and SDK have been + converted into moltemplate format using this tool.) + +---- Credit: ---- + +The "emcprm2lt.py" converter was writtin by David Stelter. +The .PRM files we use were written by Pieter J. in 't Veld. + +---- Citation request: ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py similarity index 99% rename from tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py index c924ce64e0d8e5ea85700528254cab23577d332f..7e97770899c84c9044b2f64e33582798ef255d72 100755 --- a/tools/moltemplate/moltemplate/force_fields/sdk/emcprm2lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py @@ -508,7 +508,7 @@ for i in range(len(nonbond)): atom1name = None atom2name = None stylename = pstyle - if pstyle == 'lj/sdk' or 'lj/sdk/coul/long': + if pstyle == 'lj/sdk' or pstyle == 'lj/sdk/coul/long': stylename = 'lj%s_%s' % (nonbond[i][4], nonbond[i][5]) # Cross Terms + Diagonal, normal for j in range(len(equiv)): diff --git a/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py new file mode 100755 index 0000000000000000000000000000000000000000..7c4c6abc7331a5bb95792375f38f83edb0c24ef4 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py @@ -0,0 +1,4536 @@ +#! /usr/bin/env python +# Author: Andrew Jewett (jewett.aij at g mail) +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2017, California Institute of Technology +# All rights reserved. + +""" +This standalone python script can be used to convert force-field data +in FRC files (a.k.a. "MSI", "Accelrys", "BIOSYM", "DISCOVERY" files) +...into MOLTEMPLATE/LAMMPS compatible format (.LT files). + +Once converted into moltemplate (.LT) format, users can use these files with +MOLTEMPLATE to prepare LAMMPS simulations of molecules using these force fields +(without needing any additional software such as msi2lmp). + +There are several examples of MSI files in the "tools/msi2lmp/frc_files/" +directory which is distributed with LAMMPS. + +Limitations: + +Currently (2017-10) this script ignores the "template" information in .FRC files. +When defining a new type of molecule, the user must carefully choose the +complete atom type for each type of atom in the molecule. In other words, +MOLTEMPLATE will not attempt to determine (from local context) whether +a carbon atom somewhere in your molecule happens to be an SP3 carbon +(ie. "c4" in the COMPASS force-field), or an aromatic carbon ("c3a"), +or something else (for example). This information is typically contained +in the "templates" section of these files, and this script currently ignores +that information. Instead, the user must determine which type of carbon atom +it is manually, for all of the carbon atoms in that kind of molecule. +(This only needs to be done once per molecule definition. + Once a type of molecule is defined, it can be copied indefinitely.) + +""" + + +__author__ = 'Andrew Jewett' +__version__ = '0.2.1' +__date__ = '2017-10-15' + + +import sys +import os + +from collections import defaultdict, OrderedDict +from operator import itemgetter + + +g_program_name = __file__.split('/')[-1] + + +doc_msg = \ + "Typical Usage:\n\n" + \ + " " + g_program_name + " -name COMPASS < compass_published.frc > compass.lt\n\n" + \ + " where \"compass_published.frc\" is a force-field file in MSI format.\n" + \ + " \"comass.lt\" is the corresponding file converted to moltemplate format\n" + \ + " and \"COMPASS\" is the name that future moltemplate users will use to refer\n" + \ + " to this force-field (optional).\n" + \ + "Optional Arguments\n" + \ + " -name FORCEFIELDNAME # Give the force-field a name\n" + \ + " -file FILE_NAME # Read force field parameters from a file\n" + \ + " -url URL # Read force field parameters from a file on the web\n" + \ + " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ + " Sometimes an FRC file contains multiple versions. In that case,\n"+\ + " you can select between them using these optional arguments:\n"+\ + " -pair-style \"PAIRSTYLE ARGS\" # LAMMPS pair style and cutoff arg(s)\n" + \ + " -bond-style BONDSTYLE # desired LAMMPS bond style (default: \"class2\")\n" + \ + " -angle-style ANGLESTYLE # desired LAMMPS angle style\n" + \ + " -dihedral-style DIHEDRALSTYLE # desired LAMMPS dihedral style\n" + \ + " -improper-style IMPROPERSTYLE # desired LAMMPS improper style\n" + \ + " -hbond-style \"HBONDTYLE ARGS\" # LAMMPS hydrogen-bond style and args\n" + + +# " -auto # Consider auto_equivalences in the .frc file \n"+\ + + + +class InputError(Exception): + """ A generic exception object containing a string for error reporting. + (Raising this exception implies that the caller has provided + a faulty input file or argument.) + + """ + + def __init__(self, err_msg): + self.err_msg = err_msg + + def __str__(self): + return self.err_msg + + def __repr__(self): + return str(self) + +# It seems like there are no ordered sets in python, (a set that remembers the +# order that you added elements), so I built one by wrapping OrderedDict() + +class MyOrderedSet(object): + def __init__(self, l): + self.d = OrderedDict() + for x in l: + self.d[x] = True + def __add__(self, x): + self.d[x] = True + def __delitem__(self, x): + del self.d[x] + def __contains__(self, x): + return x in self.d + def __iter__(self): + self.p = iter(self.d) + return self + def __next__(self): + return next(self.p) + # the following wrappers might be necessary for python2/3 compatibility: + def add(self, x): + self.__add__(x) + def del_item(self, x): + self.__del_item__(x) + def iter(self): + return self.__iter__() + def next(self): + return self.__next__() + # no need to bother with set unions and intersections + + +def NSplitQuotedString(string, + nmax, + quotes, + delimiters=' \t\r\f\n', + escape='\\', + comment_char='#'): + """ + Split a quoted & commented string into at most "nmax" tokens (if nmax>0), + where each token is separated by one or more delimeter characters + in the origingal string, and quoted substrings are not split, + This function returns a list of strings. Once the string is split Nmax + times, any remaining text will be appended to the last entry of the list. + Comments are stripped from the string before splitting begins. + """ + tokens = [] + token = '' + reading_token = True + escaped_state = False + quote_state = None + for c in string: + + if (c in comment_char) and (not escaped_state) and (quote_state == None): + if len(token) > 0: + tokens.append(token) + return tokens + + elif (c in delimiters) and (not escaped_state) and (quote_state == None): + if reading_token: + if (nmax == 0) or (len(tokens) < nmax-1): + if len(token) > 0: + tokens.append(token) + token = '' + reading_token = False + else: + token += c + elif c in escape: + if escaped_state: + token += c + reading_token = True + escaped_state = False + else: + escaped_state = True + # and leave c (the '\' character) out of token + elif (c in quotes) and (not escaped_state): + if (quote_state != None): + if (c == quote_state): + quote_state = None + else: + quote_state = c + token += c + reading_token = True + else: + if (c == 'n') and (escaped_state == True): + c = '\n' + elif (c == 't') and (escaped_state == True): + c = '\t' + elif (c == 'r') and (escaped_state == True): + c = '\r' + elif (c == 'f') and (escaped_state == True): + c = '\f' + token += c + reading_token = True + escaped_state = False + + if len(token) > 0: + tokens.append(token) + return tokens + + + + +def SplitQuotedString(string, + quotes='\'\"', + delimiters=' \t\r\f\n', + escape='\\', + comment_char='#'): + + return NSplitQuotedString(string, + 0, + quotes, + delimiters, + escape, + comment_char) + + + + +def RemoveOuterQuotes(text, quotes='\"\''): + if ((len(text) >= 2) and (text[0] in quotes) and (text[-1] == text[0])): + return text[1:-1] + else: + return text + + +def SortByEnds(l_orig): + """ + Convenient to have a one-line macro for swapping list order if first>last + """ + l = [x for x in l_orig] + if l[0] > l[-1]: + l.reverse() + return l + + + +#def Repl(tokens, a, b): +# return [(b if x==a else x) for x in tokens] + +def DecodeAName(s): + if s.find('auto') == 0: + s = s[4:] + if s == 'X': # special case: deal with strings like 'X' + return '*' + return s + + +def EncodeAName(s): + """ + Handle * characters in MSI atom names + """ + + if s.find('auto') == 0: + s = s[4:] + # If the atom name begins with *, then it is a wildcard + if s[:1] == '*': # special case: deal with strings like *7 + return 'X' # These have special meaning. Throw away the integer. + # (and replace the * with an X) + + # If the * character occurs later on in the atom name, then it is actually + # part of the atom's name. (MSI force fields use many strange characters in + # atom names.) Here we change the * to \* to prevent the atom name from + # being interpreted as a wild card in the rules for generating bonds, + # angles, dihedrals, and impropers. + + return s.replace('*','star').replace('\'','prime').replace('"','dblpr') + # '*' is reserved for wildcards in moltemplate + # 'star' is a string that is unused in any + # of the force fields I have seen so far. + # Similarly quote characters (' and ") confuse + # moltemplate, so we replace them with something else. + + # The following approach doesn't work (mistakenly thinks '\*' = wildcard) + #return s.replace('*','\\*') # this prevents ttree_lex.MatchesAll() + # # from interpreting the '*' as a wildcard + + +def DetermineAutoPriority(anames): + """ + Given a list of atom names (including wildcards), generate a number + indicating the priority the interaction between these atoms should have: + Scan through list of strings anames, looking for patterns of the form + *n + where n is an integer. + Make sure this pattern only appears once and return n to the caller. + (These patterns are used by MSI software when using "auto_equivalences" + to look up force field parameters for bonded interactions. + The higher the integer, the lower the priority. + For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + Ordinary wildcards ('*' characters not followed by integers) have the + lowest possible priority. (Each time a '*' string appears in the + list of arguments, the priority value increases by HUGE_VAL.) + """ + + # This is terrible code. + + n = -1.0 + num_blank_wildcards = 0 + for a in anames: + # Sometimes the first atom name contains the prefix 'auto'. Remove this + if a.find('auto') == 0: + a = a[4:] + if a[:1] == '*': + #if a[:1] == 'X': + if len(a) > 1: + if n == -1.0: + n = float(a[1:]) + elif n != float(a[1:]): + # Make sure if present, the number appears only once in the list of atom names + raise InputError('Error: Inconsistent priority integers in the following interaction:\n' + ' ' + ' '.join(anames) + '\n') + else: + num_blank_wildcards += 1 + + # A "blank" wildcard (not followed by a number eg '*') has a very low priority + # Give it a high number, because this corresponds to low priority. Very confusing + # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + HUGE_VAL = 1.0e5 + return n + num_blank_wildcards*HUGE_VAL + + + + +#def DeterminePriority(is_auto, +# anames, +# version): +# """ +# Determine the priority of an interaction from +# 1) whether or not it is an "auto" interaction +# 2) what is the force-field "version" (a number) +# 3) what are the names of the atoms (for auto_equivalences only, +# some atom "names" are wildcards followed by integers. use the integer) +# """ +# +# if is_auto: +# n = DetermineAutoPriority(anames) +# return (is_auto, n) +# else: +# return (is_auto, -version) + + +def DetermineNumericPriority(is_auto, + anames, + version): + """ + Determine the priority of an interaction from + 2) what is the force-field "version" (a number) + 3) what are the names of the atoms (for auto_equivalences only, + some atom "names" are wildcards followed by integers. use the integer) + """ + + if is_auto: + n = DetermineAutoPriority(anames) + return n # low priority integers <--> high priority () + else: + return -float(version) # later version numbers <--> higher priority + # (multiplying by -1 compensates for this) + # Note: this means auto interactions always have + # lower priority because their numeric priority + # will be a positive number. Otherwise the + # numeric priority will be a negative number + # (...corresponding to a higher priority + # I don't like this complicated priority system + # but I didn't invent it. It's not my fault.) + + +def IsAutoAtom(atom_name): + return atom_name[-1:] == '_' + + +#def PossibleAutoAtom(atom_name): +# """ Auto-equivalences are alternate atom names used in "auto" +# interactions. (These are low priority interactions used as a +# last resort when the interaction parameters could not be located +# by any other means). Each atom is given an alternate name which +# is used in this kind of interaction. These names typically end +# '_' followed by an optional integer. Example "auto" atom names +# are 'c3m_' and 'c=_3'. Unfortunately some ordinary atom names +# also end in an integer preceeded by a _ character. But they +# never end in a '_' character. Here we check for both.""" +# +# i = atom_name.rfind('_') +# if (i == -1) or str.isdigit(atom_name[i:]): +# return True +# return False + + + +def IsAutoInteraction(interaction_name): + return interaction_name.find('auto') == 0 + + +#def IsAutoInteraction(interaction_name): +# anames = ExtractAtomNames(interaction_name) +# for a in anames: +# if IsAutoAtom(a): +# return True +# if not PossibleAutoAtom(a): +# return False +# return True + + + + +def EncodeInteractionName(anames, + is_auto = False): + if is_auto == False: + is_auto = False + # Is the line containing anames from an "_auto" section of + # the FRC file? (I am trying to infer this from whether or + # not any of the atom names are followed by the '_' character.) + for s in anames: + if IsAutoAtom(s): + is_auto = True + if is_auto: + priority = DetermineAutoPriority(anames) + # (If an atom name is a wildcard '*' followed by + # an integer, DetermineAutoPriority() will return + # that integer. Otherwise it will return '') + #return str(priority)+'auto'+','.join(anames) + return 'auto'+','.join(anames) + + return ','.join(anames) + + + +def ExtractANames(interaction_name): + if IsAutoInteraction(interaction_name): + return interaction_name[4:].split(',') + return interaction_name.split(',') + + + +def OOPImproperNameSort(aorig): + assert(len(aorig) == 4) + atom_names = map(EncodeAName, aorig) + if atom_names[0] < atom_names[3]: + return (atom_names, [0,1,2,3]) + else: + return ([atom_names[3], + atom_names[1], + atom_names[2], + atom_names[0]], + [3,1,2,0]) + + +def Class2ImproperNameSort(aorig): + """ + This function takes a list of 4 strings as an argument representing 4 atom + names for atoms participating in an "improper" ("wilson-out-of-plane") + interaction. This function assumes the second atom is the central ("hub") + atom in the interaction, and it sorts the remaining atoms names. + This function also replaces any occurence of \"*\" with \"X\". + The new list is returned to the caller, along with the permutation. + """ + assert(len(aorig) == 4) + atom_names = [a for a in map(EncodeAName, aorig)] + z = [x for x in zip([atom_names[0], atom_names[2], atom_names[3]], + [0,2,3])] + z.sort() + l = [z[0][0], atom_names[1], z[1][0], z[2][0]] + p = [z[0][1], 1, z[1][1], z[2][1]] + return (l, p) + + + +def Parity(p): + """ compute the parity of a permutation + (credit: "Weeble") + """ + permutation = list(p) + length = len(permutation) + elements_seen = [False] * length + cycles = 0 + for index, already_seen in enumerate(elements_seen): + if already_seen: + continue + cycles += 1 + current = index + while not elements_seen[current]: + elements_seen[current] = True + current = permutation[current] + return (length-cycles) % 2 == 0 + + + +def ImCrossTermID(atom_names): + """ + # From a list of 4 atom names, corresponding two a pair + # of angles between atoms# 3,2,1 and 3,2,4, + # and replaces the list of atoms with a canonical tuple + # which eliminates order ambiguity. + # If you swap the first and last atom (#1 and #4), then + # the -pair- of angles is the same. Hence if atom #1 + # has a name which is lexicographically less than atom #4, + # swap atoms 1 and 4. + """ + if atom_names[0] <= atom_names[3]: + return (atom_names[0]+','+atom_names[1]+','+ + atom_names[2]+','+atom_names[3]) + else: + return (atom_names[3]+','+atom_names[1]+','+ + atom_names[2]+','+atom_names[0]) + + + + +def AtomsMatchPattern(anames, pattern): + """ + Check whether the list of atom names "anames" matches "pattern" + (Both arguments are lists of strings, but some of the strings + in pattern may contain wildcard characters followed by + "priority" numbers. Matches with lower priority numbers are + given preference whenever multiple distinct matches are found. + (Note: This function does not check patterns in reverse order.) + """ + #sys.stderr.write('DEBUG: checking whether '+str(anames)+' matches '+str(pattern)+'\n') + assert(len(anames) == len(pattern)) + matched = True + for d in range(0, len(pattern)): + if (pattern[d] == anames[d]) or (pattern[d][0] == '*'): + if pattern[d][0] == '*': + priority = int(pattern[d][1:]) + else: + priority = 0 + else: + matched = False + if matched: + #sys.stderr.write('DEBUG: '+str(anames)+' matches '+str(pattern)+'\n') + return priority + else: + return None + + +def LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto): + """ + Try to find bond parameters between atoms whose original + atom names (without equivalences) are a1 and a2. + Then return both the equilibrium bond length for that bond, + as well as the equivalent atom names used to lookup that bond. + (These could be stored in either atom2equiv_bond or atom2auto_bond.) + If a match was not found, return None. + """ + return_val = None + anames = (atom2equiv_bond[a1], atom2equiv_bond[a2]) + bond_name = EncodeInteractionName(SortByEnds(anames)) + if bond_name in bond2r0: + return_val = (bond2r0[bond_name], + [anames[0], anames[1]], + False) + # If no bond between these atoms is defined, + # check the bonds in the _auto section(s) + # This is a lot messier. + elif ((a1 in atom2auto_bond) and (a2 in atom2auto_bond)): + anames = [atom2auto_bond[a1], atom2auto_bond[a2]] + # Because _auto interactions can contain wildcards, + # there can be multiple entries in bond2r0_auto[] + # for the same list of atom names, and we have to + # consider all of them, and pick the one with the + # most priority (ie. whose priority number is lowest). + # (Note: The MSI file format uses low priority numbers + # to indicate high priority. Somewhat confusing. + # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) + HUGE_VAL = 2000000000 + best_priority = HUGE_VAL + pattern = ['',''] + for (pattern[0],pattern[1]), r0 in bond2r0_auto.items(): + priority = AtomsMatchPattern(anames, pattern) + if (priority != None) and (priority < best_priority): + best_priority = priority + return_val = (r0, anames, True) + # try again with the atom type names in reverse order + priority = AtomsMatchPattern([anames[1],anames[0]], pattern) + if ((priority != None) and + (priority < best_priority)): #(note: low priority numbers = high priority) + best_priority = priority + return_val = (r0, anames, True) + #if return_val != None: + # sys.stderr.write('DEBUG: For atoms '+str((a1,a2))+' ... bond_length, batom_names = '+str(return_val)+'\n') + return return_val + + + + + + + + +def LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + atom2auto_angle, + angle2theta0_auto_or): + """ + Try to find angle parameters between atoms whose original atom + names (without equivalences) are a1, a2, and a3. Then return + both the equilibrium rest angle for that 3body interaction + as well as the equivalent atom names used to look it up. (These + could be stored in either atom2equiv_angle or atom2auto_angle.) + If a match was not found, return None. + """ + return_val = None + anames = (atom2equiv_angle[a1], atom2equiv_angle[a2], atom2equiv_angle[a3]) + angle_name = EncodeInteractionName(SortByEnds(anames)) + if angle_name in angle2theta0_or: + return_val = (angle2theta0_or[angle_name], + [anames[0], anames[1], anames[2]], + False) + + # If no angle between these atoms is defined, + # check the angles in the _auto section(s) + # This is a lot messier. + elif ((a1 in atom2auto_angle[0]) and + (a2 in atom2auto_angle[1]) and + (a3 in atom2auto_angle[2])): + + anames = [atom2auto_angle[0][a1], + atom2auto_angle[1][a2], + atom2auto_angle[2][a3]] + #sys.stderr.write('DEBUG: LookupBondAngle(): a1,a2,a3=('+ + # a1+','+a2+','+a3+'), anames='+str(anames)+'\n') + + # Because _auto interactions can contain wildcards, + # there can be multiple entries in angle2theta0_auto_or[] + # for the same list of atom names, and we have to + # consider all of them, and pick the one with the + # most priority (ie. whose priority number is lowest). + # (Note: The MSI file format uses low priority numbers + # to indicate high priority. Somewhat confusing.) + HUGE_VAL = 2000000000 + best_priority = HUGE_VAL # (ie. low priority) + pattern = ['','',''] + for (pattern[0],pattern[1],pattern[2]), theta0 in angle2theta0_auto_or.items(): + priority = AtomsMatchPattern(anames, pattern) + if ((priority != None) and + (priority < best_priority)): #(note: low priority numbers = high priority) + best_priority = priority + return_val = (theta0, anames, True) + # try again with the atom type names in reverse order + priority = AtomsMatchPattern([anames[2],anames[1],anames[0]], pattern) + if (priority != None) and (priority < best_priority): + best_priority = priority + return_val = (theta0, anames, True) + #if return_val != None: + # sys.stderr.write('DEBUG: For atoms '+str((a1,a2,a3))+' ... rest_angle, anames = '+str(return_val)+'\n') + return return_val + + + + + + + + +def Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper): + """ + This function reads a list of lines containing "equivalences" and + "auto_equivalences" from an MSI-formatted .FRC file. + Then, for each atom type, it generates a long string which includes the + original atom type name as well as all of the equivalences it belongs to. + Later on, when it is time to generate angles, dihedrals, or impropers, + moltemplate will search for patterns contained in these strings to decide + which type of interaction to generate. + This function returns a dictionary that converts the original atom type name + into these strings. + """ + for line in lines_equivalences: + #tokens = SplitQuotedString(line.strip(), + # comment_char='!>') + + # skip past both '!' and '>' characters + ic1 = line.find('!') + ic = ic1 + ic2 = line.find('>') + if ic2 != -1 and ic2 < ic1: + ic = ic2 + if ic != -1: + line = line[:ic] + else: + line = line.rstrip('\n') + tokens = line.strip().split() + #sys.stderr.write('DEBUG Equivalences2ffids():\n' + # ' tokens = '+str(tokens)+'\n') + atype = EncodeAName(tokens[2]) + atom2equiv_pair[atype] = EncodeAName(tokens[3]) + atom2equiv_bond[atype] = EncodeAName(tokens[4]) + atom2equiv_angle[atype] = EncodeAName(tokens[5]) + atom2equiv_dihedral[atype] = EncodeAName(tokens[6]) + atom2equiv_improper[atype] = EncodeAName(tokens[7]) + + atom2ffid = OrderedDict() + for atom in atom_types: + atom2ffid[atom] = (atom + + ',p'+atom2equiv_pair.get(atom,'') + + ',b'+atom2equiv_bond.get(atom,'') + + ',a'+atom2equiv_angle.get(atom,'') + + ',d'+atom2equiv_dihedral.get(atom,'') + + ',i'+atom2equiv_improper.get(atom,'')) + return atom2ffid + + + + + + +def AutoEquivalences2ffids(lines_equivalences, + lines_auto_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper, + atom2auto_pair, + atom2auto_bondincr, + atom2auto_bond, + atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_dihedralend, + atom2auto_dihedralcenter, + atom2auto_improperend, + atom2auto_impropercenter): + """ + This function is a variant of Equivalences2ffids() which also considers + "auto_equivalences". + This function returns a dictionary that converts the original atom type name + into a string that includes that atom's "equivalences", + as well as its "auto_equivalences". + moltemplate will search for patterns contained in these strings to decide + which type of interaction to generate. + """ + Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper) + + # ------ The following lines are for processing "auto_equivalences" ----- + # + # What is the difference between "equivalences" and "auto_equivalences"? + # + # equivalences: + # Here is an excerpt from the Discover manual describing "equivalences": + # "Chemically distinct atoms often differ in some, but not all, + # of their forcefield parameters. For example, the bond parameters + # for the C-C bonds in ethene and in benzene are quite different, + # but the nonbond parameters for the carbon atoms are essentially + # the same. Rather than duplicating the nonbond parameters in the + # forcefield parameter file, the Discover program uses atom type + # equivalences to simplify the problem. In the example, the phenyl + # carbon atom type is equivalent to the pure sp2 carbons of ethene + # insofar as the nonbond parameters are concerned. The Discover + # program recognizes five types of equivalences for each atom + # type: nonbond, bond, angle, torsion, and out-of-plane. + # Cross terms such as bond-bond terms have the same equivalences + # (insofar as atom types are concerned) as the diagonal term of + # the topology of all the atoms defining the internal coordinates. + # For the bond-bond term, this means that the atom type + # equivalences for angles would be used + # + # auto_equivalences: + # Are similar to equivalences, but apparently with lower priority. + # In addition, it seems that, when looking up some of the class2 terms + # in the interaction according to atom type using "auto_equivalences" + # a distinction is made between end atoms and central atoms. + # The parameters for these interactions are also stored in different + # tables in the .frc file, with different comments/tags. + # (for example, "cff91_auto" as opposed to "cff91") + # An excerpt from the Discover manual is somewhat vague: + # "A forcefield may include automatic parameters for use when + # better-quality explicit parameters are not defined for a + # particular bond, angle, torsion, or out-of-plane interaction. + # These parameters are intended as temporary patches, to allow + # you to begin calculations immediately." + + for line in lines_auto_equivalences: + #tokens = SplitQuotedString(line.strip(), + # comment_char='!>') + + # skip past both '!' and '>' characters + ic1 = line.find('!') + ic = ic1 + ic2 = line.find('>') + if ic2 != -1 and ic2 < ic1: + ic = ic2 + if ic != -1: + line = line[:ic] + else: + line = line.rstrip('\n') + tokens = line.strip().split() + #sys.stderr.write('DEBUG Equivalences2ffids():\n' + # ' tokens = '+str(tokens)+'\n') + atype = EncodeAName(tokens[2]) + atom2auto_pair[atype] = EncodeAName(tokens[3]) + atom2auto_bondincr[atype] = EncodeAName(tokens[4]) + atom2auto_bond[atype] = EncodeAName(tokens[5]) + atom2auto_angleend[atype] = EncodeAName(tokens[6]) + atom2auto_anglecenter[atype] = EncodeAName(tokens[7]) + atom2auto_dihedralend[atype] = EncodeAName(tokens[8]) + atom2auto_dihedralcenter[atype] = EncodeAName(tokens[9]) + atom2auto_improperend[atype] = EncodeAName(tokens[10]) + atom2auto_impropercenter[atype] = EncodeAName(tokens[11]) + + atom2ffid = OrderedDict() + for atom in atom_types: + atom2ffid[atom] = (atom + + ',p'+atom2equiv_pair.get(atom,'') + + ',b'+atom2equiv_bond.get(atom,'') + + ',a'+atom2equiv_angle.get(atom,'') + + ',d'+atom2equiv_dihedral.get(atom,'') + + ',i'+atom2equiv_improper.get(atom,'') + + ',ap'+atom2auto_pair.get(atom,'') + + ',aq'+atom2auto_bondincr.get(atom,'') + + ',ab'+atom2auto_bond.get(atom,'') + + ',aae'+atom2auto_angleend.get(atom,'') + + ',aac'+atom2auto_anglecenter.get(atom,'') + + ',ade'+atom2auto_dihedralend.get(atom,'') + + ',adc'+atom2auto_dihedralcenter.get(atom,'') + + ',aie'+atom2auto_improperend.get(atom,'') + + ',aic'+atom2auto_impropercenter.get(atom,'') + + '' + ) + return atom2ffid + + + + + + +def main(): + try: + sys.stderr.write(g_program_name + ", version " + + __version__ + ", " + __date__ + "\n") + if sys.version < '2.6': + raise InputError('Error: Using python ' + sys.version + '\n' + + ' Alas, your version of python is too old.\n' + ' You must upgrade to a newer version of python (2.6 or later).') + + if sys.version < '2.7': + from ordereddict import OrderedDict + else: + from collections import OrderedDict + + if sys.version > '3': + import io + else: + import cStringIO + + # defaults: + ffname = 'BIOSYM_MSI_FORCE_FIELD' + type_subset = set([]) + filename_in = '' + file_in = sys.stdin + #file_in = open('pcff_repaired.frc','r') #CONTINUEHERE + include_auto_equivalences = False + #pair_style_name = 'lj/class2/coul/long' + #pair_style_params = "10.0 10.0" + pair_style2docs = {} + pair_style2args = defaultdict(str) + pair_style2docs['lj/cut/coul/long'] = 'http://lammps.sandia.gov/doc/pair_lj.html' + pair_style2args['lj/cut/coul/long'] = '10.0' + pair_style2docs['lj/class2/coul/long'] = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style2args['lj/class2/coul/long'] = '10.0' + pair_style2docs['lj/class2/coul/cut'] = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style2args['lj/class2/coul/cut'] = '10.0' + + bond_style2docs = {} + #bond_style2args = defaultdict(str) + bond_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/bond_harmonic.html' + bond_style2docs['class2'] = 'http://lammps.sandia.gov/doc/bond_class2.html' + bond_style2docs['morse'] = 'http://lammps.sandia.gov/doc/bond_morse.html' + bond_symmetry_subgraph = '' # default + + angle_style2docs = {} + #angle_style2args = defaultdict(str) + angle_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/angle_harmonic.html' + angle_style2docs['class2'] = 'http://lammps.sandia.gov/doc/angle_class2.html' + angle_symmetry_subgraph = '' # default + + dihedral_style2docs = {} + #dihedral_style2args = defaultdict(str) + dihedral_style2docs['charmm'] = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' + dihedral_style2docs['class2'] = 'http://lammps.sandia.gov/doc/dihedral_class2.html' + dihedral_symmetry_subgraph = '' # default + + improper_style2docs = {} + #improper_style2args = defaultdict(str) + improper_style2docs['cvff'] = 'http://lammps.sandia.gov/doc/improper_cvff.html' + improper_style2docs['class2'] = 'http://lammps.sandia.gov/doc/improper_class2.html' + improper_symmetry_subgraph = {} #'cenJsortIKL' + + pair_mixing_style = 'sixthpower tail yes' + + special_bonds_command = 'special_bonds lj/coul 0.0 0.0 1.0 dihedral yes' + # Thanks to Paul Saxe for is suggestions + # http://lammps.sandia.gov/threads/msg11270.html + + + kspace_style = 'kspace_style pppm 0.0001' + pair_styles_selected = set([]) + #pair_style_link = 'http://lammps.sandia.gov/doc/pair_class2.html' + pair_style_args = {} + pair_cutoff = '10.0' + #pair_style_command = " pair_style hybrid " + \ + # pair_style_name + " " + pair_style_args + "\n" + bond_styles_selected = set([]) + #bond_style_link = bond_style2docs[bond_style_name] + #bond_style_args = '' + angle_styles_selected = set([]) + #angle_style_link = angle_style2docs[angle_style_name] + #angle_style_args = '' + dihedral_styles_selected = set([]) + #dihedral_style_link = dihedral_style2docs[dihedral_style_name] + #dihedral_style_args = '' + improper_styles_selected = set([]) + #improper_style_link = improper_style2docs[improper_style_name] + #improper_style_args = '' + hbond_style_name = '' + hbond_style_link = '' + hbond_style_args = '' + + lines_templates = [] + lines_references = defaultdict(list) + lines_warnings = [] + + + argv = [arg for arg in sys.argv] + + i = 1 + + while i < len(argv): + + #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') + + if argv[i] == '-atoms': + if i + 1 >= len(argv): + raise InputError('Error: the \"' + argv[i] + '\" argument should be followed by a quoted string\n' + ' which contains a space-delimited list of of a subset of atom types\n' + ' you want to use from the original force-field.\n' + ' Make sure you enclose the entire list in quotes.\n') + type_subset = set(argv[i + 1].strip('\"\'').strip().split()) + del argv[i:i + 2] + + elif argv[i] == '-name': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of the force-field\n') + ffname = argv[i + 1] + del argv[i:i + 2] + + elif argv[i] in ('-file', '-in-file'): + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of a force-field file\n') + filename_in = argv[i + 1] + try: + file_in = open(filename_in, 'r') + except IOError: + sys.stderr.write('Error: Unable to open file\n' + ' \"' + filename_in + '\"\n' + ' for reading.\n') + sys.exit(1) + del argv[i:i + 2] + + elif argv[i] == '-pair-cutoff': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by a number' + ' (the distance cutoff for non-bonded (pair) interactions)\n') + pair_style_cutoff = argv[i+1] + del argv[i:i + 2] + + elif argv[i] == '-pair-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by either \"lj/class2/coul/cut\" or \"lj/class2/coul/long\"\n') + pair_style_list = argv[i + 1].split(',') + for pair_style in pair_style_list: + if pair_style == '9-6': + pair_style = 'lj/class2/coul/long' + elif pair_style in ('12-6', 'lj', 'LJ'): + pair_style = 'lj/cut/coul/long' + + if pair_style.find('lj/class2/coul/long') == 0: + kspace_style = 'kspace_style pppm 0.0001' + elif pair_style.find('lj/cut/coul/long') == 0: + kspace_style = 'kspace_style pppm 0.0001' + elif pair_style.find('lj/class2/coul/cut') == 0: + pass + #kspace_style = '' + elif pair_style.find('lj/cut') == 0: + pass + #kspace_style = '' + else: + raise InputError('Error: ' + argv[i] + ' ' + pair_style + ' not supported.\n' + ' The following pair_styles are supported:\n' + ' lj/class2/coul/cut\n' + ' lj/class2/coul/long\n' + ' lj/cut\n' + ' lj/cut/coul/long\n') + pair_styles_selected.add(pair_style) + + del argv[i:i + 2] + + elif argv[i] == '-bond-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible bond_style.\n') + bond_styles = argv[i + 1].split(',') + for bond_style in bond_styles: + bond_styles_selected.add(bond_style) + #bond_style2args[bond_style] = argv[i + 1].split()[1:] + #if bond_style_name.find('harmonic') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_harmonic.html' + #elif bond_style_name.find('morse') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_morse.html' + #elif bond_style_name.find('class2') == 0: + # pass + # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\", \"class2\", or \"morse\".\n') + del argv[i:i + 2] + + elif argv[i] == '-angle-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible angle_style.\n') + angle_styles = argv[i + 1].split(',') + for angle_style in angle_styles: + angle_styles_selected.add(angle_style) + #if angle_style_name.find('harmonic') == 0: + # pass + # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_harmonic.html' + #elif angle_style_name.find('class2') == 0: + # pass + # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-dihedral-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible dihedral_style.\n') + dihedral_styles = argv[i + 1].split(',') + for dihedral_style in dihedral_styles: + dihedral_styles_selected.add(dihedral_style) + #if dihedral_style_name.find('charmm') == 0: + # pass + # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' + #elif dihedral_style_name.find('class2') == 0: + # pass + # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-improper-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' + ' a compatible impropoer_style.\n') + improper_styles = argv[i + 1].split(',') + for improper_style in improper_styles: + improper_styles_selected.add(improper_style) + #if impropoer_style_name.find('harmonic') == 0: + # pass + # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_harmonic.html' + #elif impropoer_style_name.find('class2') == 0: + # pass + # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_class2.html' + #else: + # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' + # ' \"harmonic\" or \"class2\"\n') + del argv[i:i + 2] + + elif argv[i] == '-hbond-style': + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' ' + hbond_style_name + '\n' + ' should be followed by a compatible pair_style.\n') + hbond_style_name = argv[i + 1] + hbond_style_link = 'http://lammps.sandia.gov/doc/pair_hbond_dreiding.html' + if hbond_style_name.find('none') == 0: + hbond_style_name = '' + hbond_style_args = '' + elif hbond_style_name.find('hbond/dreiding/lj') == 0: + n = len('hbond/dreiding/lj') + hbond_style_args = hbond_style_name[n+1:] + hbond_style_name = hbond_style_name[:n] + elif hbond_style_name.find('hbond/dreiding/morse') == 0: + n = len('hbond/dreiding/morse') + hbond_style_args = hbond_style_name[n+1:] + hbond_style_name = hbond_style_name[:n] + else: + raise InputError('Error: ' + argv[i] + ' flag should be followed by either\n' + ' \"hbond/dreiding/lj\" or \"hbond/dreiding/morse"\n') + del argv[i:i + 2] + + elif argv[i] in ('-url', '-in-url'): + import urllib2 + if i + 1 >= len(argv): + raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' + ' a file containing force-field information in msi/frc format.\n') + url = argv[i + 1] + try: + request = urllib2.Request(url) + file_in = urllib2.urlopen(request) + except urllib2.URLError: + sys.stdout.write("Error: Unable to open link:\n" + url + "\n") + sys.exit(1) + del argv[i:i + 2] + + elif argv[i] == '-auto': + include_auto_equivalences = True + del argv[i:i + 1] + + elif argv[i] in ('-help', '--help', '-?', '--?'): + sys.stderr.write(doc_msg) + sys.exit(0) + del argv[i:i + 1] + + else: + i += 1 + + if len(argv) != 1: + raise InputError('Error: Unrecongized arguments: ' + ' '.join(argv[1:]) + + '\n\n' + doc_msg) + + # Default styles: + if len(bond_styles_selected) == 0: + bond_styles_selected.add('class2') + if len(angle_styles_selected) == 0: + angle_styles_selected.add('class2') + if len(dihedral_styles_selected) == 0: + dihedral_styles_selected.add('class2') + if len(improper_styles_selected) == 0: + improper_styles_selected.add('class2') + if len(pair_styles_selected) == 0: + pair_styles_selected.add('lj/class2/coul/long') + + #sys.stderr.write("Reading parameter file...\n") + + lines = file_in.readlines() + atom2charge = OrderedDict() # lookup charge from atom type + atom2mass = OrderedDict() # lookup mass from atom type + # equivalences lookup + atom2ffid = OrderedDict() # lookup "force-field-ID" a string containing + # equivalences to lookup bonded interactions + atom2equiv_pair = OrderedDict() # lookup the equivalent symbol used for + # looking up pair interactions + atom2equiv_bond = OrderedDict() + atom2equiv_angle = OrderedDict() + atom2equiv_dihedral = OrderedDict() + atom2equiv_improper = OrderedDict() + # inverse equivalences lookup + equiv_pair2atom = defaultdict(set) + equiv_bond2atom = defaultdict(set) + equiv_angle2atom = defaultdict(set) + equiv_dihedral2atom = defaultdict(set) + equiv_improper2atom = defaultdict(set) + + # auto equivalences lookup + atom2auto_pair = OrderedDict() + atom2auto_bondincr = OrderedDict() + atom2auto_bond = OrderedDict() + atom2auto_angleend = OrderedDict() + atom2auto_anglecenter = OrderedDict() + atom2auto_dihedralend = OrderedDict() + atom2auto_dihedralcenter = OrderedDict() + atom2auto_improperend = OrderedDict() + atom2auto_impropercenter = OrderedDict() + # inverse auto equivalences lookup + auto_pair2atom = defaultdict(set) + auto_bondincr2atom = defaultdict(set) + auto_bond2atom = defaultdict(set) + auto_angleend2atom = defaultdict(set) + auto_anglecenter2atom = defaultdict(set) + auto_dihedralend2atom = defaultdict(set) + auto_dihedralcenter2atom = defaultdict(set) + auto_improperend2atom = defaultdict(set) + auto_impropercenter2atom = defaultdict(set) + + + atom2element = OrderedDict() # Optional: + # which element (eg 'C', 'O') ? (Note this + # is different from atom type: 'C1', 'Oh') + atom2numbonds = OrderedDict() # Optional: how many bonds emanate from + atom2descr = OrderedDict() # Optional: a brief description + atom2ver = OrderedDict() # atoms introduced in different versions of ff + atom2ref = OrderedDict() # reference to paper where atom introduced + lines_equivalences = [] # equivalences for force-field lookup + lines_auto_equivalences = [] # auto_equivalences have lower priority + + pair2params = OrderedDict() + pair2style = OrderedDict() + pair_styles = set([]) + pair2ver = OrderedDict() + pair2ref = OrderedDict() + + bond2chargepair = OrderedDict() # a.k.a "bond increments" + charge_pair_priority = OrderedDict() # priority in case multiple entries + # exist for the same pair of atoms + charge_pair_ver = OrderedDict() # which version of the force field? + charge_pair_ref = OrderedDict() # paper introducing this chargepair + + bond2params = OrderedDict() # store a tuple with the 2-body bond + # interaction type, and its parameters + # for every type of bond + bond2priority = OrderedDict() # What is the priority of this interaction? + bond2style = OrderedDict() # What LAMMPS bond style (formula) + # is used for a given interaction? + bond_styles = set([]) # Contains all bond styles used. + bond2ver = OrderedDict() + bond2ref = OrderedDict() + bond2r0 = OrderedDict() + bond2r0_auto = OrderedDict() + + angle2params = OrderedDict() # store a tuple with the 3-body angle + # interaction type, and its parameters + # for every type of angle + + angle2params_or = OrderedDict() + # http://lammps.sandia.gov/doc/angle_class2.html + #angle2class2_a = OrderedDict() # params for the "a" class2 terms + angle2class2_bb = OrderedDict() # params for the "bb" class2 terms + angle2class2_bb_or = OrderedDict() + angle2class2_ba = OrderedDict() # params for the "ba" class2 terms + angle2class2_ba_or = OrderedDict() + angle2priority = OrderedDict() # What is the priority of this interaction? + angle2priority_or = OrderedDict() + angle_is_secondary_or = OrderedDict() + angle2style = OrderedDict() # What LAMMPS angle style (formula) + # is used for a given interaction? + angle2style_or = OrderedDict() + angle_styles = set([]) # Contains all angle styles used. + angle2ref = OrderedDict() + angle2ver = OrderedDict() + angle2ref_or = OrderedDict() + angle2ver_or = OrderedDict() + angle2ver_bb = OrderedDict() + angle2ver_bb_or = OrderedDict() + angle2ref_bb = OrderedDict() + angle2ref_bb_or = OrderedDict() + angle2ver_ba = OrderedDict() + angle2ver_ba_or = OrderedDict() + angle2ref_ba = OrderedDict() + angle2ref_ba_or = OrderedDict() + angle2theta0_or = OrderedDict() + angle2theta0_auto_or = OrderedDict() + + # http://lammps.sandia.gov/doc/dihedral_class2.html + dihedral2params = OrderedDict() # store a tuple with the 4-body dihedral + # interaction type, and its parameters + # for every type of dihedral + dihedral2params_or = OrderedDict() + #dihedral2class2_d = OrderedDict() # params for the "d" class2 term + dihedral2class2_mbt = OrderedDict() # params for the "mbt" class2 term + dihedral2class2_mbt_or = OrderedDict() + dihedral2class2_ebt = OrderedDict() # params for the "ebt" class2 term + dihedral2class2_ebt_or = OrderedDict() + #dihedral2sym_ebt = OrderedDict() + dihedral2class2_at = OrderedDict() # params for the "at" class2 term + dihedral2class2_at_or = OrderedDict() + #dihedral2sym_at = OrderedDict() + dihedral2class2_aat = OrderedDict() # params for the "aat" class2 term + dihedral2class2_aat_or = OrderedDict() + #dihedral2sym_aat = OrderedDict() + dihedral2class2_bb13 = OrderedDict() # params for the "bb13" class2 term + dihedral2class2_bb13_or = OrderedDict() + #dihedral2sym_bb13 = OrderedDict() + dihedral2priority = OrderedDict() # What is the priority of this interaction? + dihedral2priority_or = OrderedDict() + dihedral_is_secondary_or = OrderedDict() + dihedral2style = OrderedDict() # What LAMMPS dihedral style (formula) + # is used for a given interaction? + dihedral2style_or = OrderedDict() + dihedral_styles = set([]) # Contains all dihedral styles used. + dihedral2ref = OrderedDict() + dihedral2ver = OrderedDict() + dihedral2ver_or = OrderedDict() + dihedral2ref_or = OrderedDict() + dihedral2ver_mbt = OrderedDict() + dihedral2ver_mbt_or = OrderedDict() + dihedral2ref_mbt = OrderedDict() + dihedral2ref_mbt_or = OrderedDict() + dihedral2ver_ebt = OrderedDict() + dihedral2ver_ebt_or = OrderedDict() + dihedral2ref_ebt = OrderedDict() + dihedral2ref_ebt_or = OrderedDict() + dihedral2ver_at = OrderedDict() + dihedral2ver_at_or = OrderedDict() + dihedral2ref_at = OrderedDict() + dihedral2ref_at_or = OrderedDict() + dihedral2ver_aat = OrderedDict() + dihedral2ver_aat_or = OrderedDict() + dihedral2ref_aat = OrderedDict() + dihedral2ref_aat_or = OrderedDict() + dihedral2ver_bb13 = OrderedDict() + dihedral2ver_bb13_or = OrderedDict() + dihedral2ref_bb13 = OrderedDict() + dihedral2ref_bb13_or = OrderedDict() + + + # http://lammps.sandia.gov/doc/improper_class2.html + improper2params = OrderedDict() # store a tuple with the 4-body improper + # interaction type, and its parameters + # for every type of imporpoer + improper2params_or = OrderedDict() + improper2class2_aa = OrderedDict() # params for the "aa" class2 term + improper2class2_aa_or = OrderedDict() + + improper2cross = defaultdict(dict) + # improper2cross[imp_name][atoms] stores the + # coefficient (K) for the angle-angle ("aa") + # improper interactions between a pair of + # neighboring 3-body angles (in the .FRC file). + # "imp_name" is the name of the improper interaction + # (which is a concatination of the central atom and + # the 3 surrounding leaf atoms (which are sorted)) + # "atoms" indicates, for that K value, the list of + # leaf atoms for that K value as they appear in the + # corresponding line of the .frc file (however the + # and last atom names are swapped if the first + # atom name is lexicographically > the last, to + # eliminate redundancy and ambiguity.) + + improper2sym = defaultdict(set) + # improper2sym[imp_name] indicates which subset of + # leaf atoms (from 0 to 2) are equivalent and can + # tolerate having their order rearranged without + # effecting the energy. Later on this will be used + # to reduce the number of improper interactions that + # will be generated by moltemplate. + + improper2priority = OrderedDict() # What is the priority of this interaction? + improper2priority_or = OrderedDict() + improper_is_secondary_or = OrderedDict() + improper2style = OrderedDict() # What LAMMPS improper style (formula) + # is used for a given interaction? + improper2style_or = OrderedDict() + improper_styles = set([]) # Contains all improper styles used. + improper2ver = OrderedDict() + improper2ver_or = OrderedDict() + improper2ref = OrderedDict() + improper2ref_or = OrderedDict() + improper2ver_aa = OrderedDict() + improper2ver_aa_or = OrderedDict() + improper2ref_aa = OrderedDict() + improper2ref_aa_or = OrderedDict() + + + # Warn users if force field contains terms which cannot yet + # be simulated with LAMMPS (as of 2017-10-13) + display_OOP_OOP_warning = False + display_torsion_torsion_1_warning = False + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete this code in a later version + hbond2params = OrderedDict() # lookup hbond parameters and atom types + hbond2donors = OrderedDict() # according to the identifier in the 2nd + hbond2acceptors = OrderedDict() # column of the "#hbond_definition" + hbond2hydrogens = OrderedDict() # section of an .frc file. + """ + + allowed_section_names = set(['#define', + # sections used in all MSI force-fields + '#atom_types', + '#equivalence', + '#auto_equivalence', + '#nonbond(9-6)', + '#nonbond(12-6)', + '#quadratic_bond', + '#quartic_bond', + '#morse_bond', + '#quadratic_angle', + '#quartic_angle', + '#bond-bond', + '#bond-angle', + '#torsion_1', + '#torsion_3', + '#middle_bond-torsion_3', + '#end_bond-torsion_3', + '#angle-torsion_3', + '#angle-angle-torsion_1',#(class2 dihedral) + '#bond-bond_1_3', #(a class2 dihedral term) + '#out_of_plane', + '#wilson_out_of_plane', + '#angle-angle', #(a class2 improper term) + '#out_of_plane-out_of_plane', # UNSUPPORTED + '#torsion-torsion_1', # UNSUPPORTED + '#bond_increments', + '#hbond_definition', # irrelevant? + '#templates', + '#reference', + '#end' + ]) + + icol_type = icol_mass = icol_elem = icol_nbonds = icol_comment = icol_ver = icol_ref = -1 + + section_name = '' + section_is_auto = False + + sys.stderr.write("parsing file pass1: look for atom types and equivalences...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if tokens[0] in allowed_section_names: + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif not tokens[0] in ('#version', + '#define'): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + elif (len(tokens) == 8) and (section_name == '#equivalence'): + if line.lstrip().find('!') == 0: + continue + lines_equivalences.append(line) + elif (len(tokens) == 12) and (section_name == '#auto_equivalence'): + if line.lstrip().find('!') == 0: + continue + lines_auto_equivalences.append(line) + elif (len(tokens) > 0) and (section_name == '#atom_types'): + # Different FRC files put this information in different + # columns. Column order is stored in the !Ver comment line: + if line.lstrip().find('!Ver') == 0: + tokens = line.strip().split() + for i in range(0, len(tokens)): + if tokens[i].lower() == 'type': + icol_type = i + elif tokens[i].lower() == 'mass': + icol_mass = i + elif tokens[i].lower() == 'element': + icol_elem = i + elif tokens[i].lower() == 'connections': + icol_nbonds = i + elif tokens[i].lower() == 'comment': + icol_comment = i + elif tokens[i].lower() == '!ver': #(version of ff) + icol_ver = i + elif tokens[i].lower() == 'ref': + icol_ref = i + assert(icol_ver == 0) + + if -1 in (icol_type, icol_mass): + raise InputError('Error: Invalid #atom_types section.\n' + ' The meaning of each column cannot be determined.\n' + ' This file needs a valid "!Ver..." comment.\n') + if icol_comment == -1: + icol_comment = max(icol_type, icol_mass, + icol_elem, icol_nbonds) + 1 + + sys.stderr.write('icol_ver = '+str(icol_ver)+'\n') + sys.stderr.write('icol_ref = '+str(icol_ref)+'\n') + sys.stderr.write('icol_mass = '+str(icol_mass)+'\n') + sys.stderr.write('icol_nelem = '+str(icol_elem)+'\n') + sys.stderr.write('icol_nbonds = '+str(icol_nbonds)+'\n') + sys.stderr.write('icol_comment = '+str(icol_comment)+'\n') + continue + + tokens = map(RemoveOuterQuotes, + NSplitQuotedString(line.strip(), + icol_comment+1, + quotes='', + comment_char='>')) + tokens = list(tokens) + + if (len(tokens) > 4): + if ((len(type_subset) == 0) or (tokens[1] in type_subset)): + aname = EncodeAName(tokens[icol_type]) + atom2mass[aname] = str(max(float(tokens[icol_mass]), 1.0e-06)) + # Some atoms in cvff.prm have zero mass. Unfortunately this + # causes LAMMPS to crash, even if these atoms are never used, + # so I give the mass a non-zero value instead. + + if icol_elem != -1: + atom2element[aname] = tokens[icol_elem] + if icol_nbonds != -1: + atom2numbonds[aname] = int(tokens[icol_nbonds]) + atom2descr[aname] = tokens[icol_comment] + atom2ver[aname] = tokens[icol_ver] + atom2ref[aname] = tokens[icol_ref] + + elif len(tokens) > 0: + raise InputError('Error: Invalid atom line: (line#'+str(iline)+')\n' + + '\"'+line.strip()+'\"') + + atom_types = [x for x in atom2mass] + + # Now construct the lookup tables and inverse tables + # we will need to understand the remainder of the file: + if not include_auto_equivalences: + atom2ffid = Equivalences2ffids(lines_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper) + else: + atom2ffid = AutoEquivalences2ffids(lines_equivalences, + lines_auto_equivalences, + atom_types, + atom2equiv_pair, + atom2equiv_bond, + atom2equiv_angle, + atom2equiv_dihedral, + atom2equiv_improper, + atom2auto_pair, + atom2auto_bondincr, + atom2auto_bond, + atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_dihedralend, + atom2auto_dihedralcenter, + atom2auto_improperend, + atom2auto_impropercenter) + + for a,e in atom2equiv_pair.items(): + equiv_pair2atom[e].add(a) + for a,e in atom2equiv_bond.items(): + equiv_bond2atom[e].add(a) + for a,e in atom2equiv_angle.items(): + equiv_angle2atom[e].add(a) + for a,e in atom2equiv_dihedral.items(): + equiv_dihedral2atom[e].add(a) + for a,e in atom2equiv_improper.items(): + equiv_improper2atom[e].add(a) + + # the inverse lookup for '*' matches all atom types + for a in atom_types: + #equiv_pair2atom['*'].add(EncodeAName(a)) + equiv_pair2atom['X'].add(EncodeAName(a)) + #equiv_bond2atom['*'].add(EncodeAName(a)) + equiv_bond2atom['X'].add(EncodeAName(a)) + #equiv_angle2atom['*'].add(EncodeAName(a)) + equiv_angle2atom['X'].add(EncodeAName(a)) + #equiv_dihedral2atom['*'].add(EncodeAName(a)) + equiv_dihedral2atom['X'].add(EncodeAName(a)) + #equiv_improper2atom['*'].add(EncodeAName(a)) + equiv_improper2atom['X'].add(EncodeAName(a)) + + for a,e in atom2auto_pair.items(): + auto_pair2atom[e].add(a) + for a,e in atom2auto_bondincr.items(): + auto_bondincr2atom[e].add(a) + for a,e in atom2auto_bond.items(): + auto_bond2atom[e].add(a) + for a,e in atom2auto_angleend.items(): + auto_angleend2atom[e].add(a) + #auto_angle[0][e].add(a) + #auto_angle[2][e].add(a) + for a,e in atom2auto_anglecenter.items(): + auto_anglecenter2atom[e].add(a) + #auto_angle[1][e].add(a) + for a,e in atom2auto_dihedralend.items(): + auto_dihedralend2atom[e].add(a) + #auto_dihedral2atom[0][e].add(a) + #auto_dihedral2atom[3][e].add(a) + for a,e in atom2auto_dihedralcenter.items(): + auto_dihedralcenter2atom[e].add(a) + #auto_dihedral2atom[1][e].add(a) + #auto_dihedral2atom[2][e].add(a) + for a,e in atom2auto_improperend.items(): + auto_improperend2atom[e].add(a) + for a,e in atom2auto_impropercenter.items(): + auto_impropercenter2atom[e].add(a) + + # the inverse lookup for '*' matches all atom types + for a in atom_types: + #auto_pair2atom['*'].add(EncodeAName(a)) + auto_pair2atom['X'].add(EncodeAName(a)) + #auto_bondincr2atom['*'].add(EncodeAName(a)) + auto_bondincr2atom['X'].add(EncodeAName(a)) + #auto_bond2atom['*'].add(EncodeAName(a)) + auto_bond2atom['X'].add(EncodeAName(a)) + #auto_angleend2atom['*'].add(EncodeAName(a)) + auto_angleend2atom['X'].add(EncodeAName(a)) + #auto_anglecenter2atom['*'].add(EncodeAName(a)) + auto_anglecenter2atom['X'].add(EncodeAName(a)) + #auto_dihedralend2atom['*'].add(EncodeAName(a)) + auto_dihedralend2atom['X'].add(EncodeAName(a)) + #auto_dihedralcenter2atom['*'].add(EncodeAName(a)) + auto_dihedralcenter2atom['X'].add(EncodeAName(a)) + #auto_improperend2atom['*'].add(EncodeAName(a)) + auto_improperend2atom['X'].add(EncodeAName(a)) + #auto_impropercenter2atom['*'].add(EncodeAName(a)) + auto_impropercenter2atom['X'].add(EncodeAName(a)) + + + + + + + + + sys.stderr.write("parsing file pass2: look for bonds, bond_increments and nonbonded (pair) interactions...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + elif ((len(tokens) > 4) and (section_name == '#nonbond(12-6)') + and (pair_styles_selected & set(['lj','lj/cut','lj/cut/coul/long', + 'lj/cut/coul/cut','lj/cut/coul/debye', + 'lj/cut/coul/dsf','lj/cut/coul/msm', + '12-6','nonbond(12-6)']))): + + if line.lstrip().find('!') == 0: + continue + atom_name = EncodeAName(tokens[2]) + pair2ver[atom_name] = tokens[0] + pair2ref[atom_name] = tokens[1] + A = float(tokens[3]) + B = float(tokens[4]) + epsilon = B*B/(4*A) + sigma = pow(B/A, 1.0/6) + if sigma == 0.0: + sigma = 1.0 #(non-zero to avoid nan error later) + pair_styles.add('lj/cut/coul/long') + pair_style_args['lj/cut/coul/long'] = pair_cutoff + pair2style[atom_name] = 'lj/cut/coul/long' + pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) + pair_mixing_style = 'geometric tail yes' + #if pair_style_name.find('lj/cut') == 0: + # pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) + # pair_mixing_style = 'geometric tail yes' + + + elif ((len(tokens) > 4) and (section_name == '#nonbond(9-6)') + and (pair_styles_selected & + set(['class2', '9-6', 'nonbond(9-6)', + 'lj/class2/coul/long']))): + if line.lstrip().find('!') == 0: + continue + atom_name = EncodeAName(tokens[2]) + pair2ver[atom_name] = tokens[0] + pair2ref[atom_name] = tokens[1] + sigma = tokens[3] + epsilon = tokens[4] + pair_styles.add('lj/class2/coul/long') + pair_style_args['lj/class2/coul/long'] = pair_cutoff + pair2style[atom_name] = 'lj/class2/coul/long' + pair2params[atom_name] = (epsilon+' '+sigma) + pair_mixing_style = 'sixthpower tail yes' + #if pair_style_name.find('lj/class2') == 0: + # pair2params[atom_name] = (epsilon+' '+sigma) + # pair_mixing_style = 'sixthpower tail yes' + + + elif (len(tokens) == 6) and (section_name == '#bond_increments'): + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:4])] + delta_q = tokens[4:6] + atom_names = [a for a in aorig] + # swap the order of the atoms? + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + delta_q.reverse() + atom_names.reverse() + bond_name = EncodeInteractionName(atom_names, section_is_auto) + charge_pair_ver[bond_name] = tokens[0] + charge_pair_ref[bond_name] = tokens[1] + charge_pair_priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(charge_pair_ver[bond_name]))) + bond2chargepair[bond_name] = (delta_q[0] + ' ' + delta_q[1]) + + + elif ((len(tokens) > 5) and (section_name == '#quadratic_bond') + and (bond_styles_selected & set(['harmonic','quadratic','quadratic_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('harmonic') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + k = tokens[5] + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + bond2style[bond_name] = 'harmonic' + bond2params[bond_name] = (k+' '+r0) + + + elif ((len(tokens) > 6) and (section_name == '#morse_bond') + and (bond_styles_selected & set(['morse','morse_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('morse') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + D = tokens[5] + alpha = tokens[6] + sys.stderr.write('DEBUG: morse: atom_names = '+str(atom_names)+'\n') + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + bond2style[bond_name] = 'morse' + bond2params[bond_name] = (D+' '+alpha+' '+r0) + + + + elif ((len(tokens) > 7) and (section_name == '#quartic_bond') + and (bond_styles_selected & set(['class2','quartic','quartic_bond']))): + if line.lstrip().find('!') == 0: + continue + bond_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) + bond_name = EncodeInteractionName(atom_names, section_is_auto) + bond2ver[bond_name] = tokens[0] + bond2ref[bond_name] = tokens[1] + bond2priority[bond_name] = \ + (section_is_auto, + DetermineNumericPriority(section_is_auto, + tokens[2:4], + float(bond2ver[bond_name]))) + r0 = tokens[4] + if not section_is_auto: + bond2r0[bond_name] = r0 + sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') + else: + bond2r0_auto[(atom_names[0], atom_names[1])] = r0 + sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') + K2 = tokens[5] + K3 = tokens[6] + K4 = tokens[7] + bond2style[bond_name] = 'class2' + bond2params[bond_name] = (r0+' '+K2+' '+K3+' '+K4) + + + + + + sys.stderr.write("parsing file pass3: look for (3-body) angle interactions...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + + + + + + elif (len(tokens) > 6) and (section_name == '#quadratic_angle'): + if line.lstrip().find('!') == 0: + continue + atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) + angle_name = EncodeInteractionName(atom_names, section_is_auto) + + angle2ver[angle_name] = tokens[0] + angle2ref[angle_name] = tokens[1] + angle2priority_or[angle_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:5], + float(angle2ver[angle_name])) + angle_is_secondary_or[angle_name] = False + angle2priority[angle_name] = \ + (section_is_auto, + angle_is_secondary_or[angle_name], + angle2priority_or[angle_name]) + theta0 = tokens[5] + k = tokens[6] + if not section_is_auto: + angle2theta0_or[angle_name] = theta0 + sys.stderr.write('angle2theta0_or['+angle_name+'] = ' + str(theta0) + '\n') + else: + angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 + sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') + if (angle_styles_selected & set(['harmonic', + 'quadratic', + 'quadratic_angle'])): + angle_styles.add('harmonic') + angle2style[angle_name] = 'harmonic' + angle2params[angle_name] = (k+' '+theta0) + elif (angle_styles_selected & set(['class2', + 'quartic', + 'quartic_angle'])): + # Then this is a special case of the class2 angle where + # the (theta-theta0)^3 and (theta-theta0)^4 terms = 0 + angle_styles.add('class2') + angle2style_or[angle_name] = 'class2' + angle2params_or[angle_name] = (theta0+' '+k+' 0 0') + + + + elif ((len(tokens) > 8) and (section_name == '#quartic_angle') + and (angle_styles_selected & set(['class2','quartic','quartic_angle']))): + if line.lstrip().find('!') == 0: + continue + angle_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) + ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) + version = tokens[0] + reference = tokens[1] + angle2ver_or[ang_name_orig] = version + angle2ref_or[ang_name_orig] = reference + angle2priority_or[ang_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:5], + float(angle2ver_or[ang_name_orig])) + angle_is_secondary_or[ang_name_orig] = False + #angle2priority[ang_name_orig] = \ + # (section_is_auto, + # angle_is_secondary_or[ang_name_orig], + # angle2priority_or[ang_name_orig]) + theta0 = tokens[5] + if not section_is_auto: + angle2theta0_or[ang_name_orig] = theta0 + sys.stderr.write('angle2theta0_or['+ang_name_orig+'] = ' + str(theta0) + '\n') + else: + angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 + sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') + K2 = tokens[6] + K3 = tokens[7] + K4 = tokens[8] + angle2style_or[ang_name_orig] = 'class2' + angle2params_or[ang_name_orig] = [theta0, K2, K3, K4] + if not ang_name_orig in angle2class2_bb_or: + angle2class2_bb_or[ang_name_orig] = '0.0' # default value + angle2ver_bb_or[ang_name_orig] = version # default value + angle2ref_bb_or[ang_name_orig] = reference # default value + if not ang_name_orig in angle2class2_ba_or: + angle2class2_ba_or[ang_name_orig] = ['0.0', '0.0'] # default value + angle2ver_ba_or[ang_name_orig] = version # default value + angle2ref_ba_or[ang_name_orig] = reference # default value + + elif ((len(tokens) > 5) and + (section_name in ('#bond-bond', '#bond-angle')) and + (angle_styles_selected & + set(['class2', 'quartic', 'quartic_angle']))): + if line.lstrip().find('!') == 0: + continue + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:5])] + atom_names = SortByEnds(aorig) + ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) + K = ['', ''] + K[0] = tokens[5] + K[1] = K[0] + if len(tokens) > 6: + K[1] = tokens[6] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + K.reverse() + if (section_name == '#bond-bond'): + angle2class2_bb_or[ang_name_orig] = K[0] + angle2ver_bb_or[ang_name_orig] = version + angle2ref_bb_or[ang_name_orig] = reference + elif (section_name == '#bond-angle'): + angle2class2_ba_or[ang_name_orig] = [k for k in K] + angle2ver_ba_or[ang_name_orig] = version + angle2ref_ba_or[ang_name_orig] = reference + if not ang_name_orig in angle2params_or: + angle_is_secondary_or[ang_name_orig] = True #only cross terms have been defined so far + angle2params_or[ang_name_orig] = ['0.0', '0.0', '0.0', '0.0'] # default value + angle2ver_or[ang_name_orig] = version + angle2ref_or[ang_name_orig] = reference + angle2priority_or[ang_name_orig] = 0.0 + + + + + + + + + + sys.stderr.write("parsing file pass4: look for dihedrals(torsions) and impropers(out_of_plane)...") + + for iline in range(0, len(lines)): + line = lines[iline] + sys.stderr.write('line=\"' + line.strip() + '\"\n') + tokens = SplitQuotedString(line.strip(), + quotes='', + comment_char='>') + #sys.stderr.write('tokens = ' + str(tokens) + '\n') + if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': + continue + + + if line.lstrip(' ').find('#') == 0: + #sys.stderr.write('allowed_section_names = ' + + # str(allowed_section_names) + '\n') + if (tokens[0] in allowed_section_names): + section_name = tokens[0] + section_is_auto = tokens[-1].endswith('_auto') + tokens_after_section_name = tokens[1:] + sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') + continue + elif (not tokens[0] in ('#version','#define')): + raise InputError('Error: Line# '+str(iline) +'\n' + ' Unrecognized section name:\n' + ' \"' + tokens[0] + '\"\n') + + + + + elif (len(tokens) > 8) and (section_name == '#torsion_1'): + if line.lstrip().find('!') == 0: + continue + atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) + dihedral_name = EncodeInteractionName(atom_names, section_is_auto) + dihedral2ver[dihedral_name] = tokens[0] + dihedral2ref[dihedral_name] = tokens[1] + dihedral2priority_or[dihedral_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(dihedral2ver[dihedral_name])) + dihedral_is_secondary_or[dihedral_name] = False + dihedral2priority[dihedral_name] = \ + (section_is_auto, + dihedral_is_secondary_or[dihedral_name], + dihedral2priority_or[dihedral_name]) + K = tokens[6] + n = tokens[7] + d = tokens[8] + + w = '0.0' #ignore: this is only used by the CHARMM force field + + if (dihedral_styles_selected & set(['charmm','torsion_1'])): + dihedral_styles.add('charmm') + dihedral2style[dihedral_name] = 'charmm' + #dihedral2params_or[dihedral_name] = [K,n,d,w] + dihedral2params[dihedral_name] = (K+' '+n+' '+d+' '+w) + elif (dihedral_styles_selected & set(['class2','torsion_3'])): + # Then this is a special case of the class2 angle + # lacking the higher terms in the Fourier series + dihedral_styles.add('class2') + dihedral2style[dihedral_name] = 'class2' + dihedral2params_or[dihedral_name] = [K,d,0,0,0,0] + + + + + elif ((len(tokens) > 7) and (section_name == '#torsion_3') + and (dihedral_styles_selected & set(['class2','torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + version = tokens[0] + reference = tokens[1] + dihedral2priority_or[dih_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(version)) + dihedral_is_secondary_or[dih_name_orig] = False + #dihedral2priority[dih_name_orig] = \ + # (section_is_auto, + # dihedral_is_secondary_or[dih_name_orig], + # dihedral2priority_or[dih_name_orig]) + V1 = tokens[6] + phi0_1 = tokens[7] + V2 = phi0_2 = V3 = phi0_3 = '0.0' + if len(tokens) > 9: + V2 = tokens[8] + phi0_2 = tokens[9] + if len(tokens) > 11: + V3 = tokens[10] + phi0_3 = tokens[11] + dihedral2style_or[dih_name_orig] = 'class2' + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2params_or[dih_name_orig] = [V1, phi0_1, V2, phi0_2, V3, phi0_3] + # default values for cross terms: + if not dih_name_orig in dihedral2class2_mbt_or: + dihedral2class2_mbt_or[dih_name_orig] = ['0.0','0.0','0.0'] # default value + dihedral2ver_mbt_or[dih_name_orig] = version + dihedral2ref_mbt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_ebt_or: + dihedral2class2_ebt_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value + dihedral2ver_ebt_or[dih_name_orig] = version + dihedral2ref_ebt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_bb13_or: + dihedral2class2_bb13_or[dih_name_orig] = '0.0' # default value + dihedral2ver_bb13_or[dih_name_orig] = version + dihedral2ref_bb13_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_at_or: + dihedral2class2_at_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value + dihedral2ver_at_or[dih_name_orig] = version + dihedral2ref_at_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2class2_aat_or: + dihedral2class2_aat_or[dih_name_orig] = '0.0' # default value + dihedral2ver_aat_or[dih_name_orig] = version + dihedral2ref_aat_or[dih_name_orig] = reference + + + + + + elif ((len(tokens) > 6) and (section_name == '#middle_bond-torsion_3') + and (dihedral_styles_selected & set(['class2','torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + Fmbt = [tokens[6], '0.0', '0.0'] + if len(tokens) > 7: + Fmbt[1] = tokens[7] + if len(tokens) > 8: + Fmbt[2] = tokens[8] + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + #sys.stderr.write('DEBUG: (a2,a3) = '+str((a2,a3))+', ' + # ' (b1,b2) = '+str(batoms)+'\n') + dihedral2style[dih_name_orig] = 'class2' + dihedral2class2_mbt_or[dih_name_orig] = [F for F in Fmbt] + dihedral2ver_mbt_or[dih_name_orig] = version + dihedral2ref_mbt_or[dih_name_orig] = reference + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + elif ((len(tokens) > 6) and + (section_name in ('#end_bond-torsion_3', + '#bond-bond_1_3')) and + (dihedral_styles_selected & + set(['class2', 'torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + dihedral2style[dih_name_orig] = 'class2' + if section_name == '#end_bond-torsion_3': + Febt = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] + Febt[0][0] = tokens[6] + if len(tokens) > 7: + Febt[0][1] = tokens[7] + if len(tokens) > 8: + Febt[0][2] = tokens[8] + Febt[1][0] = Febt[0][0] + Febt[1][1] = Febt[0][1] + Febt[1][2] = Febt[0][2] + if len(tokens) > 9: + Febt[1][0] = tokens[9] + if len(tokens) > 10: + Febt[1][1] = tokens[10] + if len(tokens) > 11: + Febt[1][2] = tokens[11] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + Febt.reverse() + dihedral2class2_ebt_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Febt] #deep copy of Febt[][] + dihedral2ver_ebt_or[dih_name_orig] = version + dihedral2ref_ebt_or[dih_name_orig] = reference + + elif section_name == '#bond-bond_1_3': + Kbb13 = tokens[6] + #dihedral2ver_bb13[dih_name_orig] = version + dihedral2class2_bb13_or[dih_name_orig] = Kbb13 + dihedral2ver_bb13_or[dih_name_orig] = version + dihedral2ref_bb13_or[dih_name_orig] = reference + else: + assert(False) + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + + + + + + + elif ((len(tokens) > 6) and + (section_name in ('#angle-torsion_3', + '#angle-angle-torsion_1')) and + (dihedral_styles_selected & + set(['class2', 'torsion_3']))): + if line.lstrip().find('!') == 0: + continue + dihedral_styles.add('class2') + version = tokens[0] + reference = tokens[1] + if line.lstrip().find('!') == 0: + continue + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names = SortByEnds(aorig) + + dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) + + dihedral2style[dih_name_orig] = 'class2' + + if section_name == '#angle-torsion_3': + Fat = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] + Fat[0][0] = tokens[6] + if len(tokens) > 7: + Fat[0][1] = tokens[7] + if len(tokens) > 8: + Fat[0][2] = tokens[8] + Fat[1][0] = Fat[0][0] + Fat[1][1] = Fat[0][1] + Fat[1][2] = Fat[0][2] + if len(tokens) > 9: + Fat[1][0] = tokens[9] + if len(tokens) > 10: + Fat[1][1] = tokens[10] + if len(tokens) > 11: + Fat[1][2] = tokens[11] + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + Fat.reverse() + Fat[0].reverse() + Fat[1].reverse() + dihedral2class2_at_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Fat] #deep copy of Fat + dihedral2ver_at_or[dih_name_orig] = version + dihedral2ref_at_or[dih_name_orig] = reference + elif section_name == '#angle-angle-torsion_1': + Kaat = tokens[6] + dihedral2class2_aat_or[dih_name_orig] = Kaat + dihedral2ver_aat_or[dih_name_orig] = version + dihedral2ref_aat_or[dih_name_orig] = reference + else: + assert(False) + + if not dih_name_orig in dihedral2params_or: + dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far + dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] # default value + dihedral2ver_or[dih_name_orig] = version + dihedral2ref_or[dih_name_orig] = reference + dihedral2priority_or[dih_name_orig] = 0.0 + + + + + + + + + + + elif ((len(tokens) > 8) and (section_name == '#out_of_plane') + and (improper_styles_selected & set(['cvff','out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('cvff') + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names,_ignore = OOPImproperNameSort(tokens[2:6]) + improper_name = EncodeInteractionName(atom_names, section_is_auto) + imsym = improper_symmetry_subgraph[improper_name] = 'cenJflipIL' + subgraph2impname['cenJflipIL'].add(improper_name) CONTINUEHERE + improper2ver[imsym][improper_name] = tokens[0] + improper2ref[imsym][improper_name] = tokens[1] + improper2priority_or[imsym][improper_name] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(improper2ver[imsym][improper_name])) + improper_is_secondary_or[imsym][imp_name_orig] = False + improper2priority[imsym][improper_name] = \ + (section_is_auto, + improper_is_secondary_or[imsym][imp_name_orig], + improper2priority_or[imsym][improper_name]) + K = tokens[6] + n = tokens[7] + chi0 = tokens[8] + improper2style[imsym][improper_name] = 'cvff' + improper2params[imsym][improper_name] = (Kchi+' '+n+' '+chi0) + #if improper_style_name == 'cvff': + # improper2params[improper_name] = (Kchi+' '+n+' '+chi0) + # improper_symmetry_subgraph[improper_name] = 'cenJswapIL' + + + elif ((len(tokens) > 7) and (section_name == '#wilson_out_of_plane') + and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('class2') + sys.stderr.write('tokens = ' + str(tokens) + '\n') + + version = tokens[0] + reference = tokens[1] + aorig = [a for a in map(EncodeAName, tokens[2:6])] + + # To avoid redundancy, it is necessary to order the atoms + # in the interaction so that two equivalent ways of ordering + # the atoms in an improper interaction do not get misinterpreted + # as two different types of improper interactions. So we sort + # the 3 "leaf" atoms surrounding the central "hub" by name. + + atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) + + # This will effect the formula for the energy. + # (specifically the "chi0" parameter) + # When we lookup the various cross-term interactions for that + # same improper interaction, we will be sure to sort them + # in the same way to make sure those interactions are + # associated with the same improper interaction. + + imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) + #improper_symmetry_subgraph_or[improper_name] = 'dihedrals_nosym' (<--no) + imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' + improper2ver_or[imsym][imp_name_orig] = version + improper2ref_or[imsym][imp_name_orig] = reference + improper2priority_or[imsym][imp_name_orig] = \ + DetermineNumericPriority(section_is_auto, + tokens[2:6], + float(improper2ver_or[imp_name_orig])) + improper_is_secondary_or[imsym][imp_name_orig] = False + #improper2priority[imp_name_orig] = \ + # (section_is_auto, + # improper_is_secondary_or[imp_name_orig], + # improper2priority_or[imp_name_orig]) + K = tokens[6] + chi0 = tokens[7] + + if Parity(permutation) != 0: + # Each time the order of a pair of atoms is swapped in + # the interaction, all 3 of the "X" (chi) angles change sign + # The formula for the ordinary term in the improper + # interaction is Ei = K*((Xijkl + Xkjli + Xljik)/3 - chi0)^2 + # This formula is invariant if we change the sign of all + # Xijkl, Xkjli, Xljik, chi0 + # Hence, we can account for a change in atom order by + # changing the sign of the "chi0" parameter. + # We calculate the "Parity" of the permutation (ie whether + # the permutation has an even or odd number of swaps) + # and multiply chi0 by -1 for each swap. + # It's not clear if this is necessary since in practice + # the "chi0" parameter is usually zero. + + chi0 = str(-1.0*float(chi0)) # same as ('-' + chi0) + + improper2style_or[imsym][imp_name_orig] = 'class2' + improper2params_or[imsym][imp_name_orig] = [K, chi0] + #improper2params[imp_name_orig] = K + ' ' + chi0 + # default values for cross terms: + if not imp_name_orig in improper2class2_aa_or: + improper2class2_aa_or[imsym][imp_name_orig] = '0.0' #(default) + improper2ver_aa_or[imsym][imp_name_orig] = version + improper2ref_aa_or[imsym][imp_name_orig] = reference + # Initially, set all of the angle-angle cross terms to zero + # Start with the first cross term between aorig[0],aorig[1],aorig[2] & aorig[2],aorig[1],aorig[3] + improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' + # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) + improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' + improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' + + elif ((len(tokens) > 6) and (section_name == '#angle-angle') + and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): + if line.lstrip().find('!') == 0: + continue + improper_styles.add('class2') + version = tokens[0] + reference = tokens[1] + aorig = [a for a in map(EncodeAName, tokens[2:6])] + atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) + imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) + imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' + improper2ver_aa_or[imsym][imp_name_orig] = version + improper2ref_aa_or[imsym][imp_name_orig] = reference + K = tokens[6] + improper2style_or[imsym][imp_name_orig] = 'class2' + if not imp_name_orig in improper2params_or: + improper_is_secondary_or[imsym][imp_name_orig] = True #only cross terms have been defined so far + improper2params_or[imsym][imp_name_orig] = ['0.0', '0.0'] + improper2ver_or[imsym][imp_name_orig] = version + improper2ref_or[imsym][imp_name_orig] = reference + improper2priority_or[imsym][imp_name_orig] = 0.0 + if not imp_name_orig in improper2cross: + # then initialize all of the cross terms to zero + improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' + # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) + improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' + improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' + #improper2class2_aa_or[imp_name_orig] = K (not needed) + improper2cross[imp_name_orig][ImCrossTermID(aorig)] = K + + elif (len(tokens) > 0) and (section_name == '#out_of_plane-out_of_plane'): + if line.lstrip().find('!') == 0: + continue + display_OOP_OOP_warning = True + + elif (len(tokens) > 0) and (section_name == '#torsion-torsion_1'): + if line.lstrip().find('!') == 0: + continue + display_torsion_torsion_1_warning = True + + elif section_name == '#templates': + #if line.lstrip().find('!') == 0: + # continue + lines_templates.append(line) + + elif section_name == '#reference': + if line.lstrip().find('!') == 0: + continue + if len(tokens_after_section_name) > 0: + ref_number = int(tokens_after_section_name[0]) + if len(line.strip()) > 0: + lines_references[ref_number].append(line) + + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete this code in a later version + elif (len(tokens) > 3) and (section_name == '#hbond_definition'): + hbondID = tokens[1] + if tokens[2] == 'distance': + hbond2distance[hbondID] = tokens[3] + if tokens[2] == 'angle': + hbond2angle[hbondID] = tokens[3] + if tokens[2] == 'donors': + hbond2donors[hbondID] = map(EncodeAName, tokens[2:]) + if tokens[2] == 'acceptors': + hbond2acceptors[hbondID] = map(EncodeAname(),tokens[2:]) + """ + + + if display_OOP_OOP_warning: + lines_warnings.append('###########################################################\n' + '# WARNING\n' + '# ALL \"out-of-plane_out-of_plane\" INTERACTIONS ARE IGNORED.\n' + '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' + '# \"out-of-plane_out-of_plane\" interactions are not yet supported in LAMMPS\n' + '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' + '# LAMMPS compatible parameter files for these interactions.\n' + '###########################################################\n') + + if display_torsion_torsion_1_warning: + lines_warnings.append('###########################################################\n' + '# WARNING\n' + '# ALL \"torsion_torsion_1\" INTERACTIONS ARE IGNORED.\n' + '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' + '# \"torsion_torsion_1\" interactions are not yet supported in LAMMPS\n' + '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' + '# LAMMPS compatible parameter files for these interactions.\n' + '###########################################################\n') + + + sys.stderr.write(' done.\n' + 'building lookup tables...') + + + + + + + + """ + --- these next few lines of code appear to be unnecessary. + --- I'll probably delete them eventually + if len(hbond2params) > 0: + sys.stdout.write('\n\n write_once("In Settings") {\n') + if hbond_style == 'hbond/dreiding/lj': + for hbondID, angle in hbond2angle: + hbond2params[hbondID] = hbond2distance[hbondID]+' '+hbond2angle[hbondID] ##<--this is not correct + for hbondID, params in hbond2params: + for donor in hbond2donors[hbondID]: + for acceptor in hbond2acceptors[hbondID]: + for hydrogen in hbond2hydrogens[hbondID]: + sys.stdout.write('pair_coeff @atom:'+donor+' @atom:'+acceptor+' '+hbond_style+' @atom:'+hydrogen+' i '+params+'\n') + sys.stdout.write(' } # (DREIDING style H-bond parameters)\n\n\n') + """ + + + + + + + sys.stderr.write(" done.\n") + sys.stderr.write("Trying all combinations of atom types...") + + + + + + + + ##################### POST-PROCESSING ######################## + + + + + + for ang_name_orig in angle2params_or: + + is_auto = (ang_name_orig.find('auto_') == 0) + + atom_names = ExtractANames(ang_name_orig) + + num_angles = 0 + + atom_combos = [set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy BOTH angle_equivalences and bond_equivalences. + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @angle interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + auto_angle2atom = [auto_angleend2atom, + auto_anglecenter2atom, + auto_angleend2atom] + + for i in range(0, 3): + angle_atom_name = atom_names[i] + sys.stderr.write('DEBUG: angle_atom_name = '+angle_atom_name+'\n') + if not is_auto: + assert(angle_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_angle2atom['+angle_atom_name+'] = '+ + str(equiv_angle2atom[angle_atom_name])+'\n') + for a in equiv_angle2atom[angle_atom_name]: + atom_combos[i].add(a) + else: + #assert((angle_atom_name[-1] == '_') or (angle_atom_name[0] == '*')) (<--some exceptions. don't assert this) + + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_angle2atom['+str(i)+']['+angle_atom_name+'] = \n' + ' '+str(equiv_angle2atom[i][angle_atom_name])+'\n') + for a in auto_angle2atom[i][angle_atom_name]: + atom_combos[i].add(a) + + found_at_least_one = False + #for a1 in atom_combos[0]: + for a1 in sorted(list(atom_combos[0])): + #for a2 in atom_combos[1]: + for a2 in sorted(list(atom_combos[1])): + #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') + bond_data1 = LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data1 == None: # Save time by continuing only if a + continue # bond was defined between a1 and a2 + + #for a3 in atom_combos[2]: + for a3 in sorted(list(atom_combos[2])): + bond_data2 = LookupBondLength(a2, a3, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data2 == None: + continue + + #bond lengths: + r0s = [0.0, 0.0] + #equivalent atom names used to lookup the bonds: + batoms = [['', ''], ['', '']] + #were "auto" equivalences needed to lookup the bond length? + b_is_auto = [False, False] + r0s[0], batoms[0], b_is_auto[0] = bond_data1 + r0s[1], batoms[1], b_is_auto[1] = bond_data2 + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + batoms.reverse() + batoms[0].reverse() + batoms[1].reverse() + b_is_auto.reverse() + ang_name_full = (ang_name_orig + ',' + + EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + + EncodeInteractionName(batoms[1], b_is_auto[1])) + + + #sys.stderr.write('DEBUG: (a1,a2,a3) = '+str((a1,a2,a3))+', ' + # ' (b11,b12,b21,b22) = '+str(batoms)+'\n') + angle2ref_or[ang_name_full] = reference + angle2style_or[ang_name_full] = 'class2' + theta0_K_params = angle2params_or[ang_name_orig] + angle2params[ang_name_full] = ' '.join(theta0_K_params) + if ang_name_orig in angle2class2_bb_or: + Kbb = angle2class2_bb_or[ang_name_orig] + assert(ang_name_orig in angle2ver_bb_or) + assert(ang_name_orig in angle2ref_bb_or) + else: #(use default values) + Kbb = '0.0' + angle2class2_bb_or[ang_name_orig] = Kbb + angle2ver_bb_or[ang_name_orig] = angle2ver_or[ang_name_orig] + angle2ref_bb_or[ang_name_orig] = angle2ref_or[ang_name_orig] + angle2class2_bb[ang_name_full] = (Kbb+' '+r0s[0]+' '+r0s[1]) + angle2priority_bb = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[1], + float(angle2ver_bb_or[ang_name_orig])) + angle2ver_bb[ang_name_full] = angle2ver_bb_or[ang_name_orig] + angle2ref_bb[ang_name_full] = angle2ref_bb_or[ang_name_orig] + + if ang_name_orig in angle2class2_ba_or: + Kba = angle2class2_ba_or[ang_name_orig] + assert(ang_name_orig in angle2ver_ba_or) + assert(ang_name_orig in angle2ref_ba_or) + else: #(use default values) + Kba = ['0.0', '0.0'] + angle2class2_ba_or[ang_name_orig] = Kba + angle2ver_ba_or[ang_name_orig] = angle2ver_or[ang_name_orig] + angle2ref_ba_or[ang_name_orig] = angle2ref_or[ang_name_orig] + angle2class2_ba[ang_name_full] = (Kba[0]+' '+Kba[1]+' '+r0s[0]+' '+r0s[1]) + angle2sym_ba = (Kba[0] == Kba[1]) + angle2priority_ba = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[1], + angle2ver_ba_or[ang_name_orig]) + angle2ver_ba[ang_name_full] = angle2ver_ba_or[ang_name_orig] + angle2ref_ba[ang_name_full] = angle2ref_ba_or[ang_name_orig] + + version = max((angle2ver_or[ang_name_orig], + angle2ver_bb_or[ang_name_orig], + angle2ver_ba_or[ang_name_orig])) + angle2ver[ang_name_full] = version + angle2ref[ang_name_full] = angle2ref_or[ang_name_orig] + angle2style[ang_name_full] = 'class2' + angle2priority[ang_name_full] = \ + (is_auto, + angle_is_secondary_or[ang_name_orig], + angle2priority_or[ang_name_orig], + angle2priority_bb, + angle2priority_ba) + + if num_angles < len(angle2params): + sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') + sys.stderr.write('DEBUG: len(angle2class2_bb) = '+str(len(angle2class2_bb))+'\n') + sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') + #sys.stderr.write('DEBUG: len(angle2class2_ba) = '+str(len(angle2class2_ba))+'\n') + num_angles = len(angle2params) + + if ((not angle2sym_ba) + and + (atom_names[0] == atom_names[2])): + raise InputError('Error: Unsupported angle interaction: \"@angle:'+str(ang_name_orig)+'\"\n' + ' This interaction has symmetric atom names:\n' + ', '.join(atom_names)+'\n' + ' and yet it lacks symmetry in the corresponding force field parameters.\n' + ' (If this is not a mistake in the .frc file, then explain\n' + ' why to andrew so he can fix this.)\n') + + + found_at_least_one = True + + + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined bond length (r0) in angle: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction + # because at least one of the bond lengths could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + ang_name_full = (ang_name_orig + ',X,X,X,X,X,X') + version = angle2ver_or[ang_name_orig] + reference = angle2ref_or[ang_name_orig] + angle2ref[ang_name_full] = reference + angle2ver[ang_name_full] = version + angle2style[ang_name_full] = 'class2' + angle2params[ang_name_full] = ' '.join(angle2params_or[ang_name_orig]) + # substitute zeros for all the cross term interactions + angle2priority[ang_name_full] = angle2priority_or[ang_name_orig] + angle2class2_bb[ang_name_full] = '0.0 1.0 1.0' + angle2ref_bb[ang_name_full] = reference + angle2ver_bb[ang_name_full] = version + angle2class2_ba[ang_name_full] = '0.0 0.0 1.0 1.0' + angle2ref_ba[ang_name_full] = reference + angle2ver_ba[ang_name_full] = version + #sys.stderr.write('bond_names = ' + str(bond_names) + '\n') + + + + + + ############ POST-PROCESSING DIHEDRALS ########### + + + + for dih_name_orig in dihedral2params_or: + #assert(dih_name_orig in dihedral2class2_mbt_or) + #assert(dih_name_orig in dihedral2class2_ebt_or) + #assert(dih_name_orig in dihedral2class2_bb13_or) + #assert(dih_name_orig in dihedral2class2_at_or) + #assert(dih_name_orig in dihedral2class2_aat_or) + + is_auto = (dih_name_orig.find('auto_') == 0) + + atom_names = ExtractANames(dih_name_orig) + + num_dihedrals = 0 + + atom_combos = [set([]), set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy all three: + # dihedral_equivalences + # bond_equivalences + # angle_equivalences + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @dihedral interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + auto_dihedral2atom = [auto_dihedralend2atom, + auto_dihedralcenter2atom, + auto_dihedralcenter2atom, + auto_dihedralend2atom] + + for i in range(0, 4): + dihedral_atom_name = atom_names[i] + sys.stderr.write('DEBUG: dihedral_atom_name = '+dihedral_atom_name+'\n') + if not is_auto: + assert(dihedral_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_dihedral2atom['+dihedral_atom_name+'] = '+ + str(equiv_dihedral2atom[dihedral_atom_name])+'\n') + for a in equiv_dihedral2atom[dihedral_atom_name]: + atom_combos[i].add(a) + else: + assert((dihedral_atom_name[-1] == '_') or (ange_atom_name[0] == '*')) + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_dihedral2atom['+str(i)+']['+dihedral_atom_name+'] = \n' + ' '+str(equiv_dihedral2atom[i][dihedral_atom_name])+'\n') + for a in auto_dihedral2atom[i][dihedral_atom_name]: + atom_combos[i].add(a) + + found_at_least_one = False + + #for a1 in atom_combos[0]: + for a1 in sorted(list(atom_combos[0])): + + #for a2 in atom_combos[1]: + for a2 in sorted(list(atom_combos[1])): + + #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') + bond_data12 = LookupBondLength(a1, a2, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data12 == None: + # Save time by only continuing if a bond was + # found between a1 and a2 + continue + #for a3 in atom_combos[2]: + for a3 in sorted(list(atom_combos[2])): + bond_data23 = LookupBondLength(a2, a3, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data23 == None: + # Save time by only continuing if a bond was + # found between a2 and a3 + continue + + angle_data123 = LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_anglecenter], + angle2theta0_auto_or) + if angle_data123 == None: + # Save time by only continuing if an angle was + # found between a1, a2, a3 + continue + + + #for a4 in atom_combos[3]: + for a4 in sorted(list(atom_combos[3])): + bond_data34 = LookupBondLength(a3, a4, + atom2equiv_bond, + bond2r0, + atom2auto_bond, + bond2r0_auto) + if bond_data34 == None: + # Save time by only continuing if a bond was + # found between a3 and a4 + continue + + #rest bond lengths: + r0s = [0.0, 0.0, 0,0] + #equivalent atom names used to lookup the bonds: + batoms = [['', ''], ['', ''], ['','']] + #are these bond interactions "auto" interactions? + #were "auto" equivalences needed to lookup the bond length? + b_is_auto = [False, False, False] + r0s[0], batoms[0], b_is_auto[0] = bond_data12 + r0s[1], batoms[1], b_is_auto[1] = bond_data23 + r0s[2], batoms[2], b_is_auto[2] = bond_data34 + + angle_data234 = LookupBondAngle(a2, a3, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_angleend, + atom2auto_anglecenter, + atom2auto_anglecenter], + angle2theta0_auto_or) + if angle_data234 == None: + # Save time by only continuing if an angle was + # found between a2, a3, a4 + continue + + #rest angles: + theta0s = [0.0, 0.0] + #equivalent atom names used to lookup angles: + aatoms = [['', '',''], ['', '','']] + #were "auto" equivalences needed to lookup the bond-angle? + a_is_auto = [False, False] + theta0s[0], aatoms[0], a_is_auto[0] = angle_data123 + theta0s[1], aatoms[1], a_is_auto[1] = angle_data234 + order_reversed = aorig[0] > aorig[-1] + if order_reversed: + batoms.reverse() + batoms[0].reverse() + batoms[1].reverse() + batoms[2].reverse() + b_is_auto.reverse() + theta0s.reverse() + aatoms.reverse() + aatoms[0].reverse() + aatoms[1].reverse() + a_is_auto.reverse() + + #if is_auto: + dih_name_full = (dih_name_orig + ',' + + EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + + EncodeInteractionName(batoms[1], b_is_auto[1]) + ',' + + EncodeInteractionName(batoms[2], b_is_auto[2]) + ',' + + EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + + EncodeInteractionName(aatoms[1], a_is_auto[1])) + #else: + # assert(batoms[0][1] == batoms[1][0]) + # assert(batoms[1][1] == batoms[2][0]) + # assert(aatoms[0][1] == aatoms[1][0]) + # assert(aatoms[0][2] == aatoms[1][1]) + # dih_name_full = dih_name_orig + ',' + \ + # EncodeInteractionName([batoms[0][0], batoms[0][1] + # batoms[2][0], batoms[2][1], + # aatoms[0][0], aatoms[0][1], + # aatoms[0][2], aatoms[1][0]], + # False) + + ########### Fourier terms ########### + #if dih_name_orig in dihedral2param_or: + V_phi0_params = dihedral2params_or[dih_name_orig] + dihedral2params[dih_name_full] = ' '.join(V_phi0_params) + #else: + # dihedral2params[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' + + ########### "mbt", "ebt", and "aat" terms ########### + # "mbt" terms: + if dih_name_orig in dihedral2class2_mbt_or: + Fmbt = dihedral2class2_mbt_or[dih_name_orig] + else: + Fmbt = ['0.0', '0.0', '0.0'] + dihedral2class2_mbt_or[dih_name_orig] = Fmbt + dihedral2ver_mbt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_mbt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2class2_mbt[dih_name_full] = \ + (Fmbt[0]+' '+Fmbt[1]+' '+Fmbt[2]+' '+r0s[1]) + dihedral2priority_mbt = \ + DetermineNumericPriority(is_auto, + batoms[1], + float(dihedral2ver_mbt_or[dih_name_orig])) + dihedral2ver_mbt[dih_name_full] = dihedral2ver_mbt_or[dih_name_orig] + dihedral2ref_mbt[dih_name_full] = dihedral2ref_mbt_or[dih_name_orig] + + # "ebt" terms: + if dih_name_orig in dihedral2class2_ebt_or: + Febt = dihedral2class2_ebt_or[dih_name_orig] + dihedral2sym_ebt = ((Febt[0][0] == Febt[1][0]) and + (Febt[0][1] == Febt[1][1]) and + (Febt[0][2] == Febt[1][2])) + #and (r0s[0] == r0s[2])) + else: + Febt = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] + dihedral2class2_ebt_or[dih_name_orig] = Febt + dihedral2ver_ebt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_ebt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_ebt = True + dihedral2class2_ebt[dih_name_full]= (Febt[0][0] + ' ' + + Febt[0][1] + ' ' + + Febt[0][2] + ' ' + + Febt[1][0] + ' ' + + Febt[1][1] + ' ' + + Febt[1][2] + ' ' + + r0s[0]+' '+r0s[2]) + + dihedral2priority_ebt = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[2], + float(dihedral2ver_ebt_or[dih_name_orig])) + dihedral2ver_ebt[dih_name_full] = dihedral2ver_ebt_or[dih_name_orig] + dihedral2ref_ebt[dih_name_full] = dihedral2ref_ebt_or[dih_name_orig] + + #(Note: large atom_priority number <==> low priority + # Only one of the atom priority numbers should be > 0) + + # "bb13" terms: + if dih_name_orig in dihedral2class2_bb13_or: + Kbb13 = dihedral2class2_bb13_or[dih_name_orig] + #dihedral2sym_bb13 = (r0s[0] == r0s[2]) + dihedral2sym_bb13 = True + else: + Kbb13 = '0.0' + dihedral2class2_bb13_or[dih_name_orig] = Kbb13 + dihedral2ver_bb13_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_bb13_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_bb13 = True + + dihedral2class2_bb13[dih_name_full] = (Kbb13+' '+r0s[0]+' '+r0s[2]) + dihedral2priority_bb13 = \ + DetermineNumericPriority(is_auto, + batoms[0] + batoms[2], + float(dihedral2ver_bb13_or[dih_name_orig])) + dihedral2ver_bb13[dih_name_full] = dihedral2ver_bb13_or[dih_name_orig] + dihedral2ref_bb13[dih_name_full] = dihedral2ref_bb13_or[dih_name_orig] + + + ########### "at" and "aat" terms ########### + # "at" terms: + if dih_name_orig in dihedral2class2_at_or: + Fat = dihedral2class2_at_or[dih_name_orig] + dihedral2sym_at = ((Fat[0][0] == Fat[1][0]) and + (Fat[0][1] == Fat[1][1]) and + (Fat[0][2] == Fat[1][2])) + #and (theta0[0] == theta0[1])) + else: + Fat = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] + dihedral2class2_at_or[dih_name_orig] = Fat + dihedral2ver_at_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_at_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_at = True + dihedral2class2_at[dih_name_full] = \ + (Fat[0][0] + ' ' + + Fat[0][1] + ' ' + + Fat[0][2] + ' ' + + Fat[1][0] + ' ' + + Fat[1][1] + ' ' + + Fat[1][2] + ' ' + + theta0s[0] + ' ' + + theta0s[1]) + dihedral2priority_at = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1], + float(dihedral2ver_at_or[dih_name_orig])) + dihedral2ver_at[dih_name_full] = dihedral2ver_at_or[dih_name_orig] + dihedral2ref_at[dih_name_full] = dihedral2ref_at_or[dih_name_orig] + + + # "aat" terms: + if dih_name_orig in dihedral2class2_aat_or: + Kaat = dihedral2class2_aat_or[dih_name_orig] + #dihedral2sym_aat = (theta0[0] == theta0[1]) + dihedral2sym_aat = True + else: + Kaat = '0.0' + dihedral2class2_aat_or[dih_name_orig] = Kaat + dihedral2ver_aat_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] + dihedral2ref_aat_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] + dihedral2sym_aat = True + dihedral2class2_aat[dih_name_full] = \ + (Kaat+' '+theta0s[0]+' '+theta0s[1]) + dihedral2priority_aat = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1], + float(dihedral2ver_aat_or[dih_name_orig])) + dihedral2ver_aat[dih_name_full] = dihedral2ver_aat_or[dih_name_orig] + dihedral2ref_aat[dih_name_full] = dihedral2ref_aat_or[dih_name_orig] + + if len(dihedral2params) > num_dihedrals: + sys.stderr.write('DEBUG: dihedral['+dih_name_full+']:\n' + '(r12,r23,r34) = (' + +r0s[0]+','+r0s[1]+','+r0s[2]+') \n' + '(theta123,theta234) = (' + +theta0s[0]+','+theta0s[1]+') \n') + sys.stderr.write('DEBUG: num_dihedrals = len(dihedral2params) = ' + +str(len(dihedral2params))+'\n') + version = max((dihedral2ver_or[dih_name_orig], + dihedral2ver_mbt_or[dih_name_orig], + dihedral2ver_ebt_or[dih_name_orig], + dihedral2ver_bb13_or[dih_name_orig], + dihedral2ver_at_or[dih_name_orig], + dihedral2ver_aat_or[dih_name_orig])) + + dihedral2style[dih_name_full] = 'class2' + dihedral2ver[dih_name_full] = version + dihedral2ref[dih_name_full] = dihedral2ref_or[dih_name_orig] + dihedral2priority[dih_name_full] = \ + (is_auto, + dihedral_is_secondary_or[dih_name_orig], + dihedral2priority_or[dih_name_orig], + dihedral2priority_mbt, + dihedral2priority_ebt, + dihedral2priority_bb13, + dihedral2priority_at, + dihedral2priority_aat) + + num_dihedrals = len(dihedral2params) + + if ((not (dihedral2sym_ebt and + #dihedral2sym_mbt and + # (note: symmetry doesn't make sense for mbt) + dihedral2sym_at and + dihedral2sym_aat and + dihedral2sym_bb13)) + and + ((atom_names[0] == atom_names[3]) and + (atom_names[1] == atom_names[2]))): + raise InputError('Error: Unsupported dihedral interaction: \"@dihedral:'+str(dih_name_orig)+'\"\n' + ' This interaction has symmetric atom names:\n'+ + ', '.join(atom_names)+'\n'+ + ' and yet it lacks symmetry in the corresponding force field parameters.\n'+ + ' (If this is not a mistake in the .frc file, then explain\n'+ + ' why to andrew so he can fix this.)\n') + + found_at_least_one = True + + + #sys.stderr.write('DEBUG: number of interactions = '+str(len(dihedral2class2_bb))+'\n') + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: ' + + #'# the dihedral interaction between: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction because + # at least one of the bond lengths or bond angles could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + dih_name_full = (dih_name_orig + ',X,X,X,X,X,X,X,X,X,X,X,X') + reference = dihedral2ref_or[dih_name_orig] + version = dihedral2ver_or[dih_name_orig] + dihedral2ref[dih_name_full] = reference + dihedral2ver[dih_name_full] = version + dihedral2style[dih_name_full] = 'class2' + dihedral2priority[dih_name_full] = dihedral2priority_or[dih_name_orig] + dihedral2params[dih_name_full] = ' '.join(dihedral2params_or[dih_name_orig]) + # substitute zeros for all the cross term interactions + + dihedral2class2_mbt[dih_name_full] = '0.0 0.0 0.0 1.0' + dihedral2ref_mbt[dih_name_full] = reference + dihedral2ver_mbt[dih_name_full] = version + + dihedral2class2_ebt[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0' + dihedral2ref_ebt[dih_name_full] = reference + dihedral2ver_ebt[dih_name_full] = version + + dihedral2class2_bb13[dih_name_full] = '0.0 1.0 1.0' + dihedral2ref_bb13[dih_name_full] = reference + dihedral2ver_bb13[dih_name_full] = version + + dihedral2class2_at[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0' + dihedral2ref_at[dih_name_full] = reference + dihedral2ver_at[dih_name_full] = version + + dihedral2class2_aat[dih_name_full] = '0.0 120.0 120.0' + dihedral2ref_aat[dih_name_full] = reference + dihedral2ver_aat[dih_name_full] = version + + + + + + + + + ############ POST-PROCESSING IMPROPERS ########### + + + + + imsym = 'cenJsortIKL' + for imp_name_orig in improper2cross[imsym]: + + if improper2style_or[imsym][imp_name_orig] != 'class2': + continue + + assert(imp_name_orig in improper2params_or[imsym]) + assert(imp_name_orig in improper2class2_aa_or[imsym]) + + is_auto = (imp_name_orig.find('auto') == 0) + + atom_names = ExtractANames(imp_name_orig) + + num_impropers = 0 + + atom_combos = [set([]), set([]), set([]), set([])] + + # We must consider every possible combination of atom types + # which satisfy both: + # improper_equivalences + # angle_equivalences + # ...AND we must consider BOTH regular AND auto equivalences. + # For each combination generate a separate @improper interaction. + # (I fear this will make the resulting .LT file large.) + + # Use different auto equivalence lookup tables for different + # atoms in the interaction. (ie the "center" and "end" atoms) + + auto_improper2atom = [auto_improperend2atom, + auto_impropercenter2atom, + auto_improperend2atom, + auto_improperend2atom] + + for i in range(0, 4): + improper_atom_name = atom_names[i] + sys.stderr.write('DEBUG: improper_atom_name = '+improper_atom_name+'\n') + if not is_auto: + assert(improper_atom_name[-1] != '_') + # assume regular equivalences when looking up atom types + sys.stderr.write('DEBUG: equiv_improper2atom['+improper_atom_name+'] = '+ + str(equiv_improper2atom[improper_atom_name])+'\n') + for a in equiv_improper2atom[improper_atom_name]: + atom_combos[i].add(a) + else: + assert((improper_atom_name[-1] == '_') or (improper_atom_name[0] == 'X')) + # assume "auto" equivalences when looking up atom types + sys.stderr.write('DEBUG: auto_improper2atom['+str(i)+']['+improper_atom_name+'] = \n' + ' '+str(auto_improper2atom[i][improper_atom_name])+'\n') + for a in auto_improper2atom[i][improper_atom_name]: + atom_combos[i].add(a) + + is_auto = IsAutoInteraction(imp_name_orig) # is this an "auto" interaction? + + atom_names = ExtractANames(imp_name_orig) # names of all 4 atoms + lnames = [atom_names[0], atom_names[2], atom_names[3]] # names of "leaf" atoms + + #M1 = improper2cross[imp_name_orig][ 2 ] + #M2 = improper2cross[imp_name_orig][ 0 ] + #M3 = improper2cross[imp_name_orig][ 3 ] + + #try: + M1 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], + atom_names[1], + atom_names[2], + atom_names[3]])] + #except KeyError: + # M1 = '0.0' + + #try: + M2 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[2], + atom_names[1], + atom_names[0], + atom_names[3]])] + #except KeyError: + # M2 = '0.0' + + #try: + M3 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], + atom_names[1], + atom_names[3], + atom_names[2]])] + #except KeyError: + # M3 = '0.0' + + + + + + + # ###### Symmetry: ###### + # Unfortunately, it's time to wade into the messy issue of symmetry. + # We desire a way to detect whether an improper interaction + # between 4 atoms is invariant with respect to atom reordering + # of the 3 peripheral "leaf" atoms which surround the central atom. + # In principle, any rearrangement of atoms would require a separate + # class2 improper interaction. However, in some cases, when the + # parameters for these rearrangements are symmetric, we can detect + # that and warn moltemplate that it is not necessary to generate new + # improper interactions for every conceivable permutation of these + # atoms. Figuring out when it is safe to do that is a headache. + # (...but it's necessary. Otherwise each junction in the molecule + # will generate 3*2*1=6 improper interactions which are usually + # redundant. This will slow down the simulation significantly + # and may make it difficult to compare the resulting LAMMPS + # input files with those generated by other tools like msi2lmp.) + # + # To make this easier, I store the parameters in arrays which + # are arranged in a more symmetric way + M = [0.0, 0.0, 0.0] + theta0 = [0.0, 0.0, 0.0] + # noti3[i] = the sorted tuple of integers from the + # set {0,1,2} which remain after deleting i + noti3 = ((1,2), (0,2), (0,1)) + i_neigh = [ ([0,2,3][ noti3[i][0] ], # neighbor leaves of ith leaf + [0,2,3][ noti3[i][1] ]) for i in range(0,3)] + for i in range(0, 3): + # You will notice the pattern "[0,2,3][i]" appears often in the + # code below because for class 2 force-fields, the second atom + # (with index 1) is the central atom ("hub" atom), and the three + # that surround it ("leaf" atoms) have indices 0,2,3. I want + # to skip over the central atoms and loop over the leaf atoms + imTermID = ImCrossTermID([atom_names[ i_neigh[i][0] ], + atom_names[ 1 ], + atom_names[ [0,2,3][i] ], + atom_names[ i_neigh[i][1] ]]) + M[i] = float(improper2cross[imp_name_orig][imTermID]) + ##i_leaf = [0,2,3][i] + ##M[i] = float(improper2cross[imp_name_orig][ i_leaf ]) + #angle_name_l = SortByEnds([atom_names[i_neigh[i][0]], + # atom_names[ 1 ], + # atom_names[i_neigh[i][1]]]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + #theta0[i] = float(angle2theta0_or[angle_name]) + + for i in range(0, 3): + if (M[ noti3[i][0] ] == M[ noti3[i][1] ]): + #and (theta0[ noti3[i][0] ] == theta0[ noti3[i][1] ])): + # Then it is safe to swap the order of these two atoms in + # the list of atoms when looking up force-field parameters + improper2sym[imp_name_orig].add(i_neigh[i][0]) + improper2sym[imp_name_orig].add(i_neigh[i][1]) + # Later, I can use these to decide whether or not I need to + # change the default script with symmetry rules. (I'm hoping + # that "cenJsortIKL.py" should work in most cases.) + # CONTINUEHERE: FIGURE OUT WHETHER TO WORRY ABOUT improper2sym + else: + if atom_names[i_neigh[i][0]] == atom_names[i_neigh[i][1]]: + raise InputError('Error: Unsupported improper interaction: \"@improper:'+str(imp_name_orig)+'\"\n' + ' This interaction has matching atom aliases:\n' + ' (@atom:'+str(atom_names[i_neigh[i][0]])+ + ', @atom:'+str(atom_names[i_neigh[i][1]])+')\n' + ' and yet it lacks symmetry in the corresponding force field parameters.\n' + ' (If this is not a mistake in the .frc file, then ask andrew to\n' + ' fix this limitation.)\n') + + + found_at_least_one = False + for a1 in sorted(list(atom_combos[0])): + for a2 in sorted(list(atom_combos[1])): + sys.stderr.write('DEBUG: improper '+imp_name_orig+' substitutions: '+a1+','+a2+',...\n') + for a3 in sorted(list(atom_combos[2])): + #(Note: sorting "atom_combos" makes it faster and easier + # to follow the loop's progress. This nested loop can be very slow.) + theta0s = ['0.0', '0.0', '0.0'] + aatoms = [['', '',''], ['', '',''], ['', '', '']] + #were "auto" equivalences needed to lookup the bond-angle? + a_is_auto = [False, False, False] + # Collect information from the different terms in a class2 improper: + # http://lammps.sandia.gov/doc/improper_class2.html + + # Loop over the neighbors of the central atom in each improper + # interaction and collect all the Mi and Ti parameters. Collect + # them in the order they appear in the formula for the Eaa + # term as it appears in the documentation for improper_style class2: + # + # http://lammps.sandia.gov/doc/improper_class2.html + # + # Eaa = M1 (Tijk - T0)(Tkjl - T2) + #common leaf node: k (index 2) + # M2 (Tijk - T0)(Tijl - T1) + #common leaf node: i (index 0) + # M3 (Tijl - T1)(Tkjl - T2) #common leaf node: l (index 3) + # (I'm trying to match the variable names used in this web page + # I wish the author had chosen the M1,M2,M3, T1,T2,T3 order in more + # symmetric way, or at least in a way that makes more sense to me.) + + #angle_name_l = SortByEnds([atom_names[0], atom_names[1], atom_names[2]]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + #theta01 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a1, a2, a3, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a1, a2, a3 + continue + theta0s[0], aatoms[0], a_is_auto[0] = angle_data + + + for a4 in sorted(list(atom_combos[3])): + theta0s[1] = theta0s[2] = '0.0' + aatoms[1] = aatoms[2] = ['', '',''] + + #angle_name_l = SortByEnds(aatoms[0]) + #angle_name = EncodeInteractionName(angle_name_l[0], is_auto) + + #theta02 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a1, a2, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a1, a2, a4 + continue + theta0s[1], aatoms[1], a_is_auto[1] = angle_data + + #angle_name_l = SortByEnds(aatoms[1]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + + + #theta03 = angle2theta0_or[angle_name] + angle_data = LookupBondAngle(a3, a2, a4, + atom2equiv_angle, + angle2theta0_or, + [atom2auto_improperend, + atom2auto_impropercenter, + atom2auto_improperend], + angle2theta0_auto_or) + if angle_data == None: + # Save time by only continuing if an angle was + # found between a3, a2, a4 + continue + theta0s[2], aatoms[2], a_is_auto[2] = angle_data + + + # The following asserts checks that the two theta0s + # are defined whenever the corresponding M is defined. + # (Note: The order is LAMMPS-implementation specific. + # See http://lammps.sandia.gov/doc/improper_class2.html) + assert((float(theta0s[0]) != 0) or (float(M1) == 0)) + assert((float(theta0s[2]) != 0) or (float(M1) == 0)) + assert((float(theta0s[0]) != 0) or (float(M2) == 0)) + assert((float(theta0s[1]) != 0) or (float(M2) == 0)) + assert((float(theta0s[1]) != 0) or (float(M3) == 0)) + assert((float(theta0s[2]) != 0) or (float(M3) == 0)) + + #angle_name_l = SortByEnds(aatoms[2]) + #angle_name = EncodeInteractionName(angle_name_l, is_auto) + + + imp_name_full = (imp_name_orig + ',' + + EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + + EncodeInteractionName(aatoms[1], a_is_auto[1]) + ',' + + EncodeInteractionName(aatoms[2], a_is_auto[2])) + + #if imp_name_orig in improper2params_or[imsym][imp_name_orig]: + improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imsym][imp_name_orig]) + #else: + # improper2params[imsym][imp_name_full] = '0.0 0.0' + + #if imp_name_orig in improper2cross: + improper2class2_aa[imsym][imp_name_full] = \ + (str(M1)+' '+str(M2)+' '+str(M3)+' '+ + str(theta0s[0])+' '+str(theta0s[1])+' '+str(theta0s[2])) + #else: + # improper2class2_aa[imsym][imp_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' + # improper2ver_aa_or[imsym][imp_name_orig] = improper2ver_or[imsym][imp_name_orig] + # improper2ref_aa_or[imsym][imp_name_orig] = improper2ref_or[imsym][imp_name_orig] + + improper2priority_aa = \ + DetermineNumericPriority(is_auto, + aatoms[0] + aatoms[1] + aatoms[2], + float(improper2ver_aa_or[imsym][imp_name_orig])) + improper2ver_aa[imsym][imp_name_full] = improper2ver_aa_or[imsym][imp_name_orig] + improper2ref_aa[imsym][imp_name_full] = improper2ref_aa_or[imsym][imp_name_orig] + + + version = max((improper2ver_or[imsym][imp_name_orig], + improper2ver_aa_or[imsym][imp_name_orig])) + improper2style[imsym][imp_name_full] = 'class2' + improper2ref[imsym][imp_name_full] = improper2ref_or[imsym][imp_name_orig] + improper2ver[imsym][imp_name_full] = version + improper2priority[imsym][imp_name_full] = \ + (is_auto, + improper_is_secondary_or[imsym][imp_name_orig], + improper2priority_or[imsym][imp_name_orig], + improper2priority_aa) + + if len(improper2params) > num_impropers: + sys.stderr.write('DEBUG: improper['+imp_name_full+']:\n' + 'theta0 = (' + +theta0s[0]+','+theta0s[1]+','+theta0s[2]+')\n') + sys.stderr.write('DEBUG: num_impropers = len(improper2params) = ' + +str(len(improper2params))+'\n') + num_impropers = len(improper2params) + + + found_at_least_one = True + + + if not found_at_least_one: + lines_warnings.append('# WARNING: Undefined rest angle (theta0) in improper: ' + + #'# the improper interaction between: ' + + ' '.join(atom_names)+'\n') + # Then we were unable to define cross terms for this interaction because + # at least one of the equilibrium rest angles could not be determined. + # This usually occurs because most of the .FRC files which are + # in circulation are incomplete. We have to handle this gracefully. + imp_name_full = (imp_name_orig + ',X,X,X,X,X,X,X,X,X') + reference = improper2ref_or[imsym][imp_name_orig] + version = improper2ver_or[imsym][imp_name_orig] + improper2ref[imsym][imp_name_full] = reference + improper2ver[imsym][imp_name_full] = version + improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imp_name_orig]) + CONTINUEHERE + improper2style[imp_name_full] = 'class2' + improper2priority[imp_name_full] = improper2priority_or[imp_name_orig] + # substitute zeros for the cross term interactions + improper2class2_aa[imp_name_full] = '0.0 0.0 0.0 120.0 120.0 120.0' + improper2ref_aa[imp_name_full] = reference + improper2ver_aa[imp_name_full] = version + + + + + + sys.stderr.write("done\n") + sys.stderr.write("Converting to moltemplate format...\n") + + + + + + ##################### BEGIN WRITING FILE ##################### + + + + + + sys.stdout.write("# This file was generated automatically using:\n") + sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") + sys.stdout.write("\n\n") + sys.stdout.write(ffname + " {\n\n") + + sys.stdout.write("\n" + " # AtomType Mass # \"Description\" (version, reference)\n\n") + sys.stdout.write(" write_once(\"Data Masses\") {\n") + for atype in atom2mass: + sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype])) + sys.stdout.write(" # ") + if atype in atom2element: + sys.stdout.write(atom2element[atype] + ", ") + #sys.stdout.write(atom2descr[atype]) + sys.stdout.write("\"" + atom2descr[atype] + "\"") + sys.stdout.write(" (") + if atype in atom2numbonds: + sys.stdout.write("nbonds="+str(atom2numbonds[atype])+", ") + sys.stdout.write("ver=" + atom2ver[atype] + + ", ref=" + atom2ref[atype]) + sys.stdout.write(")\n") + sys.stdout.write(" } #(end of atom masses)\n\n\n") + + + + + + + + + + + + + sys.stdout.write(" # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ----------\n" + " # Each type of atom has a separate ID used for looking up bond parameters\n" + " # and a separate ID for looking up 3-body angle interaction parameters\n" + " # and a separate ID for looking up 4-body dihedral interaction parameters\n" + " # and a separate ID for looking up 4-body improper interaction parameters\n" + #" # (This is because there are several different types of sp3 carbon atoms\n" + #" # which have the same torsional properties when within an alkane molecule,\n" + #" # for example. If they share the same dihedral-ID, then this frees us\n" + #" # from being forced define separate dihedral interaction parameters\n" + #" # for all of them.)\n" + " # The complete @atom type name includes ALL of these ID numbers. There's\n" + " # no need to force the end-user to type the complete name of each atom.\n" + " # The \"replace\" command used below informs moltemplate that the short\n" + " # @atom names we have been using abovee are equivalent to the complete\n" + " # @atom names used below:\n\n") + + for atype in atom2ffid: + #ffid = atype + "_ffid" + atom2ffid[atype] + sys.stdout.write(" replace{ @atom:" + atype + + " @atom:" + atom2ffid[atype] + " }\n") + + sys.stdout.write("\n\n\n\n") + + + sys.stdout.write(" # --------------- Non-Bonded Interactions: ---------------------\n" + " # Syntax:\n" + " # pair_coeff AtomType1 AtomType2 pair_style_name parameters...\n\n") + + sys.stdout.write(" write_once(\"In Settings\") {\n") + + for atype in pair2params: + assert(atype in pair2style) + if IsAutoInteraction(bond_name): + assert(atype in atom2auto_pair) + if include_auto_equivalences: + sys.stdout.write(' pair_coeff @atom:*,ap' + atom2auto_pair[atype] + + ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap' + atom2auto_pair[atype] + + ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic* ' + + pair2style[atype] + ' ' + + pair2params[atype] + + ' # (ver=' + pair2ver[atype] + + ', ref=' +pair2ref[atype] + ')\n') + else: + continue + else: + assert(atype in atom2equiv_pair) + sys.stdout.write(' pair_coeff ' + + '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + + '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + + pair2style[atype] + ' ' + + pair2params[atype] + + ' # (ver=' + pair2ver[atype] + + ', ref=' +pair2ref[atype] + ')\n') + sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") + + + + + + + + ################# Print Charge By Bond Interactions ################## + charge_pair_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(charge_pair_priority.items())], + key=itemgetter(1), + reverse=True)] + + if len(charge_pair_priority) > 0: + sys.stdout.write(" # ---------- Charge By Bond (a.k.a. \"bond equivalences\") ----------\n") + # Print rules for generating (2-body) "bond" interactions: + sys.stdout.write('\n\n\n' + ' write_once("Data Charge By Bond") {\n') + for bond_name in charge_pair_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(bond_name)] + # Did the user ask us to include "auto" interactions? + if IsAutoInteraction(bond_name): + if include_auto_equivalences: + sys.stdout.write(' @atom:*,ap*,aq' + anames[0] + + ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap*,aq' + anames[1] + + ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + + ' ' + bond2chargepair[bond_name] + + " # (ver=" + charge_pair_ver[bond_name] + + ", ref=" + charge_pair_ref[bond_name] + ")\n") + else: + continue + else: + sys.stdout.write(' @atom:*,p*,b' + anames[0] + ',a*,d*,i* ' + + ' @atom:*,p*,b' + anames[1] + ',a*,d*,i* ' + + ' ' + bond2chargepair[bond_name] + + " # (ver=" + charge_pair_ver[bond_name] + + ", ref=" + charge_pair_ref[bond_name] + ")\n") + sys.stdout.write(' } #(end of Charge by Bond (bond equivalences))\n\n' + '\n\n\n\n') + + + + + + + + ################# Print 2-body Bond Interactions ################## + + bond_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(bond2priority.items())], + key=itemgetter(1), + reverse=True)] + + if len(bond2priority) > 0: + sys.stdout.write(" # --------------- Bond Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (2-body) "bond" interactions: --\n' + ' # BondType AtomType1 AtomType2\n') + sys.stdout.write('\n' + ' write_once("Data Bonds By Type') + if bond_symmetry_subgraph != '': + sys.stdout.write(' ('+bond_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for bond_name in bond_names_priority_high_to_low: + if not (bond2style[bond_name] in + bond_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(bond_name)] + # Did the user ask us to include "auto" interactions? + if IsAutoInteraction(bond_name): + if include_auto_equivalences: + sys.stdout.write(' @bond:' + bond_name + ' ' + + ' @atom:*,ap*,aq*,ab' + anames[0] + + ',aae*,aac*,ade*,adc*,aie*,aic*' + + ' @atom:*,ap*,aq*,ab' + anames[1] + + ',aae*,aac*,ade*,adc*,aie*,aic*' + + '\n') + else: + continue + else: + sys.stdout.write(' @bond:' + bond_name + ' ' + + ' @atom:*,b' + anames[0] + ',a*,d*,i* ' + + ' @atom:*,b' + anames[1] + ',a*,d*,i* ' + + '\n') + + sys.stdout.write(' } # end of "Data Bonds By Type" section\n' + '\n') + + # Print the force-field parameters for these bond interactions: + sys.stdout.write('\n\n' + ' # ------------ Bond Parameters: ----------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # bond_coeff BondTypeName BondStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for bond_name in bond_names_priority_high_to_low: + if not (bond2style[bond_name] in + bond_styles_selected): + continue + # Did the user ask us to include "auto" interactions? + if (IsAutoInteraction(bond_name) and + (not include_auto_equivalences)): + continue + sys.stdout.write(' bond_coeff @bond:'+bond_name+' '+ + bond2style[bond_name] + ' ' + + bond2params[bond_name] + + " # (ver=" + bond2ver[bond_name] + + ", ref=" +bond2ref[bond_name] + ")\n") + + sys.stdout.write(' } # end of bond_coeff commands\n' + '\n\n') + + + + + + + ################# Print 3-body Angle Interactions ################## + + ang_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(angle2priority.items())], + key=itemgetter(1), + reverse=True)] + + ang_name_abbr = {} #optional abbreviated name for each interaction + ang_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(angle2priority) > 0: + sys.stdout.write(" # --------------- Angle Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (3-body) "angle" interactions: --\n' + ' # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2]\n') + sys.stdout.write('\n' + ' write_once("Data Angles By Type') + if angle_symmetry_subgraph != '': + sys.stdout.write(' ('+angle_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for angle_name in ang_names_priority_high_to_low: + if not (angle2style[angle_name] in + angle_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(angle_name)] + + angle_is_auto = IsAutoInteraction(angle_name) + if angle2style[angle_name] == 'class2': + anm = [a for a in map(DecodeAName, anames)] + bnames = [[a for a in map(DecodeAName, anames[3:5])], + [a for a in map(DecodeAName, anames[5:7])]] + bond_is_auto1 = IsAutoInteraction(anames[3]) + bond_is_auto2 = IsAutoInteraction(anames[5]) + + if ((angle_is_auto or bond_is_auto1 or bond_is_auto2) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (angle_is_auto or bond_is_auto1 or bond_is_auto2): + if angle2style[angle_name] == 'class2': + assert(bnames[0][1] == bnames[1][0]) + # Optional: Shorten the angle name since some of the atom's bond names are redundant: + ang_name_abbr[angle_name] = EncodeInteractionName(map(EncodeAName, + anm[0:3] + + #[anm[3],anm[4],anm[6]], + [bnames[0][0],bnames[0][1],bnames[1][1]]), + angle_is_auto) + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b'+bnames[0][0]+',a'+anames[0]+',d*,i* ' + + ' @atom:*,p*,b'+bnames[0][1]+',a'+anames[1]+',d*,i* ' + + ' @atom:*,p*,b'+bnames[1][1]+',a'+anames[2]+',d*,i*' + '\n') + else: + ang_name_abbr[angle_name] = angle_name + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b*,a'+anames[0]+',d*,i* ' + + ' @atom:*,p*,b*,a'+anames[1]+',d*,i* ' + + ' @atom:*,p*,b*,a'+anames[2]+',d*,i*' + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + ang_name_abbr[angle_name] = angle_name #(full name) + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ') + + if angle2style[angle_name] == 'class2': + + bshared = 'b*' #(default. overidden below) + abshared = 'ab*' #(default. overidden below) + + if angle_is_auto: + a1 = a2 = a3 = 'a*' #Then, dont use regular equivalences for these atoms. + aa1 = 'aae' + anames[0] + ',aac*' #Instead use the corresponding "auto" equivalence names + aa2 = 'aae*,aac*' + anames[1] #for these atoms. (There are different auto equivalence names depending + aa3 = 'aae' + anames[2] + ',aac*' #on if the atom appears in the center (c) or end(e) of the 3-body angle) + else: + a1 = 'a' + anames[0] #In this case, use use (regular) equivalence names + a2 = 'a' + anames[1] #for these atoms + a3 = 'a' + anames[2] + aa1 = aa2 = aa3 = 'aae*,aac*' + + if not bond_is_auto1: + b11 = 'b' + bnames[0][0] #(bond atom equivalent name) + b12 = 'b' + bnames[0][1] #(bond atom equivalent name) + bshared = 'b' + bnames[0][1] #(bond atom equivalent name) + ab11 = ab12 = 'ab*' + else: + b11 = b12 = 'b*' + ab11 = 'ab' + bnames[0][0] #(auto bond atom name) + ab12 = 'ab' + bnames[0][1] #(auto bond atom name) + abshared = 'ab' + bnames[0][1] #(auto bond atom name) + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,'+b11+','+a1+',d*,i*,' + + 'ap*,aq*,'+ab11+','+aa1+ + ',ade*,adc*,aie*,aic*') + if not bond_is_auto2: + b21 = 'b' + bnames[1][0] #(bond atom equivalent name) + b22 = 'b' + bnames[1][1] #(bond atom equivalent name) + assert((bshared == 'b*') or (bshared == 'b' + bnames[1][0])) + bshared = 'b' + bnames[1][0] + ab21 = ab22 = 'ab*' + else: + b21 = b22 = 'b*' + ab21 = 'ab' + bnames[1][0] #(auto bond atom name) + ab22 = 'ab' + bnames[1][1] #(auto bond atom name) + assert((abshared == 'ab*') or (abshared == 'ab' + bnames[1][0])) + abshared = 'ab' + bnames[1][0] + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,'+bshared+','+a2+',d*,i*,' + + 'ap*,aq*,'+abshared+','+aa2+ + ',ade*,adc*,aie*,aic*') + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,'+b22+','+a3+',d*,i*,' + + 'ap*,aq*,'+ab22+','+aa3+ + ',ade*,adc*,aie*,aic*') + sys.stdout.write('\n') + else: + sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae'+anames[0]+'aac*,ade*,adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac'+anames[1]+',ade*,adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae'+anames[2]+'aac*,ade*,adc*,aie*,aic* ' + '\n') + + assert(ang_name_abbr[angle_name] not in ang_name_abbr_used) + ang_name_abbr_used.add(ang_name_abbr[angle_name]) + + sys.stdout.write(' } # end of "Data Angles By Type" section\n' + '\n') + + # Print the force-field parameters for these angle interactions: + sys.stdout.write('\n\n' + ' # ------- Angle Force Field Parameters: -------') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # angle_coeff AngleTypeName AngleStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for angle_name in ang_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(angle_name)] + if not (angle2style[angle_name] in + angle_styles_selected): + continue + + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(angle_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if angle_name not in ang_name_abbr: + continue + + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' ' + + angle2params[angle_name] + + " # (ver=" + angle2ver[angle_name] + + ", ref=" + angle2ref[angle_name] + ")\n") + if angle_name in angle2class2_bb: + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' bb ' + + angle2class2_bb[angle_name] + + " # (ver=" + angle2ver_bb[angle_name] + + ", ref=" + angle2ref_bb[angle_name] + ")\n") + + assert(angle_name in angle2class2_ba) + sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ + angle2style[angle_name] + ' ba ' + + angle2class2_ba[angle_name] + + " # (ver=" + angle2ver_ba[angle_name] + + ", ref=" + angle2ref_ba[angle_name] + ")\n") + sys.stdout.write(' } # end of angle_coeff commands\n' + '\n\n') + + + + + + + + ################# Print 4-body Dihedral Interactions ################## + + dih_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(dihedral2priority.items())], + key=itemgetter(1), + reverse=True)] + + dih_name_abbr = {} #optional abbreviated name for each interaction + dih_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(dih_names_priority_high_to_low) > 0: + sys.stdout.write(' # --------------- Dihedral Interactions: ---------------------\n') + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (4-body) "dihedral" interactions: --\n' + ' # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') + sys.stdout.write('\n\n' + ' write_once("Data Dihedrals By Type') + if dihedral_symmetry_subgraph != '': + sys.stdout.write(' ('+dihedral_symmetry_subgraph+')') + sys.stdout.write('") {\n') + + + + for dihedral_name in dih_names_priority_high_to_low: + if not (dihedral2style[dihedral_name] in + dihedral_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(dihedral_name)] + + dihedral_is_auto = IsAutoInteraction(dihedral_name) + if dihedral2style[dihedral_name] == 'class2': + anm = [a for a in map(DecodeAName, anames)] + bnames = [[a for a in map(DecodeAName, anames[4:6])], + [a for a in map(DecodeAName, anames[6:8])], + [a for a in map(DecodeAName, anames[8:10])]] + bond_is_auto1 = IsAutoInteraction(anames[4]) + bond_is_auto2 = IsAutoInteraction(anames[6]) + bond_is_auto3 = IsAutoInteraction(anames[8]) + ang_names = [[a for a in map(DecodeAName, anames[10:13])], + [a for a in map(DecodeAName, anames[13:16])]] + angle_is_auto1 = IsAutoInteraction(anames[10]) + angle_is_auto2 = IsAutoInteraction(anames[13]) + + if ((dihedral_is_auto or + angle_is_auto1 or angle_is_auto2 or + bond_is_auto1 or bond_is_auto2 or bond_is_auto3) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (dihedral_is_auto or + angle_is_auto1 or angle_is_auto2 or + bond_is_auto1 or bond_is_auto2 or bond_is_auto3): + + if dihedral2style[dihedral_name] == 'class2': + assert(bnames[0][1] == bnames[1][0]) + assert(bnames[1][1] == bnames[2][0]) + assert(ang_names[0][1] == ang_names[1][0]) + assert(ang_names[0][2] == ang_names[1][1]) + + # Optional: Shorten the dihedral name since some of the atom's bond names are redundant: + dih_name_abbr[dihedral_name] = EncodeInteractionName(map(EncodeAName, + anm[0:4] + + #[bnames[0][0], bnames[0][1], + # bnames[1][1], bnames[2][1]] + [anm[4],anm[5],anm[7],anm[9]]+ + #[ang_names[0][0], + # ang_names[0][1], + # ang_names[0][2], + # ang_names[1][2]] + [anm[10],anm[11],anm[12],anm[15]]), + is_auto) + + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b'+bnames[0][0]+',a'+ang_names[0][0]+',d'+anames[0]+',i* ' + + ' @atom:*,p*,b'+bnames[0][1]+',a'+ang_names[0][1]+',d'+anames[1]+',i* ' + + ' @atom:*,p*,b'+bnames[1][1]+',a'+ang_names[0][2]+',d'+anames[2]+',i* ' + ' @atom:*,p*,b'+bnames[2][1]+',a'+ang_names[1][2]+',d'+anames[3]+',i*' + '\n') + else: + dih_name_abbr[dihedral_name] = dihedral_name + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b*,a*,d'+anames[0]+',i* ' + + ' @atom:*,p*,b*,a*,d'+anames[1]+',i* ' + + ' @atom:*,p*,b*,a*,d'+anames[2]+',i* ' + ' @atom:*,p*,b*,a*,d'+anames[3]+',i*' + + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + dih_name_abbr[dihedral_name] = dihedral_name #(full name) + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ') + + if dihedral2style[dihedral_name] == 'class2': + + # equivalent names of atoms shared by more than one bond: + # (names ending in * mean they were unspecified for this + # dihedral interaction. By default, this is the case.) + bshared1 = 'b*' #(default. overidden below) + bshared2 = 'b*' #(default. overidden below) + abshared1 = 'ab*' #(default. overidden below) + abshared2 = 'ab*' #(default. overidden below) + + # equivalent names of atoms shared by more than one angle interaction: + # (names ending in * mean they were unspecified for this + # dihedral interaction. By default, this is the case.) + ashared1 = 'a*' #(default. overidden below) + ashared2 = 'a*' #(default. overidden below) + aac_shared1 = 'aac*' #(default. overidden below) + aae_shared1 = 'aae*' #(default. overidden below) + aac_shared2 = 'aac*' #(default. overidden below) + aae_shared2 = 'aae*' #(default. overidden below) + + if dihedral_is_auto: + d1 = d2 = d3 = d4 = 'd*' #Then, dont use regular equivalences for these atoms. + ad1 = 'ade' + anames[0] + ',adc*' #Instead use the corresponding "auto" + ad2 = 'ade*,adc*' + anames[1] #equivalence names for these atoms. + ad3 = 'ade*,adc*' + anames[1] #(There are different auto equivalence names depending upon + ad4 = 'ade' + anames[2] + ',adc*' # if the atom appears in the center (c) or end(e) of the dihedral) + else: + d1 = 'd' + anames[0] # In this case, use use (regular) equivalence names + d2 = 'd' + anames[1] # for these atoms + d3 = 'd' + anames[2] + d4 = 'd' + anames[3] + ad1 = ad2 = ad3 = ad4 = 'ade*,adc*' + + if not bond_is_auto1: + b11 = 'b' + bnames[0][0] #(bond atom equivalent name) + b12 = 'b' + bnames[0][1] #(bond atom equivalent name) + bshared1 = 'b' + bnames[0][1] #(bond atom equivalent name) + ab11 = ab12 = 'ab*' + else: + b11 = b12 = 'b*' + ab11 = 'ab' + bnames[0][0] #(auto bond atom name) + ab12 = 'ab' + bnames[0][1] #(auto bond atom name) + abshared1 = 'ab' + bnames[0][1] #(auto bond atom name) + + if not bond_is_auto2: + b21 = 'b' + bnames[1][0] #(bond atom equivalent name) + b22 = 'b' + bnames[1][1] #(bond atom equivalent name) + assert((bshared1 == 'b*') or (bshared1 == 'b' + bnames[1][0])) + bshared1 = 'b' + bnames[1][0] #(bond atom equivalent name) + assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[1][1])) + bshared2 = 'b' + bnames[1][1] #(bond atom equivalent name) + ab21 = ab22 = 'ab*' + else: + b21 = b22 = 'b*' + ab21 = 'ab' + bnames[1][0] #(auto bond atom name) + ab22 = 'ab' + bnames[1][1] #(auto bond atom name) + assert((abshared1 == 'ab*') or (abshared1 == 'ab' + bnames[1][0])) + abshared1 = 'ab' + bnames[1][0] #(auto bond atom name) + assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[1][1])) + abshared2 = 'ab' + bnames[1][1] #(auto bond atom name) + + if not bond_is_auto3: + b31 = 'b' + bnames[2][0] #(bond atom equivalent name) + b32 = 'b' + bnames[2][1] #(bond atom equivalent name) + assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[2][0])) + bshared2 = 'b' + bnames[2][0] #(bond atom equivalent name) + ab31 = ab32 = 'ab*' + else: + b31 = b32 = 'b*' + ab31 = 'ab' + bnames[2][0] #(auto bond atom name) + ab32 = 'ab' + bnames[2][1] #(auto bond atom name) + assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[2][0])) + abshared2 = 'ab' + bnames[2][0] #(auto bond atom name) + + if not angle_is_auto1: + a11 = 'a' + ang_names[0][0] #(angle atom equivalent name) + a12 = 'a' + ang_names[0][1] #(angle atom equivalent name) + a13 = 'a' + ang_names[0][2] #(angle atom equivalent name) + ashared1 = 'a' + ang_names[0][1] #(angle atom equivalent name) + ashared2 = 'a' + ang_names[0][2] #(angle atom equivalent name) + aa11 = 'aae*,aac*' + aa12 = 'aae*,aac*' + aa13 = 'aae*,aac*' + else: + a11 = a12 = a13 = 'a*' + aa11 = 'aae'+ang_names[0][0]+'aac*' #(auto angle atom name) + aa12 = 'aae*,aac'+ang_names[0][1] #(auto angle atom name) + aa13 = 'aae'+ang_names[0][2]+'aac*' #(auto angle atom name) + aac_shared1 = 'aac'+ang_names[0][1] #(auto angle atom name) + aae_shared2 = 'aae'+ang_names[0][2] #(auto angle atom name) + + if not angle_is_auto2: + a21 = 'a' + ang_names[1][0] #(angle atom equivalent name) + a22 = 'a' + ang_names[1][1] #(angle atom equivalent name) + a23 = 'a' + ang_names[1][2] #(angle atom equivalent name) + assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) + ashared1 = 'a' + ang_names[1][0] #(angle atom equivalent name) + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) + ashared2 = 'a' + ang_names[1][1] #(angle atom equivalent name) + aa21 = 'aae*,aac*' + aa22 = 'aae*,aac*' + aa23 = 'aae*,aac*' + else: + a21 = a22 = a23 = 'a*' + aa21 = 'aae'+ang_names[1][0]+',aac*' #(auto angle atom name) + aa22 = 'aae*,aac'+ang_names[1][1] #(auto angle atom name) + aa23 = 'aae'+ang_names[1][2]+',aac*' #(auto angle atom name) + aae_shared1 = 'aae'+ang_names[1][0] #(auto angle atom name) + aac_shared2 = 'aac'+ang_names[1][1] #(auto angle atom name) + + + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,'+b11+','+a11+','+d1+',i*,' + + 'ap*,aq*,'+ab11+','+aa11+',' + + ad1+',aie*,aic*') + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,'+bshared1+','+ashared1+','+d2+',i*,' + + 'ap*,aq*,'+abshared1+','+aae_shared1+','+aac_shared1+',' + + ad2+',aie*,aic*') + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,'+bshared2+','+ashared2+','+d3+',i*,' + + 'ap*,aq*,'+abshared2+','+aae_shared2+','+aac_shared2+',' + + ad3+',aie*,aic*') + # print atom 4 information: + sys.stdout.write(' @atom:*,p*,'+b32+','+a23+','+d4+',i*,' + + 'ap*,aq*,'+ab32+','+aa23+',' + + ad4+',aie*,aic*') + sys.stdout.write('\n') + else: + assert(dihedral_is_auto) #(so we should use "auto" equivalence names for these atoms) + sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade'+anames[0]+',adc*,aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[1]+',aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[2]+',aie*,aic* ' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade'+anames[3]+',adc*,aie*,aic* ' + '\n') + + + + + assert(dih_name_abbr[dihedral_name] not in dih_name_abbr_used) + dih_name_abbr_used.add(dih_name_abbr[dihedral_name]) + + sys.stdout.write(' } # end of "Data Dihedrals By Type" section\n' + '\n') + + # Print the force-field parameters for these dihedral interactions: + sys.stdout.write('\n\n' + ' # ------- Dihedral Force Field Parameters: -------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') + sys.stdout.write('\n' + ' # Syntax: \n' + ' # dihedral_coeff DihedralTypeName DihedralStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for dihedral_name in dih_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(dihedral_name)] + #if (len(anames) == 4) and dihedral2style[dihedral_name] == 'class2': + # continue + if not (dihedral2style[dihedral_name] in + dihedral_styles_selected): + continue + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(dihedral_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if dihedral_name not in dih_name_abbr: + continue + + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' ' + + dihedral2params[dihedral_name] + + " # (ver=" + dihedral2ver[dihedral_name] + + ", ref=" + dihedral2ref[dihedral_name] + ")\n") + if dihedral_name in dihedral2class2_mbt: + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' mbt ' + + dihedral2class2_mbt[dihedral_name] + + " # (ver=" + dihedral2ver_mbt[dihedral_name] + + ", ref=" + dihedral2ref_mbt[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_ebt) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' ebt ' + + dihedral2class2_ebt[dihedral_name] + + " # (ver=" + dihedral2ver_ebt[dihedral_name] + + ", ref=" + dihedral2ref_ebt[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_at) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' at ' + + dihedral2class2_at[dihedral_name] + + " # (ver=" + dihedral2ver_at[dihedral_name] + + ", ref=" + dihedral2ref_at[dihedral_name] + ")\n") + + assert(dihedral_name in dihedral2class2_aat) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' aat ' + + dihedral2class2_aat[dihedral_name] + + " # (ver=" + dihedral2ver_aat[dihedral_name] + + ", ref=" + dihedral2ref_aat[dihedral_name] + ")\n") + assert(dihedral_name in dihedral2class2_bb13) + sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ + dihedral2style[dihedral_name] + ' bb13 ' + + dihedral2class2_bb13[dihedral_name] + + " # (ver=" + dihedral2ver_bb13[dihedral_name] + + ", ref=" + dihedral2ref_bb13[dihedral_name] + ")\n") + sys.stdout.write(' } # end of dihedral_coeff commands\n' + '\n\n') + + + + + + ################# Print 4-body Improper Interactions ################## + + imp_names_priority_high_to_low = [x[0] for x in + sorted([x for x in reversed(improper2priority.items())], + key=itemgetter(1), + reverse=True)] + + imp_name_abbr = {} #optional abbreviated name for each interaction + imp_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names + + if len(imp_names_priority_high_to_low) > 0: + sys.stdout.write(" # --------------- Improper Interactions: ---------------------\n") + sys.stdout.write('\n' + '\n' + ' # -- Rules for generating (4-body) "improper" interactions: --\n' + ' # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') + sys.stdout.write('\n' + ' write_once("Data Impropers By Type') + if improper_symmetry_subgraph != '': + sys.stdout.write(' ('+improper_symmetry_subgraph+')') + sys.stdout.write('") {\n') + for improper_name in imp_names_priority_high_to_low: + if not (improper2style[improper_name] in + improper_styles_selected): + continue + anames = ['*' if x=='X' else x + for x in ExtractANames(improper_name)] + #if (len(anames) == 4) and improper2style[improper_name] == 'class2': + # continue + ang_names = [[a for a in map(DecodeAName, anames[4:7])], + [a for a in map(DecodeAName, anames[7:10])], + [a for a in map(DecodeAName, anames[10:13])]] + anm = [a for a in map(DecodeAName, anames)] + + improper_is_auto = IsAutoInteraction(improper_name) + if improper2style[improper_name] == 'class2': + angle_is_auto1 = IsAutoInteraction(anames[4]) + angle_is_auto2 = IsAutoInteraction(anames[7]) + angle_is_auto3 = IsAutoInteraction(anames[10]) + + if ((improper_is_auto or + angle_is_auto1 or + angle_is_auto2 or + angle_is_auto3) and + (not include_auto_equivalences)): + continue + + # Can we ignore "auto" interactions? + # (If so, life is much easier) + if not (improper_is_auto or + angle_is_auto1 or + angle_is_auto2 or + angle_is_auto3): + if improper2style[improper_name] == 'class2': + # NOTE: atom orderings here are LAMMPS implementation specific. + # http://lammps.sandia.gov/doc/improper_class2.html + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + assert(ang_names[0][1] == ang_names[1][1] == ang_names[2][1]) + assert(ang_names[0][0] == ang_names[1][0]) + assert(ang_names[1][2] == ang_names[2][2]) + assert(ang_names[2][0] == ang_names[0][2]) + + # Optional: Shorten the improper name since some of the atom's bond names are redundant: + imp_name_abbr[improper_name] = EncodeInteractionName(map(EncodeAName, anm[0:4] + + [ang_names[0][0], + ang_names[0][1], + ang_names[0][2], + ang_names[1][2]]), + #[anm[4],anm[5],anm[6], + #anm[9]], + improper_is_auto) + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,a'+ang_names[0][0]+',d*,i' + anames[0] + + ' @atom:*,p*,b*,a'+ang_names[0][1]+',d*,i' + anames[1] + + ' @atom:*,p*,b*,a'+ang_names[0][2]+',d*,i' + anames[2] + + ' @atom:*,p*,b*,a'+ang_names[1][2]+',d*,i' + anames[3] + + '\n') + else: + imp_name_abbr[improper_name] = improper_name + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,a*,d*,i' + anames[0] + + ' @atom:*,p*,b*,a*,d*,i' + anames[1] + + ' @atom:*,p*,b*,a*,d*,i' + anames[2] + + ' @atom:*,p*,b*,a*,d*,i' + anames[3] + + '\n') + else: + # Consider "auto" interactions and "auto" atom equivalences + imp_name_abbr[improper_name] = improper_name #(full name) + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ') + + if improper2style[improper_name] == 'class2': + + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + + # default angle atom equivalence names: + ashared1 = 'a*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) + ashared2 = 'a*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) + ashared3 = 'a*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) + ashared4 = 'a*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) + + # default auto angle atom equivalence names: + aashared1 = 'aae*,aac*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) + aashared2 = 'aae*,aac*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) + aashared3 = 'aae*,aac*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) + aashared4 = 'aae*,aac*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) + + if improper_is_auto: + i1 = i2 = i3 = i4 = 'i*' #Then, dont use regular equivalences for these atoms. + ai1 = 'aie' + anames[0] + ',aic*' #Instead use the corresponding "auto" equivalence names + ai2 = 'aie*,aic*' + anames[1] #for these atoms. (There are different auto equivalence names depending + ai3 = 'aie' + anames[2] + ',aic*' #on if the atom appears in the center (c) or end(e) + ai4 = 'aie' + anames[3] + ',aic*' + else: + i1 = 'i' + anames[0] #In this case, use use (regular) equivalence names + i2 = 'i' + anames[1] #for these atoms + i3 = 'i' + anames[2] + i4 = 'i' + anames[3] + ai1 = ai2 = ai3 = 'aie*,aic*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto1: + ashared1 = 'a' + ang_names[0][0] + ashared2 = 'a' + ang_names[0][1] + ashared3 = 'a' + ang_names[0][2] + else: + aashared1 = 'aae' + ang_names[0][0] + ',aac*' + aashared2 = 'aae*,aac' + ang_names[0][1] + aashared3 = 'aae' + ang_names[0][2] + ',aac*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto2: + assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) + ashared1 = 'a' + ang_names[1][0] + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) + ashared2 = 'a' + ang_names[1][1] + ashared4 = 'a' + ang_names[1][2] + else: + assert((aashared1 == 'aae*,aac*') or (aashared1 == 'aae' + ang_names[1][0] + ',aac*')) + aashared1 = 'aae' + ang_names[1][0] + ',aac*' + assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[1][1])) + aashared2 = 'aae*,aac' + ang_names[1][1] + aashared4 = 'aae' + ang_names[1][2] + ',aac*' + + #For reference, LAMMPS-specific atom ordering: + #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) + #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) + #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) + if not angle_is_auto3: + assert((ashared3 == 'a*') or (ashared3 == 'a' + ang_names[2][0])) + ashared3 = 'a' + ang_names[2][0] + assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[2][1])) + ashared2 = 'a' + ang_names[2][1] + assert((ashared4 == 'a*') or (ashared4 == 'a' + ang_names[2][2])) + ashared4 = 'a' + ang_names[2][2] + else: + assert((aashared3 == 'aae*,aac*') or (aashared3 == 'aae' + ang_names[2][0] + ',aac*')) + aashared3 = 'aae' + ang_names[2][0] + ',aac*' + assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[2][1])) + aashared2 = 'aae*,aac' + ang_names[2][1] + assert((aashared4 == 'aae*,aac*') or (aashared4 == 'aae' + ang_names[2][2] + ',aac*')) + aashared4 = 'aae' + ang_names[2][2] + ',aac*' + + # print atom 1 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared1+',d*,'+i1+','+ + 'ap*,aq*,ab*,'+aashared1+',ad*,'+ai1) + # print atom 2 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared2+',d*,'+i2+','+ + 'ap*,aq*,ab*,'+aashared2+',ad*,'+ai2) + # print atom 3 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared3+',d*,'+i3+','+ + 'ap*,aq*,ab*,'+aashared3+',ad*,'+ai3) + # print atom 4 information: + sys.stdout.write(' @atom:*,p*,b*,'+ashared4+',d*,'+i4+','+ + 'ap*,aq*,ab*,'+aashared4+',ad*,'+ai4) + sys.stdout.write('\n') + else: + sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[0]+',aic*' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie*,aic'+anames[1]+ + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[2]+',aic*' + ' @atom:*,p*,b*,d*,i*,' + + 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[3]+',aic*' + '\n') + + assert(imp_name_abbr[improper_name] not in imp_name_abbr_used) + imp_name_abbr_used.add(imp_name_abbr[improper_name]) + + + + + sys.stdout.write(' } # end of "Data Impropers By Type" section\n' + '\n') + + # Print the force-field parameters for these improper interactions: + sys.stdout.write('\n\n' + ' # ------- Improper Force Field Parameters: -------\n') + sys.stdout.write(' # For an explanation of these parameters, visit:\n') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') + sys.stdout.write('\n' + '# Syntax: \n' + ' # improper_coeff ImproperTypeName ImproperStyle parameters...\n\n') + sys.stdout.write('\n' + ' write_once("In Settings") {\n') + for improper_name in imp_names_priority_high_to_low: + anames = ['*' if x=='X' else x + for x in ExtractANames(improper_name)] + #if (len(anames) == 4) and improper2style[improper_name] == 'class2': + # continue + # Optional: Shorten the angle name since some of the bnames are redundant: + + is_auto = IsAutoInteraction(improper_name) + + if not (improper2style[improper_name] in + improper_styles_selected): + continue + + # Did the user ask us to include "auto" interactions? + #if (IsAutoInteraction(improper_name) and + # (not include_auto_equivalences)): + # continue + # the if statement above is covered by the following: + if improper_name not in imp_name_abbr: + continue + + sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ + improper2style[improper_name] + ' ' + + improper2params[improper_name] + + " # (ver=" + improper2ver[improper_name] + + ", ref=" + improper2ref[improper_name] + ")\n") + if improper_name in improper2class2_aa: + sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ + improper2style[improper_name] + ' aa ' + + improper2class2_aa[improper_name] + + " # (ver=" + improper2ver_aa[improper_name] + + ", ref=" + improper2ref[improper_name] + ")\n") + sys.stdout.write(' } # end of improper_coeff commands\n' + '\n\n') + + + + sys.stdout.write('\n\n\n\n' + ' # -------------------- Select LAMMPS style(s) ------------------\n' + '\n') + + + sys.stdout.write('\n' + ' # LAMMPS supports many different kinds of bonded and non-bonded\n' + ' # interactions which can be selected at run time. Eventually\n' + ' # we must inform LAMMPS which of them we will need. We specify\n' + ' # this in the "In Init" section: \n\n') + + sys.stdout.write(' write_once("In Init") {\n') + sys.stdout.write(' units real\n') + sys.stdout.write(' atom_style full\n') + + if len(bond_styles) > 0: + sys.stdout.write(' bond_style hybrid') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' ' + bond_style) + sys.stdout.write('\n') + for bond_style in bond_styles: + if not (bond_style in bond_styles_selected): + continue + sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') + sys.stdout.write('\n') + + if len(angle_styles) > 0: + sys.stdout.write(' angle_style hybrid') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' ' + angle_style) + sys.stdout.write('\n') + for angle_style in angle_styles: + if not (angle_style in angle_styles_selected): + continue + sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') + sys.stdout.write('\n') + + if len(dihedral_styles) > 0: + sys.stdout.write(' dihedral_style hybrid') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' ' + dihedral_style) + sys.stdout.write('\n') + for dihedral_style in dihedral_styles: + if not (dihedral_style in dihedral_styles_selected): + continue + sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') + sys.stdout.write('\n') + + if len(improper_styles) > 0: + sys.stdout.write(' improper_style hybrid') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' ' + improper_style) + sys.stdout.write('\n') + for improper_style in improper_styles: + if not (improper_style in improper_styles_selected): + continue + sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') + sys.stdout.write('\n') + + if len(pair_styles) > 0: + sys.stdout.write(' pair_style hybrid') + for pair_style in pair_styles: + if not (pair_style in pair_styles_selected): + continue + sys.stdout.write(' ' + pair_style + + ' ' + pair_style_args[pair_style]) + sys.stdout.write('\n') + for pair_style in pair_styles: + sys.stdout.write(' # '+pair_style2docs[pair_style]+'\n') + sys.stdout.write('\n') + + sys.stdout.write(' pair_modify mix ' + pair_mixing_style + '\n') + sys.stdout.write(' ' + special_bonds_command + '\n') + sys.stdout.write(' ' + kspace_style + '\n') + sys.stdout.write(' } #end of init parameters\n\n') + sys.stdout.write('} # ' + ffname + '\n\n') + + + sys.stdout.write("#\n" + "# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n") + sys.stdout.write("# " + special_bonds_command + "\n") + sys.stdout.write("# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n") + + #sys.stderr.write(' done.\n') + + + if len(lines_templates) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- templates from the original .frc file used for atom type selection: ---\n') + for line in lines_templates: + sys.stdout.write('# '+line) + + if len(lines_references) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- references from the original .frc file: ----\n\n') + for ref_number,lines in sorted(lines_references.items()): + sys.stdout.write('# reference '+str(ref_number)+'\n') + for line in lines: + sys.stdout.write('# '+line) + sys.stdout.write('\n') + + + if len(lines_warnings) > 0: + sys.stdout.write('\n\n\n\n' + '# ---- additional warnings: ----\n') + for line in lines_warnings: + sys.stdout.write(line) + + + if filename_in != '': + file_in.close() + + + + + except InputError as err: + sys.stderr.write('\n\n' + str(err) + '\n') + sys.exit(1) + + + +if __name__ == '__main__': + main() diff --git a/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py similarity index 76% rename from tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py rename to tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py index acb3db5e5c92fe7ed9004dcfda9f0168def1e15d..c5bf317e52b242e61e243a17009219a10c882ef1 100755 --- a/tools/moltemplate/moltemplate/force_fields/tinker/tinkerparm2lt.py +++ b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py @@ -17,8 +17,8 @@ to my knowledge, have not yet been implemented in LAMMPS as of 2017-2-01.) __author__ = 'Jason Lambert and Andrew Jewett' # (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others) -__version__ = '0.2.1' -__date__ = '2017-17-18' +__version__ = '0.3.2' +__date__ = '2018-6-15' import sys @@ -38,10 +38,12 @@ doc_msg = \ " and \"OPLS\" is the name that future moltemplate users will use to refer to\n" + \ " this force-field (optional).\n" + \ "Optional Arguments\n" + \ - " -name FORCEFIELDNAME # Give the force-field a name\n" + \ + " -name FORCEFIELDNAME # Give the force-field a name (recommended)\n" + \ " -file FILE_NAME # Read force field parameters from a file\n" + \ - " -url URL # Read force field parameters from a file on the web\n" + \ - " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + " -url URL # Read force field parameters from a file online\n" + \ + " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ + " -hybrid # Optional LAMMPS \"hybrid\" style compatibility\n" + \ + " -zeropad N # Optional zero-padding for bonded interactions\n" def SplitQuotedString(string, @@ -142,9 +144,13 @@ def main(): dihedral_style_link = "http://lammps.sandia.gov/doc/dihedral_fourier.html" improper_style_name = "harmonic" improper_style_link = "http://lammps.sandia.gov/doc/improper_harmonic.html" + #improper_style_name = "cvff" + #improper_style_link = "http://lammps.sandia.gov/doc/improper_cvff.html" special_bonds_command = "special_bonds lj/coul 0.0 0.0 0.5" mixing_style = "geometric" + use_hybrid = False contains_united_atoms = False + zeropad_ffid = 1 argv = [arg for arg in sys.argv] @@ -183,7 +189,7 @@ def main(): ' for reading.\n') sys.exit(1) del argv[i:i + 2] - + elif argv[i] == '-dihedral-style': if i + 1 >= len(argv): raise Exception( @@ -201,8 +207,9 @@ def main(): elif argv[i] in ('-url', '-in-url'): import urllib2 if i + 1 >= len(argv): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by the name of a force-field file.\n') + raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' + + ' a TINKER file containing force-field information.\n') url = argv[i + 1] try: request = urllib2.Request(url) @@ -211,6 +218,17 @@ def main(): sys.stdout.write("Error: Unable to open link:\n" + url + "\n") sys.exit(1) del argv[i:i + 2] + + elif argv[i] == '-hybrid': + use_hybrid = True + del argv[i:i + 1] + + elif (argv[i] == '-zeropad' or argv[i] == '-zero-pad'): + if (i + 1 >= len(argv)) or (argv[i+1][1:] == '-'): + raise Exception( + 'Error: ' + argv[i] + ' flag should be followed by a positive integer\n') + zeropad_ffid = int(argv[i+1]) + del argv[i:i + 2] elif argv[i] in ('-help', '--help', '-?', '--?'): sys.stderr.write(doc_msg) @@ -276,11 +294,14 @@ def main(): elif (len(tokens) > 4) and (tokens[0] == 'bond'): k = float(tokens[3]) r0 = float(tokens[4]) - bonds_by_type[tokens[1], tokens[2]] = (k, r0) + bonds_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0')] = (k, r0) elif (len(tokens) > 5) and (tokens[0] == 'angle'): k = float(tokens[4]) angle0 = float(tokens[5]) - angles_by_type[tokens[1], tokens[2], tokens[3]] = (k, angle0) + angles_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0')] = (k, angle0) elif (len(tokens) > 11) and (tokens[0] == 'torsion'): if dihedral_style_name == 'fourier': # http://lammps.sandia.gov/doc/dihedral_fourier.html @@ -292,8 +313,10 @@ def main(): K[i] = float(tokens[5 + 3 * i]) d[i] = float(tokens[5 + 3 * i + 1]) n[i] = float(tokens[5 + 3 * i + 2]) - dihedrals_by_type[tokens[1], tokens[2], - tokens[3], tokens[4]] = (K, n, d) + dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (K, n, d) elif dihedral_style_name == 'opls': # http://lammps.sandia.gov/doc/dihedral_opls.html K1 = float(tokens[5]) @@ -311,8 +334,10 @@ def main(): (float(tokens[16]) != 4.0)))): raise Exception("Error: This parameter file is incompatible with -dihedral-style \"" + dihedral_style_name + "\"\n" + " (See line number " + str(iline + 1) + " of parameter file.)\n") - dihedrals_by_type[tokens[1], tokens[2], - tokens[3], tokens[4]] = (K1, K2, K3, K4) + dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (K1, K2, K3, K4) else: assert(False) @@ -320,8 +345,10 @@ def main(): k = float(tokens[5]) angle0 = float(tokens[6]) multiplicity = float(tokens[7]) - impropers_by_type[tokens[1], tokens[2], tokens[ - 3], tokens[4]] = (k / multiplicity, angle0) + impropers_by_type[tokens[1].rjust(zeropad_ffid,'0'), + tokens[2].rjust(zeropad_ffid,'0'), + tokens[3].rjust(zeropad_ffid,'0'), + tokens[4].rjust(zeropad_ffid,'0')] = (k / multiplicity, angle0) elif ((len(tokens) > 0) and (tokens[0] == 'biotype')): # I'm not sure what to do with these, so I'll store them for now and # append them as comments to the .lt file generated by the program. @@ -351,13 +378,28 @@ def main(): " to consider alternate mixing rules.\n\n" + "The offending line from the file is line number " + str(iline) + ":\n" + line + "\n") - - - + + # Zero-pad the atom2ffid values so that they have the same number + # of digits. This is usually not necessary, but it can be helpful + # to remove uncertainty about the meaning of '4*' which could + # pattern match with '4', '4L', '47', '47L'... If you replace '4' + # with '04', '04*' becomes distinguishable from '47*'. + # This can be useful if you want to augment the force field later, + # (for example, adding additional atoms to the LOPLSAA variant of OPLSAA) + + for k in atom2ffid.keys(): + atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid, '0') + + # Horrible hack: for LOPLSAA, uncomment the next 3 lines: + #ki = atom2ffid[k].find('L') + #if ki!=-1: + # atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid + len(atom2ffid[k]) - ki, '0') + + #sys.stderr.write(" done.\n") #sys.stderr.write("Converting to moltemplate format...\n") - - + + system_is_charged = False for atom_type in atom2charge: if atom2charge[atom_type] != 0.0: @@ -373,10 +415,9 @@ def main(): pair_style_params = "10.0" kspace_style = "" pair_style_link = "http://lammps.sandia.gov/doc/pair_lj.html" - - pair_style_command = " pair_style hybrid " + \ - pair_style_name + " " + pair_style_params + "\n" - + + pair_style_command = " pair_style " + ("hybrid " if use_hybrid else "") + \ + pair_style_name + " " + pair_style_params + "\n" sys.stdout.write("# This file was generated automatically using:\n") sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") @@ -442,8 +483,10 @@ def main(): sys.stdout.write(" # --------------- Non-Bonded interactions: ---------------------\n" " # " + pair_style_link + "\n" " # Syntax:\n" - " # pair_coeff AtomType1 AtomType2 pair_style_name parameters...\n\n") - + " # pair_coeff AtomType1 AtomType2 " + + ("PairStyleName " if use_hybrid else "") + + "parameters...\n\n") + sys.stdout.write(" write_once(\"In Settings\") {\n") for atype in atom2vdw_e: assert(atype in atom2vdw_s) @@ -454,7 +497,7 @@ def main(): "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[ atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " + - pair_style_name + + (pair_style_name if use_hybrid else "") + " " + str(atom2vdw_e[atype]) + " " + str(atom2vdw_s[atype]) + "\n") sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") @@ -463,15 +506,18 @@ def main(): sys.stdout.write(" # ------- Bonded Interactions: -------\n" " # " + bond_style_link + "\n" " # Syntax: \n" - " # bond_coeff BondTypeName BondStyle parameters...\n\n") + " # bond_coeff BondTypeName " + + ("BondStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != "0" else "X" - ffid2 = btype[1] if btype[1] != "0" else "X" + ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" (k, r0) = bonds_by_type[btype] - sys.stdout.write(" bond_coeff @bond:" + ffid1 + "-" + ffid2 + " " + - bond_style_name + " " + str(k) + " " + str(r0) + "\n") + sys.stdout.write(" bond_coeff @bond:" + ffid1 + "_" + ffid2 + " " + + (bond_style_name if use_hybrid else "") + + " " + str(k) + " " + str(r0) + "\n") sys.stdout.write(" } #(end of bond_coeffs)\n\n") sys.stdout.write(" # Rules for assigning bond types by atom type:\n" @@ -480,13 +526,13 @@ def main(): sys.stdout.write(" write_once(\"Data Bonds By Type\") {\n") for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != "0" else "X" - ffid2 = btype[1] if btype[1] != "0" else "X" - sys.stdout.write(" @bond:" + ffid1 + "-" + ffid2) + ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @bond:" + ffid1 + "_" + ffid2) ffid1 = "@atom:*_b" + btype[0] + \ - "_a*_d*_i*" if btype[0] != "0" else "@atom:*" + "*_a*_d*_i*" if btype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b" + btype[1] + \ - "_a*_d*_i*" if btype[1] != "0" else "@atom:*" + "*_a*_d*_i*" if btype[1] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + "\n") sys.stdout.write(" } #(end of bonds by type)\n\n\n\n\n") @@ -494,16 +540,19 @@ def main(): sys.stdout.write(" # ------- Angle Interactions: -------\n" " # " + angle_style_link + "\n" " # Syntax: \n" - " # angle_coeff AngleTypeName AngleStyle parameters...\n\n") + " # angle_coeff AngleTypeName "+ + ("AngleStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != "0" else "X" - ffid2 = atype[1] if atype[1] != "0" else "X" - ffid3 = atype[2] if atype[2] != "0" else "X" + ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" (k, angle0) = angles_by_type[atype] - sys.stdout.write(" angle_coeff @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3 + " " + - angle_style_name + " " + str(k) + " " + str(angle0) + "\n") + sys.stdout.write(" angle_coeff @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3 + " " + + (angle_style_name if use_hybrid else "") + + " " + str(k) + " " + str(angle0) + "\n") sys.stdout.write(" } #(end of angle_coeffs)\n\n") @@ -513,16 +562,16 @@ def main(): sys.stdout.write(" write_once(\"Data Angles By Type\") {\n") for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != "0" else "X" - ffid2 = atype[1] if atype[1] != "0" else "X" - ffid3 = atype[2] if atype[2] != "0" else "X" - sys.stdout.write(" @angle:" + ffid1 + "-" + ffid2 + "-" + ffid3) + ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3) ffid1 = "@atom:*_b*_a" + atype[0] + \ - "_d*_i*" if atype[0] != "0" else "@atom:*" + "*_d*_i*" if atype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b*_a" + atype[1] + \ - "_d*_i*" if atype[1] != "0" else "@atom:*" + "*_d*_i*" if atype[1] != ("0"*zeropad_ffid) else "@atom:*" ffid3 = "@atom:*_b*_a" + atype[2] + \ - "_d*_i*" if atype[2] != "0" else "@atom:*" + "*_d*_i*" if atype[2] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + "\n") sys.stdout.write(" } #(end of angles by type)\n\n\n\n\n") @@ -530,17 +579,20 @@ def main(): sys.stdout.write(" # ----------- Dihedral Interactions: ------------\n" " # " + dihedral_style_link + "\n" " # Syntax:\n" - " # dihedral_coeff DihedralTypeName DihedralStyle parameters...\n\n") + " # dihedral_coeff DihedralTypeName " + + ("DihedralStyleName " if use_hybrid else "") + + "parameters...\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != "0" else "X" - ffid2 = dtype[1] if dtype[1] != "0" else "X" - ffid3 = dtype[2] if dtype[2] != "0" else "X" - ffid4 = dtype[3] if dtype[3] != "0" else "X" + ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" sys.stdout.write(" dihedral_coeff @dihedral:" + - ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " + - dihedral_style_name + " ") + ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + + (dihedral_style_name if use_hybrid else "") + + " ") if dihedral_style_name == 'fourier': # http://lammps.sandia.gov/doc/dihedral_fourier.html (K, n, d) = dihedrals_by_type[dtype] @@ -567,20 +619,22 @@ def main(): sys.stdout.write(" write_once(\"Data Dihedrals By Type\") {\n") for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != "0" else "X" - ffid2 = dtype[1] if dtype[1] != "0" else "X" - ffid3 = dtype[2] if dtype[2] != "0" else "X" - ffid4 = dtype[3] if dtype[3] != "0" else "X" - sys.stdout.write(" @dihedral:" + ffid1 + "-" + - ffid2 + "-" + ffid3 + "-" + ffid4) + ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @dihedral:" + + ffid1 + "_" + ffid2 + "_" + + ffid3 + "_" + ffid4) ffid1 = "@atom:*_b*_a*_d" + dtype[0] + \ - "_i*" if dtype[0] != "0" else "@atom:*" + "*_i*" if dtype[0] != ("0"*zeropad_ffid) else "@atom:*" ffid2 = "@atom:*_b*_a*_d" + dtype[1] + \ - "_i*" if dtype[1] != "0" else "@atom:*" + "*_i*" if dtype[1] != ("0"*zeropad_ffid) else "@atom:*" ffid3 = "@atom:*_b*_a*_d" + dtype[2] + \ - "_i*" if dtype[2] != "0" else "@atom:*" + "*_i*" if dtype[2] != ("0"*zeropad_ffid) else "@atom:*" ffid4 = "@atom:*_b*_a*_d" + dtype[3] + \ - "_i*" if dtype[3] != "0" else "@atom:*" + "*_i*" if dtype[3] != ("0"*zeropad_ffid) else "@atom:*" + sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + " " + ffid4 + "\n") sys.stdout.write(" } #(end of dihedrals by type)\n\n\n\n\n") @@ -589,37 +643,41 @@ def main(): sys.stdout.write(" # ---------- Improper Interactions: ----------\n" " # " + improper_style_link + "\n" " # Syntax:\n" - " # improper_coeff ImproperTypeName ImproperStyle parameters\n\n") + " # improper_coeff ImproperTypeName " + + ("ImproperStyleName " if use_hybrid else "") + + "parameters\n\n") sys.stdout.write(" write_once(\"In Settings\") {\n") for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != "0" else "X" - ffid2 = itype[1] if itype[1] != "0" else "X" - ffid3 = itype[2] if itype[2] != "0" else "X" - ffid4 = itype[3] if itype[3] != "0" else "X" + ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" (k, angle0) = impropers_by_type[itype] sys.stdout.write(" improper_coeff @improper:" + - ffid1 + "-" + ffid2 + "-" + ffid3 + "-" + ffid4 + " " + - improper_style_name + " " + str(k) + " " + str(angle0) + "\n") + ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + + (improper_style_name if use_hybrid else "") + + " " + str(k) + " " + str(angle0) + "\n") sys.stdout.write(" } #(end of improper_coeffs)\n\n") - sys.stdout.write(" # Rules for creating dihedral interactions according to atom type:\n" + sys.stdout.write(" # Rules for creating improper interactions according to atom type:\n" " # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4\n" " # (* = wildcard)\n") sys.stdout.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != "0" else "X" - ffid2 = itype[1] if itype[1] != "0" else "X" - ffid3 = itype[2] if itype[2] != "0" else "X" - ffid4 = itype[3] if itype[3] != "0" else "X" - sys.stdout.write(" @improper:" + ffid1 + "-" + - ffid2 + "-" + ffid3 + "-" + ffid4) - ffid1 = "@atom:*_b*_a*_d*_i" + itype[0] if itype[0] != "0" else "@atom:*" - ffid2 = "@atom:*_b*_a*_d*_i" + itype[1] if itype[1] != "0" else "@atom:*" - ffid3 = "@atom:*_b*_a*_d*_i" + itype[2] if itype[2] != "0" else "@atom:*" - ffid4 = "@atom:*_b*_a*_d*_i" + itype[3] if itype[3] != "0" else "@atom:*" + ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" + ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" + ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" + ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" + sys.stdout.write(" @improper:" + + ffid1 + "_" + ffid2 + "_" + + ffid3 + "_" + ffid4) + ffid1 = "@atom:*_b*_a*_d*_i" + itype[0]+"*" if itype[0] != ("0"*zeropad_ffid) else "@atom:*" + ffid2 = "@atom:*_b*_a*_d*_i" + itype[1]+"*" if itype[1] != ("0"*zeropad_ffid) else "@atom:*" + ffid3 = "@atom:*_b*_a*_d*_i" + itype[2]+"*" if itype[2] != ("0"*zeropad_ffid) else "@atom:*" + ffid4 = "@atom:*_b*_a*_d*_i" + itype[3]+"*" if itype[3] != ("0"*zeropad_ffid) else "@atom:*" sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + " " + ffid4 + "\n") sys.stdout.write(" } #(end of impropers by type)\n\n\n\n\n") @@ -639,10 +697,18 @@ def main(): sys.stdout.write(" write_once(\"In Init\") {\n") sys.stdout.write(" units real\n") sys.stdout.write(" atom_style full\n") - sys.stdout.write(" bond_style hybrid " + bond_style_name + "\n") - sys.stdout.write(" angle_style hybrid " + angle_style_name + "\n") - sys.stdout.write(" dihedral_style hybrid " + dihedral_style_name + "\n") - sys.stdout.write(" improper_style hybrid " + improper_style_name + "\n") + sys.stdout.write(" bond_style " + + ("hybrid " if use_hybrid else "") + + bond_style_name + "\n") + sys.stdout.write(" angle_style " + + ("hybrid " if use_hybrid else "") + + angle_style_name + "\n") + sys.stdout.write(" dihedral_style " + + ("hybrid " if use_hybrid else "") + + dihedral_style_name + "\n") + sys.stdout.write(" improper_style " + + ("hybrid " if use_hybrid else "") + + improper_style_name + "\n") sys.stdout.write(pair_style_command) sys.stdout.write(" pair_modify mix " + mixing_style + "\n") sys.stdout.write(" " + special_bonds_command + "\n") diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/README b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/README rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/gen_potential-cooke.py b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/gen_potential-cooke.py rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno/tabulated_potential.dat b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/cooke_deserno/tabulated_potential.dat rename to tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat diff --git a/tools/moltemplate/moltemplate/force_fields/gaff.lt b/tools/moltemplate/moltemplate/force_fields/gaff.lt index 683dbf4ee42e01d7556487963fa1a659809b2b53..d9e367e8cee126dbc3e379f4236d900f342163ce 100644 --- a/tools/moltemplate/moltemplate/force_fields/gaff.lt +++ b/tools/moltemplate/moltemplate/force_fields/gaff.lt @@ -30,15 +30,14 @@ #(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) #################################################################### # Moltemplate can not assign atom charge. You must assign atomic -# charges yourself. (Moltemplate is only a simple text manipulation tool.) +# charges yourself. (Moltemplate is only a simple text manipulation tool. +# You can do this afterwards using commands like "set atom 70 charge -0.212" +# For details, see http://lammps.sandia.gov/doc/set.html) #################################################################### - - - GAFF { # ---------------------------------------------------------------------- diff --git a/tools/moltemplate/moltemplate/force_fields/gaff2.lt b/tools/moltemplate/moltemplate/force_fields/gaff2.lt new file mode 100644 index 0000000000000000000000000000000000000000..9063b28cb9133c18f98b6b4e928b2bb34d78d05a --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/gaff2.lt @@ -0,0 +1,13357 @@ +# This is the 2.1 version of GAFF (April 2016) +#################################################################### +# This moltemplate (LT) file was generated automatically using +# amberparm2lt.sh gaff2.dat GAFF2 > gaff2.lt +#################################################################### +# WARNING: As of 2017-10-03 this file has not yet been tested with +# moltemplate. Please report issues to jewett.aij -at- gmail.com +#################################################################### +# Background information and usage explanation: +# This file contanis a list of atom types and rules for generating bonded +# interactions between these atoms (hopefully) according to AMBER conventions. +# By using the atom types shown below in your own molecules, bonds and angular +# interactions will be automatically generated. +# AMBER (GAFF) force-field parameters will also be assigned to each angle +# interaction (according to these atom types). +# One way to apply the GAFF force field to a particular type of molecule, is +# to use the "inherits" keyword when you define that molecule. For example: +# import("gaff.lt") +# MoleculeType inherits GAFF { +# write_once("Data Atoms") { +# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 +# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 +# : : : +# } +# } +#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) +#################################################################### +# Moltemplate can not assign atom charge. You must assign atomic +# charges yourself. (Moltemplate is only a simple text manipulation tool. +# You can do this afterwards using commands like "set atom 70 charge -0.212" +# For details, see http://lammps.sandia.gov/doc/set.html) +#################################################################### + + +GAFF2 { + + # ---------------------------------------------------------------------- + # The basic atom nomenclature and conventions are explained here: + # http://ambermd.org/antechamber/gaff.pdf + # For reference, the original gaff.dat file and format documentation are here: + # http://ambermd.org/AmberTools-get.html + # http://ambermd.org/formats.html#parm.dat + # ---------------------------------------------------------------------- + + write_once("Data Masses") { + @atom:c 12.01 # Sp2 C carbonyl group + @atom:cs 12.01 # Sp2 C in c=S + @atom:c1 12.01 # Sp C + @atom:c2 12.01 # Sp2 C + @atom:c3 12.01 # Sp3 C + @atom:ca 12.01 # Sp2 C in pure aromatic systems + @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. + @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp + @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems + @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc + @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems + @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce + @atom:cg 12.01 # Inner Sp carbons in conjugated systems + @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg + @atom:cx 12.01 # Sp3 carbons in triangle systems + @atom:cy 12.01 # Sp3 carbons in square systems + @atom:cu 12.01 # Sp2 carbons in triangle systems + @atom:cv 12.01 # Sp2 carbons in square systems + @atom:cz 12.01 # Sp2 carbon in guanidine group + @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group + @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group + @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group + @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group + @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group + @atom:ha 1.008 # H bonded to aromatic carbon + @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group + @atom:hn 1.008 # H bonded to nitrogen atoms + @atom:ho 1.008 # Hydroxyl group + @atom:hp 1.008 # H bonded to phosphate + @atom:hs 1.008 # Hydrogen bonded to sulphur + @atom:hw 1.008 # Hydrogen in water + @atom:hx 1.008 # H bonded to C next to positively charged group + @atom:f 19.00 # Fluorine + @atom:cl 35.45 # Chlorine + @atom:br 79.90 # Bromine + @atom:i 126.9 # Iodine + @atom:n 14.01 # Sp2 nitrogen in amide groups + @atom:n1 14.01 # Sp N + @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms + @atom:n3 14.01 # Sp3 N with three connected atoms + @atom:n4 14.01 # Sp3 N with four connected atoms + @atom:na 14.01 # Sp2 N with three connected atoms + @atom:nb 14.01 # Sp2 N in pure aromatic systems + @atom:nc 14.01 # Sp2 N in non-pure aromatic systems + @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc + @atom:ne 14.01 # Inner Sp2 N in conjugated systems + @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne + @atom:nh 14.01 # Amine N connected one or more aromatic rings + @atom:no 14.01 # Nitro N + @atom:ns 14.01 # amind N, with 1 attached hydrogen atom + @atom:nt 14.01 # amide N, with 2 attached hydrogen atoms + @atom:nx 14.01 # like n4, but only has one hydrogen atom + @atom:ny 14.01 # like n4, but only has two hydrogen atoms + @atom:nz 14.01 # like n4, but only has three three hydrogen atoms + @atom:n+ 14.01 # NH4+ + @atom:nu 14.01 # like nh, but only has one attached hydrogen atom + @atom:nv 14.01 # like nh, but only has two attached hydrogen atoms + @atom:n7 14.01 # like n3, but only has one attached hydrogen atom + @atom:n8 14.01 # like n3, but only has two attached hydrogen atoms + @atom:n9 14.01 # NH3 + @atom:o 16.00 # Oxygen with one connected atom + @atom:oh 16.00 # Oxygen in hydroxyl group + @atom:os 16.00 # Ether and ester oxygen + @atom:ow 16.00 # Oxygen in water + @atom:p2 30.97 # Phosphate with two connected atoms + @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 + @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 + @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 + @atom:pb 30.97 # Sp2 P in pure aromatic systems + @atom:pc 30.97 # Sp2 P in non-pure aromatic systems + @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc + @atom:pe 30.97 # Inner Sp2 P in conjugated systems + @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe + @atom:px 30.97 # Special p4 in conjugated systems + @atom:py 30.97 # Special p5 in conjugated systems + @atom:s 32.06 # S with one connected atom + @atom:s2 32.06 # S with two connected atom, involved at least one double bond + @atom:s4 32.06 # S with three connected atoms + @atom:s6 32.06 # S with four connected atoms + @atom:sh 32.06 # Sp3 S connected with hydrogen + @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether + @atom:sx 32.06 # Special s4 in conjugated systems + @atom:sy 32.06 # Special s6 in conjugated systems + } # (end of masses) + + write_once("In Settings") { + pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0208 2.60017699876 + pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0161 2.62547852236 + pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0100 1.10649620793 + pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0047 0.537924646013 + pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0124 1.08903459305 + pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0144 1.07460203382 + pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.1463 3.04812087425 + pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.0726 3.15609779888 + pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.0930 3.24287133403 + pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1636 3.18086478325 + pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.0832 3.03422285424 + pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.2638 3.46595237305 + pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.3932 3.61259430206 + pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.4955 3.84119891313 + pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1098 3.27351824993 + pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.0858 3.36510263816 + pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.2042 3.20580994736 + pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.2150 3.18995195017 + pair_coeff @atom:n+ @atom:n+ lj/charmm/coul/long 0.7828 2.85586493087 + pair_coeff @atom:n9 @atom:n9 lj/charmm/coul/long 0.0095 4.04468018036 + pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0208 2.42199725514 + pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0208 2.24381751151 + pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0208 2.06563776788 + pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0208 1.88745802425 + pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0161 2.53638865055 + pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0161 2.44729877873 + pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.1078 3.39770953124 + pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cs @atom:cs lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.1596 3.47895949434 + pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0988 3.31521230994 + pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.0941 3.38416787073 + pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.0858 3.36510263816 + pair_coeff @atom:n7 @atom:n7 lj/charmm/coul/long 0.0522 3.50764643306 + pair_coeff @atom:n8 @atom:n8 lj/charmm/coul/long 0.0323 3.65019022796 + pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 3.8748 2.49950544361 + pair_coeff @atom:nx @atom:nx lj/charmm/coul/long 2.5453 2.58859531543 + pair_coeff @atom:ny @atom:ny lj/charmm/coul/long 1.6959 2.67768518724 + pair_coeff @atom:nz @atom:nz lj/charmm/coul/long 1.1450 2.76677505906 + pair_coeff @atom:ns @atom:ns lj/charmm/coul/long 0.1174 3.26995465506 + pair_coeff @atom:nt @atom:nt lj/charmm/coul/long 0.0851 3.35904452688 + pair_coeff @atom:nu @atom:nu lj/charmm/coul/long 0.1545 3.27904182199 + pair_coeff @atom:nv @atom:nv lj/charmm/coul/long 0.1120 3.3681316938 + pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2824 3.53241341743 + pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2295 3.6940224449 + pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2295 3.6940224449 + } # (end of pair_coeffs) + + write_once("In Settings") { + bond_coeff @bond:ow-hw harmonic 612.98 0.957 # TIP3P_Water 1 + bond_coeff @bond:hw-hw harmonic 15.17 1.514 # TIP3P_Water 1 + bond_coeff @bond:br-br harmonic 81.01 2.542 # SOURCE1 4 + bond_coeff @bond:br-c1 harmonic 227.01 1.787 # SOURCE2 4 0.0024 + bond_coeff @bond:br-c2 harmonic 168.91 1.893 # SOURCE1_SOURCE5 25 0.0078 + bond_coeff @bond:br-c harmonic 146.48 1.946 # SOURCE2 2 0.0285 + bond_coeff @bond:br-c3 harmonic 134.73 1.978 # SOURCE1_SOURCE5 146 0.0118 + bond_coeff @bond:br-ca harmonic 162.15 1.908 # SOURCE1_SOURCE5 462 0.0052 + bond_coeff @bond:br-cc harmonic 172.53 1.885 # SOURCE4_SOURCE5 128 0.0078 + bond_coeff @bond:br-cx harmonic 154.63 1.926 # SOURCE1_SOURCE5 11 0.0019 + bond_coeff @bond:br-n1 harmonic 141.51 1.860 # SOUECE3 1 + bond_coeff @bond:br-n2 harmonic 88.47 2.038 # SOURCE3 5 0.1082 + bond_coeff @bond:br-n harmonic 136.53 1.873 # SOURCE3 4 0.0046 + bond_coeff @bond:br-n3 harmonic 110.41 1.952 # SOURCE3 2 + bond_coeff @bond:br-n4 harmonic 118.29 1.926 # SOURCE3 3 0.0013 + bond_coeff @bond:br-na harmonic 96.95 2.002 # SOURCE3 7 0.2156 + bond_coeff @bond:br-nh harmonic 112.77 1.944 # SOURCE3 1 + bond_coeff @bond:br-no harmonic 75.65 2.101 # SOURCE3 1 + bond_coeff @bond:br-o harmonic 193.58 1.800 # SOUECE3 1 + bond_coeff @bond:br-oh harmonic 160.87 1.866 # SOURCE3 1 + bond_coeff @bond:br-os harmonic 151.88 1.887 # SOURCE3 2 + bond_coeff @bond:br-p2 harmonic 133.12 2.210 # SOURCE3 9 0.0510 + bond_coeff @bond:br-p3 harmonic 126.80 2.231 # SOURCE3 3 0.0101 + bond_coeff @bond:br-p4 harmonic 145.88 2.171 # SOUECE3 1 + bond_coeff @bond:br-p5 harmonic 137.54 2.196 # SOURCE3 3 0.0099 + bond_coeff @bond:br-s harmonic 169.20 2.220 # SOUECE3 1 + bond_coeff @bond:br-s4 harmonic 128.80 2.341 # SOURCE3 1 + bond_coeff @bond:br-s6 harmonic 171.57 2.214 # SOURCE3 3 0.0443 + bond_coeff @bond:br-sh harmonic 173.58 2.209 # SOURCE3 1 + bond_coeff @bond:br-ss harmonic 176.02 2.203 # SOURCE3 3 0.0035 + bond_coeff @bond:c1-c1 harmonic 837.28 1.198 # SOURCE1_SOURCE5 659 0.0039 + bond_coeff @bond:c1-c2 harmonic 535.85 1.307 # SOURCE1 18 + bond_coeff @bond:c1-c3 harmonic 295.86 1.467 # SOURCE1_SOURCE5 795 0.0034 + bond_coeff @bond:c1-ca harmonic 325.62 1.440 # SOUECE3 1 + bond_coeff @bond:c1-ce harmonic 518.69 1.315 # SOURCE4 6 0.0086 + bond_coeff @bond:c1-cg harmonic 776.82 1.216 # SOURCE3_SOURCE5 179 0.0036 + bond_coeff @bond:c1-ch harmonic 765.43 1.219 # SOURCE3_SOURCE5 13 0.0016 + bond_coeff @bond:c1-cl harmonic 261.49 1.631 # SOURCE2 6 0.0050 + bond_coeff @bond:c1-cx harmonic 320.55 1.444 # SOURCE1_SOURCE5 24 0.0043 + bond_coeff @bond:c1-f harmonic 482.19 1.270 # SOURCE2 2 0.0085 + bond_coeff @bond:c1-ha harmonic 433.72 1.067 # SOURCE3_SOURCE5 343 0.0013 + bond_coeff @bond:c1-hc harmonic 448.21 1.060 # SOUECE3 1 + bond_coeff @bond:c1-i harmonic 153.51 1.989 # SOURCE2 4 0.0032 + bond_coeff @bond:c1-n1 harmonic 891.54 1.153 # SOURCE1_SOURCE5 481 0.0035 + bond_coeff @bond:c1-n2 harmonic 736.75 1.197 # SOURCE3_SOURCE5 36 0.0076 + bond_coeff @bond:c1-n3 harmonic 400.99 1.347 # SOURCE2_SOURCE5 10 0.0093 + bond_coeff @bond:c1-n4 harmonic 309.65 1.417 # SOURCE3 3 0.0032 + bond_coeff @bond:c1-n harmonic 428.86 1.330 # SOUECE3 1 + bond_coeff @bond:c1-na harmonic 379.52 1.362 # SOURCE3 8 0.0034 + bond_coeff @bond:c1-ne harmonic 720.51 1.202 # SOURCE4_SOURCE5 31 0.0124 + bond_coeff @bond:c1-nf harmonic 720.51 1.202 # SOURCE4_SOURCE5 21 0.0141 + bond_coeff @bond:c1-nh harmonic 409.04 1.342 # SOURCE4_SOURCE5 33 0.0061 + bond_coeff @bond:c1-no harmonic 323.48 1.405 # SOURCE3 3 0.0005 + bond_coeff @bond:c1-o harmonic 794.98 1.172 # SOURCE2_SOURCE5 31 0.0068 + bond_coeff @bond:c1-oh harmonic 422.21 1.326 # SOURCE3 1 + bond_coeff @bond:c1-os harmonic 435.38 1.318 # SOURCE3_SOURCE5 8 0.0079 + bond_coeff @bond:c1-p2 harmonic 215.98 1.770 # SOUECE3 1 + bond_coeff @bond:c1-p3 harmonic 203.86 1.790 # SOUECE3 1 + bond_coeff @bond:c1-p4 harmonic 203.86 1.790 # SOUECE3 1 + bond_coeff @bond:c1-p5 harmonic 226.96 1.753 # SOURCE3 2 + bond_coeff @bond:c1-s2 harmonic 380.51 1.595 # SOURCE3 1 + bond_coeff @bond:c1-s harmonic 370.61 1.603 # SOURCE1_SOURCE5 37 0.0043 + bond_coeff @bond:c1-s4 harmonic 239.03 1.746 # SOURCE3 2 + bond_coeff @bond:c1-s6 harmonic 256.65 1.722 # SOURCE3 2 + bond_coeff @bond:c1-sh harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:c1-ss harmonic 282.80 1.690 # SOURCE1_SOURCE5 49 0.0113 + bond_coeff @bond:c2-c2 harmonic 481.83 1.334 # SOURCE1_SOURCE5 3727 0.0053 + bond_coeff @bond:c2-c3 harmonic 255.56 1.510 # SOURCE1_SOURCE5 10204 0.0042 + bond_coeff @bond:c2-ca harmonic 398.37 1.385 # SOUECE3_SOURCE5 9 0.0149 + bond_coeff @bond:c2-cc harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 + bond_coeff @bond:c2-cd harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 + bond_coeff @bond:c2-ce harmonic 460.51 1.346 # SOURCE3_SOURCE5 3239 0.0058 + bond_coeff @bond:c2-cf harmonic 460.51 1.346 # SOURCE3_SOURCE5 3177 0.0057 + bond_coeff @bond:c2-cl harmonic 192.70 1.731 # SOURCE1_SOURCE5 290 0.0098 + bond_coeff @bond:c2-cu harmonic 500.05 1.325 # SOURCE2_SOURCE5 11 0.0010 + bond_coeff @bond:c2-cx harmonic 278.37 1.485 # SOURCE4_SOURCE5 102 0.0061 + bond_coeff @bond:c2-cy harmonic 255.91 1.509 # SOURCE4_SOURCE5 30 0.0063 + bond_coeff @bond:c2-f harmonic 368.08 1.339 # SOURCE1_SOURCE5 35 0.0085 + bond_coeff @bond:c2-h4 harmonic 394.23 1.087 # SOURCE3_SOURCE5 517 0.0028 + bond_coeff @bond:c2-h5 harmonic 386.13 1.091 # SOURCE4_SOURCE5 116 0.0021 + bond_coeff @bond:c2-ha harmonic 392.18 1.088 # SOURCE3_SOURCE5 5991 0.0019 + bond_coeff @bond:c2-hc harmonic 393.86 1.087 # SOURCE3 789 0.0046 + bond_coeff @bond:c2-hx harmonic 401.39 1.083 # SOURCE3 3 0.0008 + bond_coeff @bond:c2-i harmonic 98.09 2.170 # SOURCE3_SOURCE5 7 0.0194 + bond_coeff @bond:c2-n1 harmonic 470.94 1.306 # SOURCE3 4 0.0161 + bond_coeff @bond:c2-n2 harmonic 518.67 1.282 # SOURCE1_SOURCE5 1004 0.0051 + bond_coeff @bond:c2-n3 harmonic 412.66 1.340 # SOUECE3 1 + bond_coeff @bond:c2-n harmonic 330.19 1.399 # SOURCE3_SOURCE5 174 0.0100 + bond_coeff @bond:c2-n4 harmonic 221.45 1.512 # SOURCE3_SOURCE5 21 0.0133 + bond_coeff @bond:c2-na harmonic 327.66 1.401 # SOURCE3_SOURCE5 65 0.0179 + bond_coeff @bond:c2-nc harmonic 458.17 1.313 # SOURCE1 99 0.0095 + bond_coeff @bond:c2-nd harmonic 458.17 1.313 # SOURCE1 99 + bond_coeff @bond:c2-ne harmonic 498.75 1.292 # SOURCE3_SOURCE5 310 0.0099 + bond_coeff @bond:c2-nf harmonic 498.75 1.292 # SOURCE3_SOURCE5 273 0.0098 + bond_coeff @bond:c2-nh harmonic 345.39 1.387 # SOURCE3_SOURCE5 1559 0.0120 + bond_coeff @bond:c2-no harmonic 276.95 1.448 # SOURCE4_SOURCE5 27 0.0139 + bond_coeff @bond:c2-o harmonic 635.23 1.225 # SOURCE4_SOURCE5 35 0.0033 + bond_coeff @bond:c2-oh harmonic 402.33 1.339 # SOURCE1_SOURCE5 85 0.0126 + bond_coeff @bond:c2-os harmonic 371.26 1.360 # SOURCE1_SOURCE5 548 0.0107 + bond_coeff @bond:c2-p2 harmonic 292.48 1.669 # SOURCE3_SOURCE5 87 0.0126 + bond_coeff @bond:c2-p3 harmonic 179.93 1.834 # SOURCE3 5 0.0042 + bond_coeff @bond:c2-p4 harmonic 186.11 1.822 # SOUECE3 1 + bond_coeff @bond:c2-p5 harmonic 166.18 1.863 # SOURCE4_SOURCE5 15 0.0083 + bond_coeff @bond:c2-pe harmonic 275.11 1.689 # SOURCE3_SOURCE5 60 0.0472 + bond_coeff @bond:c2-pf harmonic 275.11 1.689 # SOURCE3_SOURCE5 8 0.0019 + bond_coeff @bond:c2-s2 harmonic 362.64 1.610 # SOURCE2 1 + bond_coeff @bond:c2-s harmonic 247.65 1.734 # SOURCE3 4 0.0034 + bond_coeff @bond:c2-s4 harmonic 229.42 1.760 # SOUECE3 1 + bond_coeff @bond:c2-s6 harmonic 229.42 1.760 # SOUECE3 1 + bond_coeff @bond:c2-sh harmonic 215.23 1.782 # SOURCE4_SOURCE5 13 0.0077 + bond_coeff @bond:c2-ss harmonic 246.19 1.736 # SOURCE1 209 0.0155 + bond_coeff @bond:c3-c3 harmonic 232.52 1.538 # SOURCE1_SOURCE5 88072 0.0058 + bond_coeff @bond:c3-ca harmonic 250.32 1.516 # SOURCE1_SOURCE5 10699 0.0054 + bond_coeff @bond:c3-cc harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 + bond_coeff @bond:c3-cd harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 + bond_coeff @bond:c3-ce harmonic 250.06 1.516 # SOURCE3_SOURCE5 1210 0.0060 + bond_coeff @bond:c3-cf harmonic 250.23 1.516 # SOURCE3_SOURCE5 345 0.0071 + bond_coeff @bond:c3-cl harmonic 155.52 1.804 # SOURCE1_SOURCE5 1173 0.0119 + bond_coeff @bond:c3-cu harmonic 284.82 1.478 # SOURCE1 7 + bond_coeff @bond:c3-cv harmonic 274.17 1.489 # SOURCE1 11 + bond_coeff @bond:c3-cx harmonic 247.95 1.518 # SOURCE1_SOURCE5 1561 0.0054 + bond_coeff @bond:c3-cy harmonic 236.93 1.532 # SOURCE1_SOURCE5 522 0.0055 + bond_coeff @bond:c3-f harmonic 352.65 1.350 # SOURCE1_SOURCE5 2188 0.0139 + bond_coeff @bond:c3-h1 harmonic 375.92 1.097 # SOURCE3_SOURCE5 112144 0.0055 + bond_coeff @bond:c3-h2 harmonic 377.33 1.096 # SOURCE3_SOURCE5 2681 0.0032 + bond_coeff @bond:c3-h3 harmonic 379.47 1.095 # SOURCE4_SOURCE5 64 0.0028 + bond_coeff @bond:c3-hc harmonic 375.92 1.097 # SOURCE3_SOURCE5 133628 0.0015 + bond_coeff @bond:c3-hx harmonic 386.49 1.091 # SOURCE3_SOURCE5 6495 0.0022 + bond_coeff @bond:c3-i harmonic 88.97 2.212 # SOURCE1_SOURCE5 35 0.0128 + bond_coeff @bond:c3-n1 harmonic 292.28 1.433 # SOURCE3_SOURCE5 7 0.0033 + bond_coeff @bond:c3-n2 harmonic 259.91 1.466 # SOURCE1_SOURCE5 816 0.0087 + bond_coeff @bond:c3-n harmonic 263.77 1.462 # SOURCE1_SOURCE5 4576 0.0061 + bond_coeff @bond:c3-n3 harmonic 261.19 1.465 # SOURCE1_SOURCE5 15206 0.0039 + bond_coeff @bond:c3-n4 harmonic 222.58 1.511 # SOURCE1_SOURCE5 2375 0.0125 + bond_coeff @bond:c3-na harmonic 262.85 1.463 # SOURCE3_SOURCE5 1732 0.0077 + bond_coeff @bond:c3-nc harmonic 269.31 1.456 # SOURCE3 9 0.0109 + bond_coeff @bond:c3-nd harmonic 269.31 1.456 # SOURCE3 9 + bond_coeff @bond:c3-nh harmonic 261.84 1.464 # SOURCE3_SOURCE5 3492 0.0064 + bond_coeff @bond:c3-no harmonic 206.37 1.533 # SOURCE1_SOURCE5 150 0.0187 + bond_coeff @bond:c3-o harmonic 438.11 1.317 # SOURCE4 8 0.0193 + bond_coeff @bond:c3-oh harmonic 293.40 1.423 # SOURCE1_SOURCE5 8884 0.0067 + bond_coeff @bond:c3-os harmonic 284.76 1.432 # SOURCE1_SOURCE5 17971 0.0103 + bond_coeff @bond:c3-p2 harmonic 169.71 1.855 # SOURCE3 9 0.0125 + bond_coeff @bond:c3-p3 harmonic 168.21 1.858 # SOURCE3_SOURCE5 221 0.0094 + bond_coeff @bond:c3-p4 harmonic 177.58 1.839 # SOURCE3_SOURCE5 45 0.0106 + bond_coeff @bond:c3-p5 harmonic 177.19 1.839 # SOURCE1_SOURCE5 408 0.0183 + bond_coeff @bond:c3-px harmonic 182.68 1.829 # SOURCE3_SOURCE5 35 0.0083 + bond_coeff @bond:c3-py harmonic 177.09 1.840 # SOURCE3_SOURCE5 39 0.0126 + bond_coeff @bond:c3-s harmonic 180.03 1.845 # SOURCE3 4 0.0185 + bond_coeff @bond:c3-s4 harmonic 187.48 1.831 # SOURCE1_SOURCE5 326 0.0096 + bond_coeff @bond:c3-s6 harmonic 200.07 1.808 # SOURCE1_SOURCE5 644 0.0143 + bond_coeff @bond:c3-sh harmonic 180.78 1.843 # SOURCE3_SOURCE5 189 0.0058 + bond_coeff @bond:c3-ss harmonic 182.96 1.839 # SOURCE1_SOURCE5 2732 0.0105 + bond_coeff @bond:c3-sx harmonic 181.64 1.842 # SOURCE3_SOURCE5 99 0.0121 + bond_coeff @bond:c3-sy harmonic 199.39 1.809 # SOURCE3_SOURCE5 162 0.0094 + bond_coeff @bond:ca-ca harmonic 378.57 1.398 # SOURCE1_SOURCE5 121206 0.0061 + bond_coeff @bond:ca-cc harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 + bond_coeff @bond:ca-cd harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 + bond_coeff @bond:ca-ce harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 + bond_coeff @bond:ca-cf harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 + bond_coeff @bond:ca-cg harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 + bond_coeff @bond:ca-ch harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 + bond_coeff @bond:ca-cl harmonic 181.97 1.750 # SOURCE1_SOURCE5 2919 0.0059 + bond_coeff @bond:ca-cp harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 + bond_coeff @bond:ca-cq harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 + bond_coeff @bond:ca-cx harmonic 273.13 1.490 # SOURCE1_SOURCE5 165 0.0091 + bond_coeff @bond:ca-cy harmonic 250.49 1.515 # SOURCE4_SOURCE5 35 0.0055 + bond_coeff @bond:ca-f harmonic 353.59 1.349 # SOURCE1_SOURCE5 1239 0.0057 + bond_coeff @bond:ca-h4 harmonic 390.15 1.089 # SOURCE3_SOURCE5 2643 0.0010 + bond_coeff @bond:ca-h5 harmonic 392.37 1.088 # SOURCE3_SOURCE5 299 0.0007 + bond_coeff @bond:ca-ha harmonic 395.72 1.086 # SOURCE3_SOURCE5 65456 0.0010 + bond_coeff @bond:ca-i harmonic 108.27 2.129 # SOURCE1_SOURCE5 61 0.0076 + bond_coeff @bond:ca-n1 harmonic 420.66 1.335 # SOURCE3_SOURCE5 6 0.0078 + bond_coeff @bond:ca-n2 harmonic 476.53 1.303 # SOURCE4 7 0.0058 + bond_coeff @bond:ca-n harmonic 315.21 1.412 # SOURCE3_SOURCE5 1254 0.0090 + bond_coeff @bond:ca-n4 harmonic 244.03 1.484 # SOURCE1_SOURCE5 28 0.0065 + bond_coeff @bond:ca-na harmonic 349.52 1.384 # SOURCE1_SOURCE5 2751 0.0095 + bond_coeff @bond:ca-nb harmonic 414.24 1.339 # SOURCE3_SOURCE5 6806 0.0055 + bond_coeff @bond:ca-nc harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 + bond_coeff @bond:ca-nd harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 + bond_coeff @bond:ca-ne harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 + bond_coeff @bond:ca-nf harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 + bond_coeff @bond:ca-nh harmonic 347.06 1.386 # SOURCE1_SOURCE5 2785 0.0134 + bond_coeff @bond:ca-no harmonic 257.38 1.469 # SOURCE1_SOURCE5 454 0.0049 + bond_coeff @bond:ca-o harmonic 606.45 1.236 # SOURCE4_SOURCE5 17 0.0088 + bond_coeff @bond:ca-oh harmonic 365.55 1.364 # SOURCE1_SOURCE5 3637 0.0062 + bond_coeff @bond:ca-os harmonic 357.53 1.370 # SOURCE1_SOURCE5 6900 0.0064 + bond_coeff @bond:ca-p2 harmonic 176.94 1.840 # SOUECE3 1 + bond_coeff @bond:ca-p3 harmonic 184.18 1.826 # SOURCE1_SOURCE5 156 0.0180 + bond_coeff @bond:ca-p4 harmonic 194.74 1.806 # SOUECE3 1 + bond_coeff @bond:ca-p5 harmonic 200.84 1.795 # SOURCE1_SOURCE5 577 0.0028 + bond_coeff @bond:ca-pe harmonic 182.48 1.829 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-pf harmonic 182.48 1.829 # SOURCE3 10 0.0042 + bond_coeff @bond:ca-px harmonic 184.54 1.825 # SOURCE3 5 0.0168 + bond_coeff @bond:ca-py harmonic 189.18 1.816 # SOURCE4_SOURCE5 34 0.0098 + bond_coeff @bond:ca-s harmonic 244.02 1.739 # SOURCE3 2 + bond_coeff @bond:ca-s4 harmonic 211.54 1.788 # SOURCE1 51 0.0048 + bond_coeff @bond:ca-s6 harmonic 224.85 1.767 # SOURCE1_SOURCE5 258 0.0041 + bond_coeff @bond:ca-sh harmonic 215.91 1.781 # SOURCE4_SOURCE5 40 0.0053 + bond_coeff @bond:ca-ss harmonic 216.10 1.781 # SOURCE1_SOURCE5 1016 0.0068 + bond_coeff @bond:ca-sx harmonic 190.35 1.825 # SOURCE4_SOURCE5 90 0.0050 + bond_coeff @bond:ca-sy harmonic 209.78 1.791 # SOURCE3_SOURCE5 703 0.0076 + bond_coeff @bond:c-c1 harmonic 303.33 1.460 # SOUECE3 1 + bond_coeff @bond:c-c2 harmonic 368.17 1.406 # SOURCE3 2 0.0370 + bond_coeff @bond:c-c harmonic 224.38 1.548 # SOURCE1_SOURCE5 254 0.0090 + bond_coeff @bond:c-c3 harmonic 243.22 1.524 # SOURCE1_SOURCE5 12697 0.0077 + bond_coeff @bond:c-ca harmonic 272.66 1.491 # SOURCE1_SOURCE5 4357 0.0085 + bond_coeff @bond:c-cc harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 + bond_coeff @bond:cc-cc harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 + bond_coeff @bond:cc-cd harmonic 416.13 1.373 # SOURCE3_SOURCE5 8451 0.0091 + bond_coeff @bond:cc-ce harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 + bond_coeff @bond:cc-cf harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 + bond_coeff @bond:cc-cg harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 + bond_coeff @bond:cc-ch harmonic 341.16 1.427 # SOURCE1 560 + bond_coeff @bond:cc-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 + bond_coeff @bond:cc-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 + bond_coeff @bond:c-cd harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 + bond_coeff @bond:c-ce harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 + bond_coeff @bond:c-cf harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 + bond_coeff @bond:cc-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 70 0.0039 + bond_coeff @bond:c-cg harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 + bond_coeff @bond:c-ch harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 + bond_coeff @bond:cc-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 + bond_coeff @bond:cc-h5 harmonic 403.49 1.082 # SOURCE3_SOURCE5 879 0.0012 + bond_coeff @bond:cc-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 + bond_coeff @bond:c-cl harmonic 156.23 1.803 # SOURCE3_SOURCE5 16 0.0187 + bond_coeff @bond:cc-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 + bond_coeff @bond:cc-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 + bond_coeff @bond:cc-n4 harmonic 236.72 1.493 # SOURCE4 7 0.0148 + bond_coeff @bond:cc-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 + bond_coeff @bond:cc-nc harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 + bond_coeff @bond:cc-nd harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 + bond_coeff @bond:cc-ne harmonic 356.61 1.379 # SOURCE4_SOURCE5 82 0.0119 + bond_coeff @bond:cc-nf harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 + bond_coeff @bond:cc-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 + bond_coeff @bond:cc-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 386 0.0074 + bond_coeff @bond:cc-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 + bond_coeff @bond:cc-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 + bond_coeff @bond:cc-pd harmonic 240.75 1.733 # SOURCE3 84 0.0161 + bond_coeff @bond:cc-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 22 0.0030 + bond_coeff @bond:cc-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 + bond_coeff @bond:cc-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 44 0.0033 + bond_coeff @bond:cc-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 + bond_coeff @bond:c-cu harmonic 360.20 1.412 # SOURCE2 1 + bond_coeff @bond:c-cx harmonic 265.90 1.498 # SOURCE1_SOURCE5 246 0.0109 + bond_coeff @bond:c-cy harmonic 222.38 1.551 # SOURCE1_SOURCE5 374 0.0059 + bond_coeff @bond:cd-cd harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 + bond_coeff @bond:cd-ce harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 + bond_coeff @bond:cd-cf harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 + bond_coeff @bond:cd-cg harmonic 341.16 1.427 # SOURCE1 560 + bond_coeff @bond:cd-ch harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 + bond_coeff @bond:cd-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 + bond_coeff @bond:cd-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 + bond_coeff @bond:cd-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 21 0.0007 + bond_coeff @bond:cd-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 + bond_coeff @bond:cd-h5 harmonic 403.68 1.082 # SOURCE3_SOURCE5 578 0.0013 + bond_coeff @bond:cd-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 + bond_coeff @bond:cd-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 + bond_coeff @bond:cd-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 + bond_coeff @bond:cd-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 + bond_coeff @bond:cd-nc harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 + bond_coeff @bond:cd-nd harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 + bond_coeff @bond:cd-ne harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 + bond_coeff @bond:cd-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 + bond_coeff @bond:cd-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 + bond_coeff @bond:cd-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 + bond_coeff @bond:cd-pc harmonic 240.75 1.733 # SOURCE3 84 + bond_coeff @bond:cd-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 + bond_coeff @bond:cd-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 + bond_coeff @bond:ce-ce harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 + bond_coeff @bond:ce-cf harmonic 452.16 1.351 # SOURCE1_SOURCE5 1908 0.0059 + bond_coeff @bond:ce-cg harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 + bond_coeff @bond:ce-ch harmonic 336.29 1.431 # SOURCE1 22 + bond_coeff @bond:ce-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 90 0.0111 + bond_coeff @bond:ce-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 31 0.0075 + bond_coeff @bond:ce-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 53 0.0043 + bond_coeff @bond:ce-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 + bond_coeff @bond:ce-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 + bond_coeff @bond:ce-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 + bond_coeff @bond:ce-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 + bond_coeff @bond:ce-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 + bond_coeff @bond:ce-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 11 0.0050 + bond_coeff @bond:ce-ne harmonic 336.57 1.394 # SOURCE3_SOURCE5 69 0.0151 + bond_coeff @bond:ce-nf harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 + bond_coeff @bond:ce-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 + bond_coeff @bond:ce-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 + bond_coeff @bond:ce-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 + bond_coeff @bond:ce-p2 harmonic 190.37 1.814 # SOUECE3 1 + bond_coeff @bond:ce-pe harmonic 188.22 1.818 # SOURCE3 8 0.0108 + bond_coeff @bond:ce-px harmonic 186.64 1.821 # SOURCE3 6 0.0046 + bond_coeff @bond:ce-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 22 0.0142 + bond_coeff @bond:ce-s harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:ce-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 56 0.0098 + bond_coeff @bond:ce-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 30 0.0101 + bond_coeff @bond:ce-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 41 0.0169 + bond_coeff @bond:c-f harmonic 387.77 1.325 # SOURCE2 6 0.0147 + bond_coeff @bond:cf-cf harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 + bond_coeff @bond:cf-cg harmonic 336.29 1.431 # SOURCE1 22 + bond_coeff @bond:cf-ch harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 + bond_coeff @bond:cf-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 + bond_coeff @bond:cf-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 + bond_coeff @bond:cf-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 + bond_coeff @bond:cf-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 + bond_coeff @bond:cf-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 + bond_coeff @bond:cf-ne harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 + bond_coeff @bond:cf-nf harmonic 336.57 1.394 # SOURCE3_SOURCE5 62 0.0156 + bond_coeff @bond:cf-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 + bond_coeff @bond:cf-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 + bond_coeff @bond:cf-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 + bond_coeff @bond:cf-p2 harmonic 190.37 1.814 # SOUECE3 1 + bond_coeff @bond:cf-pf harmonic 188.22 1.818 # SOURCE3 8 + bond_coeff @bond:cf-px harmonic 186.64 1.821 # SOURCE3 6 + bond_coeff @bond:cf-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 17 0.0171 + bond_coeff @bond:cf-s harmonic 291.39 1.680 # SOUECE3 1 + bond_coeff @bond:cf-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 25 0.0105 + bond_coeff @bond:cf-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 36 0.0177 + bond_coeff @bond:cg-cg harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 + bond_coeff @bond:cg-ch harmonic 811.54 1.206 # SOURCE1_SOURCE5 156 0.0023 + bond_coeff @bond:cg-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 + bond_coeff @bond:cg-ne harmonic 435.38 1.326 # SOURCE4_SOURCE5 68 0.0013 + bond_coeff @bond:cg-pe harmonic 339.39 1.621 # SOURCE3 11 0.2008 + bond_coeff @bond:c-h4 harmonic 350.25 1.112 # SOURCE4_SOURCE5 506 0.0025 + bond_coeff @bond:c-h5 harmonic 361.80 1.105 # SOURCE4_SOURCE5 163 0.0038 + bond_coeff @bond:c-ha harmonic 368.78 1.101 # SOURCE3 53 0.0102 + bond_coeff @bond:ch-ch harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 + bond_coeff @bond:ch-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 + bond_coeff @bond:ch-nf harmonic 435.38 1.326 # SOURCE4_SOURCE5 51 0.0014 + bond_coeff @bond:ch-pf harmonic 339.39 1.621 # SOURCE3 11 + bond_coeff @bond:c-i harmonic 89.53 2.209 # SOURCE3 4 0.0365 + bond_coeff @bond:cl-cl harmonic 79.29 2.267 # SOURCE1 2 0.0395 + bond_coeff @bond:cl-cx harmonic 172.69 1.768 # SOURCE1_SOURCE5 42 0.0071 + bond_coeff @bond:cl-cy harmonic 161.13 1.792 # SOURCE2_SOURCE5 28 0.0103 + bond_coeff @bond:cl-n1 harmonic 217.59 1.630 # SOUECE3 1 + bond_coeff @bond:cl-n2 harmonic 123.81 1.819 # SOURCE3 6 0.1020 + bond_coeff @bond:cl-n3 harmonic 139.52 1.777 # SOURCE4_SOURCE5 16 0.0044 + bond_coeff @bond:cl-n harmonic 167.01 1.716 # SOURCE4_SOURCE5 17 0.0049 + bond_coeff @bond:cl-n4 harmonic 149.71 1.753 # SOURCE3 4 0.0098 + bond_coeff @bond:cl-na harmonic 118.36 1.835 # SOURCE3 7 0.2083 + bond_coeff @bond:cl-nh harmonic 145.39 1.763 # SOURCE3 1 + bond_coeff @bond:cl-no harmonic 116.71 1.840 # SOURCE2 1 + bond_coeff @bond:cl-o harmonic 331.00 1.483 # SOURCE3 4 + bond_coeff @bond:cl-oh harmonic 169.11 1.690 # SOURCE2 1 + bond_coeff @bond:cl-os harmonic 149.95 1.730 # SOURCE3 4 + bond_coeff @bond:cl-p2 harmonic 143.51 2.070 # SOURCE3 6 0.0108 + bond_coeff @bond:cl-p3 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-p4 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-p5 harmonic 167.79 2.008 # SOURCE1 111 + bond_coeff @bond:cl-pb harmonic 172.59 1.997 # SOURCE1 46 + bond_coeff @bond:cl-s harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-s2 harmonic 185.62 2.161 # SOURCE2 1 + bond_coeff @bond:cl-s4 harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-s6 harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sh harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-ss harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sx harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:cl-sy harmonic 230.41 2.072 # SOURCE1 6 + bond_coeff @bond:c-n2 harmonic 306.30 1.420 # SOUECE3 1 + bond_coeff @bond:c-n4 harmonic 197.87 1.546 # SOURCE3 4 0.0388 + bond_coeff @bond:c-n harmonic 356.21 1.379 # SOURCE1_SOURCE5 9463 0.0137 + bond_coeff @bond:c-nc harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 + bond_coeff @bond:c-nd harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 + bond_coeff @bond:c-ne harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 + bond_coeff @bond:c-nf harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 + bond_coeff @bond:c-no harmonic 201.86 1.540 # SOUECE3 1 + bond_coeff @bond:c-o harmonic 652.57 1.218 # SOURCE1_SOURCE5 27083 0.0110 + bond_coeff @bond:c-oh harmonic 383.13 1.351 # SOURCE1_SOURCE5 3610 0.0055 + bond_coeff @bond:c-os harmonic 372.94 1.358 # SOURCE1_SOURCE5 5555 0.0163 + bond_coeff @bond:c-p2 harmonic 150.04 1.900 # SOUECE3 1 + bond_coeff @bond:c-p3 harmonic 157.13 1.883 # SOURCE3 6 0.0129 + bond_coeff @bond:c-p4 harmonic 158.42 1.880 # SOUECE3 1 + bond_coeff @bond:c-p5 harmonic 157.64 1.882 # SOURCE4_SOURCE5 25 0.0081 + bond_coeff @bond:cp-cp harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 + bond_coeff @bond:cp-cq harmonic 309.60 1.454 # SOURCE4_SOURCE5 34 0.0159 + bond_coeff @bond:c-pe harmonic 145.65 1.911 # SOURCE3 3 0.0025 + bond_coeff @bond:c-pf harmonic 145.65 1.911 # SOURCE3 3 + bond_coeff @bond:cp-na harmonic 349.52 1.384 # SOURCE4 7 0.0181 + bond_coeff @bond:cp-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 190 0.0068 + bond_coeff @bond:c-px harmonic 148.42 1.904 # SOURCE3 1 + bond_coeff @bond:c-py harmonic 164.17 1.867 # SOURCE3_SOURCE5 17 0.0103 + bond_coeff @bond:cq-cq harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 + bond_coeff @bond:c-s harmonic 298.35 1.672 # SOURCE1_SOURCE5 875 0.0114 + bond_coeff @bond:c-s4 harmonic 167.99 1.870 # SOUECE3 1 + bond_coeff @bond:c-s6 harmonic 167.99 1.870 # SOUECE3 1 + bond_coeff @bond:c-sh harmonic 206.09 1.797 # SOURCE3_SOURCE5 39 0.0097 + bond_coeff @bond:c-ss harmonic 204.39 1.800 # SOURCE1_SOURCE5 249 0.0157 + bond_coeff @bond:c-sx harmonic 161.23 1.885 # SOURCE3 5 0.0088 + bond_coeff @bond:c-sy harmonic 170.32 1.865 # SOURCE3 5 0.0085 + bond_coeff @bond:cu-cu harmonic 564.10 1.294 # SOURCE1 10 + bond_coeff @bond:cu-cx harmonic 277.70 1.485 # SOURCE1_SOURCE5 31 0.0066 + bond_coeff @bond:cu-ha harmonic 405.22 1.081 # SOURCE2 3 0.0111 + bond_coeff @bond:cv-cv harmonic 480.53 1.335 # SOURCE1 25 + bond_coeff @bond:cv-cy harmonic 250.66 1.515 # SOURCE1_SOURCE5 19 0.0057 + bond_coeff @bond:cv-ha harmonic 393.86 1.087 # SOURCE3 2 + bond_coeff @bond:cx-cv harmonic 256.87 1.508 # SOURCE1 2536 + bond_coeff @bond:cx-cx harmonic 260.31 1.504 # SOURCE1_SOURCE5 2781 0.0136 + bond_coeff @bond:cx-cy harmonic 250.83 1.515 # SOURCE3 2 + bond_coeff @bond:cx-f harmonic 339.01 1.360 # SOURCE2_SOURCE5 10 0.0045 + bond_coeff @bond:cx-h1 harmonic 390.15 1.089 # SOURCE3_SOURCE5 1142 0.0013 + bond_coeff @bond:cx-h2 harmonic 395.91 1.086 # SOURCE3_SOURCE5 5 0.0014 + bond_coeff @bond:cx-hc harmonic 393.86 1.087 # SOURCE3_SOURCE5 1702 0.0009 + bond_coeff @bond:cx-hx harmonic 397.60 1.085 # SOURCE4_SOURCE5 19 0.0002 + bond_coeff @bond:cx-n2 harmonic 245.89 1.482 # SOURCE3 2 + bond_coeff @bond:cx-n3 harmonic 256.30 1.470 # SOURCE1_SOURCE5 227 0.0050 + bond_coeff @bond:cx-n harmonic 283.33 1.442 # SOURCE4_SOURCE5 39 0.0103 + bond_coeff @bond:cx-na harmonic 264.52 1.461 # SOURCE4_SOURCE5 49 0.0026 + bond_coeff @bond:cx-nh harmonic 270.65 1.455 # SOURCE4_SOURCE5 192 0.0076 + bond_coeff @bond:cx-oh harmonic 369.30 1.361 # SOURCE3 3 0.0018 + bond_coeff @bond:cx-os harmonic 279.50 1.437 # SOURCE3_SOURCE5 703 0.0071 + bond_coeff @bond:cx-p3 harmonic 164.17 1.867 # SOURCE2 1 + bond_coeff @bond:cx-s4 harmonic 192.02 1.822 # SOURCE2 1 + bond_coeff @bond:cx-s6 harmonic 249.87 1.731 # SOURCE2 1 + bond_coeff @bond:cx-ss harmonic 186.43 1.833 # SOURCE2_SOURCE5 5 0.0011 + bond_coeff @bond:cy-cy harmonic 218.51 1.556 # SOURCE1_SOURCE5 1665 0.0053 + bond_coeff @bond:cy-f harmonic 344.83 1.356 # SOURCE4_SOURCE5 36 0.0095 + bond_coeff @bond:cy-h1 harmonic 379.11 1.095 # SOURCE3_SOURCE5 477 0.0019 + bond_coeff @bond:cy-h2 harmonic 382.87 1.093 # SOURCE4_SOURCE5 210 0.0017 + bond_coeff @bond:cy-hc harmonic 379.47 1.095 # SOURCE3_SOURCE5 840 0.0011 + bond_coeff @bond:cy-n harmonic 256.66 1.470 # SOURCE4_SOURCE5 618 0.0101 + bond_coeff @bond:cy-n3 harmonic 248.73 1.479 # SOURCE1_SOURCE5 67 0.0083 + bond_coeff @bond:cy-oh harmonic 305.23 1.412 # SOURCE3_SOURCE5 13 0.0082 + bond_coeff @bond:cy-os harmonic 277.32 1.439 # SOURCE4_SOURCE5 81 0.0141 + bond_coeff @bond:cy-s6 harmonic 177.00 1.851 # SOURCE4_SOURCE5 39 0.0142 + bond_coeff @bond:cy-ss harmonic 177.89 1.849 # SOURCE4_SOURCE5 201 0.0086 + bond_coeff @bond:cz-nh harmonic 414.24 1.339 # SOURCE4_SOURCE5 85 0.0046 + bond_coeff @bond:f-n1 harmonic 167.33 1.410 # SOUECE3 1 + bond_coeff @bond:f-n2 harmonic 148.04 1.444 # SOURCE3 5 0.0377 + bond_coeff @bond:f-n3 harmonic 169.79 1.406 # SOURCE1 9 + bond_coeff @bond:f-n harmonic 175.49 1.397 # SOURCE3 3 0.0112 + bond_coeff @bond:f-n4 harmonic 246.14 1.308 # SOURCE3 2 + bond_coeff @bond:f-na harmonic 166.72 1.411 # SOURCE3 7 0.0611 + bond_coeff @bond:f-nh harmonic 157.90 1.426 # SOURCE3 3 0.0085 + bond_coeff @bond:f-no harmonic 136.49 1.467 # SOURCE2 1 + bond_coeff @bond:f-o harmonic 198.07 1.330 # SOUECE3 1 + bond_coeff @bond:f-oh harmonic 129.79 1.444 # SOURCE3 1 + bond_coeff @bond:f-os harmonic 139.94 1.423 # SOURCE3 2 + bond_coeff @bond:f-p2 harmonic 522.31 1.536 # SOURCE3 7 0.2054 + bond_coeff @bond:f-p3 harmonic 454.68 1.578 # SOURCE2 8 0.0103 + bond_coeff @bond:f-p4 harmonic 437.32 1.590 # SOUECE3 1 + bond_coeff @bond:f-p5 harmonic 442.73 1.586 # SOURCE1_SOURCE5 18 0.0161 + bond_coeff @bond:f-s2 harmonic 363.47 1.643 # SOURCE2 1 + bond_coeff @bond:f-s harmonic 344.73 1.660 # SOUECE3 1 + bond_coeff @bond:f-s4 harmonic 428.80 1.591 # SOURCE2 4 0.0065 + bond_coeff @bond:f-s6 harmonic 400.85 1.612 # SOURCE2_SOURCE5 15 0.0133 + bond_coeff @bond:f-sh harmonic 356.72 1.649 # SOURCE3 1 + bond_coeff @bond:f-ss harmonic 373.87 1.634 # SOURCE3 3 0.0156 + bond_coeff @bond:hn-n1 harmonic 605.55 0.986 # SOURCE2 1 + bond_coeff @bond:hn-n2 harmonic 501.09 1.023 # SOURCE3_SOURCE5 732 0.0030 + bond_coeff @bond:hn-n3 harmonic 511.28 1.019 # SOURCE3_SOURCE5 5944 0.0012 + bond_coeff @bond:hn-n harmonic 527.31 1.013 # SOURCE3_SOURCE5 7593 0.0034 + bond_coeff @bond:hn-n4 harmonic 482.87 1.030 # SOURCE3_SOURCE5 756 0.0122 + bond_coeff @bond:hn-na harmonic 535.14 1.010 # SOURCE3_SOURCE5 1755 0.0019 + bond_coeff @bond:hn-nh harmonic 529.46 1.012 # SOURCE3_SOURCE5 7230 0.0022 + bond_coeff @bond:hn-no harmonic 501.09 1.023 # SOURCE3 1 + bond_coeff @bond:ho-o harmonic 540.28 0.981 # SOURCE3 1 + bond_coeff @bond:ho-oh harmonic 563.51 0.973 # SOURCE3_SOURCE5 21237 0.0034 + bond_coeff @bond:hp-p2 harmonic 266.54 1.336 # SOURCE3 87 0.1706 + bond_coeff @bond:hp-p3 harmonic 200.57 1.412 # SOURCE3_SOURCE5 123 0.0510 + bond_coeff @bond:hp-p4 harmonic 253.60 1.349 # SOURCE3 17 0.1577 + bond_coeff @bond:hp-p5 harmonic 196.39 1.418 # SOURCE3_SOURCE5 31 0.0077 + bond_coeff @bond:hs-s harmonic 288.27 1.353 # SOURCE3 1 + bond_coeff @bond:hs-s4 harmonic 265.33 1.375 # SOURCE3 5 0.0004 + bond_coeff @bond:hs-s6 harmonic 281.78 1.359 # SOURCE3 5 0.0015 + bond_coeff @bond:hs-sh harmonic 294.59 1.347 # SOURCE3_SOURCE5 477 0.0118 + bond_coeff @bond:i-i harmonic 50.27 2.917 # SOURCE1 1 + bond_coeff @bond:i-n1 harmonic 105.51 2.060 # SOUECE3 1 + bond_coeff @bond:i-n2 harmonic 59.35 2.304 # SOURCE3 6 0.1186 + bond_coeff @bond:i-n harmonic 96.05 2.098 # SOURCE3 5 0.0156 + bond_coeff @bond:i-n3 harmonic 77.95 2.185 # SOURCE3 3 0.0437 + bond_coeff @bond:i-n4 harmonic 83.69 2.155 # SOURCE3 3 0.0168 + bond_coeff @bond:i-na harmonic 89.07 2.129 # SOURCE3 8 0.1276 + bond_coeff @bond:i-nh harmonic 84.69 2.150 # SOURCE3 1 + bond_coeff @bond:i-no harmonic 70.03 2.231 # SOURCE3 1 + bond_coeff @bond:i-o harmonic 106.33 1.980 # SOUECE3 1 + bond_coeff @bond:i-oh harmonic 78.38 2.101 # SOURCE3 2 + bond_coeff @bond:i-os harmonic 73.23 2.129 # SOURCE3 3 0.0146 + bond_coeff @bond:i-p2 harmonic 66.30 2.643 # SOURCE3 6 0.0297 + bond_coeff @bond:i-p3 harmonic 77.18 2.566 # SOURCE3 3 0.0016 + bond_coeff @bond:i-p4 harmonic 120.75 2.352 # SOURCE3 4 0.2600 + bond_coeff @bond:i-p5 harmonic 72.70 2.596 # SOURCE3 3 0.0143 + bond_coeff @bond:i-s harmonic 115.77 2.430 # SOUECE3 1 + bond_coeff @bond:i-s4 harmonic 49.21 2.870 # SOUECE3 1 + bond_coeff @bond:i-s6 harmonic 49.21 2.870 # SOURCE3 1 + bond_coeff @bond:i-sh harmonic 88.56 2.560 # SOUECE3 1 + bond_coeff @bond:i-ss harmonic 86.63 2.571 # SOURCE3 3 0.0065 + bond_coeff @bond:n1-n1 harmonic 750.98 1.135 # SOURCE1_SOURCE5 78 0.0044 + bond_coeff @bond:n1-n2 harmonic 494.86 1.230 # SOURCE1_SOURCE5 36 0.0029 + bond_coeff @bond:n1-n3 harmonic 307.19 1.350 # SOUECE3 1 + bond_coeff @bond:n1-n4 harmonic 295.75 1.360 # SOUECE3 1 + bond_coeff @bond:n1-na harmonic 307.19 1.350 # SOUECE3 1 + bond_coeff @bond:n1-nc harmonic 525.73 1.216 # SOURCE1 38 + bond_coeff @bond:n1-nd harmonic 525.73 1.216 # SOURCE1 38 + bond_coeff @bond:n1-ne harmonic 452.52 1.252 # SOURCE2 1 + bond_coeff @bond:n1-nf harmonic 452.52 1.252 # SOURCE2 1 + bond_coeff @bond:n1-nh harmonic 319.16 1.340 # SOUECE3 1 + bond_coeff @bond:n1-no harmonic 254.81 1.400 # SOUECE3 1 + bond_coeff @bond:n1-o harmonic 298.40 1.277 # SOURCE3 5 0.0438 + bond_coeff @bond:n1-oh harmonic 272.24 1.300 # SOUECE3 1 + bond_coeff @bond:n1-os harmonic 261.73 1.310 # SOUECE3 1 + bond_coeff @bond:n1-p2 harmonic 268.95 1.678 # SOURCE3 2 0.0282 + bond_coeff @bond:n1-p3 harmonic 284.28 1.660 # SOUECE3 1 + bond_coeff @bond:n1-p4 harmonic 267.31 1.680 # SOURCE3 0 + bond_coeff @bond:n1-p5 harmonic 377.36 1.571 # SOURCE1 132 + bond_coeff @bond:n1-s2 harmonic 681.10 1.449 # SOURCE2 2 0.0010 + bond_coeff @bond:n1-s harmonic 339.70 1.659 # SOURCE3 6 0.0789 + bond_coeff @bond:n1-s4 harmonic 349.33 1.650 # SOUECE3 1 + bond_coeff @bond:n1-s6 harmonic 766.72 1.416 # SOURCE2 2 + bond_coeff @bond:n1-sh harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n1-ss harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n2-n2 harmonic 425.99 1.267 # SOURCE3_SOURCE5 40 0.0268 + bond_coeff @bond:n2-n3 harmonic 332.97 1.329 # SOURCE2 1 + bond_coeff @bond:n2-n4 harmonic 100.13 1.679 # SOURCE3 7 0.3138 + bond_coeff @bond:n2-na harmonic 287.40 1.368 # SOURCE4_SOURCE5 49 0.0087 + bond_coeff @bond:n2-nc harmonic 446.98 1.255 # SOURCE1 13 + bond_coeff @bond:n2-nd harmonic 446.98 1.255 # SOURCE1 13 + bond_coeff @bond:n2-ne harmonic 418.13 1.271 # SOURCE3_SOURCE5 57 0.0194 + bond_coeff @bond:n2-nf harmonic 418.13 1.271 # SOURCE3_SOURCE5 27 0.0074 + bond_coeff @bond:n2-nh harmonic 304.40 1.352 # SOURCE3_SOURCE5 210 0.0159 + bond_coeff @bond:n2-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 15 0.0628 + bond_coeff @bond:n2-o harmonic 381.83 1.217 # SOURCE3_SOURCE5 112 0.0102 + bond_coeff @bond:n2-oh harmonic 192.13 1.391 # SOURCE1_SOURCE5 149 0.0171 + bond_coeff @bond:n2-os harmonic 184.98 1.401 # SOURCE3_SOURCE5 108 0.0101 + bond_coeff @bond:n2-p2 harmonic 338.04 1.605 # SOURCE3 35 0.0737 + bond_coeff @bond:n2-p3 harmonic 208.02 1.764 # SOURCE3 7 0.0374 + bond_coeff @bond:n2-p4 harmonic 234.05 1.724 # SOUECE3 1 + bond_coeff @bond:n2-p5 harmonic 344.61 1.599 # SOURCE1 7 + bond_coeff @bond:n2-pe harmonic 418.07 1.540 # SOURCE3 20 0.1392 + bond_coeff @bond:n2-pf harmonic 418.07 1.540 # SOURCE3 20 + bond_coeff @bond:n2-s2 harmonic 491.26 1.544 # SOURCE2_SOURCE5 11 0.0086 + bond_coeff @bond:n2-s4 harmonic 396.29 1.610 # SOUECE3 1 + bond_coeff @bond:n2-s harmonic 496.36 1.541 # SOURCE1 37 + bond_coeff @bond:n2-s6 harmonic 475.70 1.554 # SOURCE4_SOURCE5 16 0.0041 + bond_coeff @bond:n2-sh harmonic 267.45 1.738 # SOURCE3 5 0.0511 + bond_coeff @bond:n2-ss harmonic 342.87 1.656 # SOURCE1 36 + bond_coeff @bond:n3-n3 harmonic 219.29 1.442 # SOURCE1_SOURCE5 48 0.0063 + bond_coeff @bond:n3-n4 harmonic 228.50 1.430 # SOURCE1_SOURCE5 9 0.0040 + bond_coeff @bond:n3-na harmonic 236.90 1.420 # SOURCE1 68 + bond_coeff @bond:n3-nh harmonic 240.71 1.416 # SOURCE1_SOURCE5 66 0.0085 + bond_coeff @bond:n3-no harmonic 256.88 1.398 # SOURCE3_SOURCE5 19 0.0132 + bond_coeff @bond:n3-o harmonic 269.04 1.303 # SOURCE3 4 0.1217 + bond_coeff @bond:n3-oh harmonic 176.15 1.415 # SOURCE1_SOURCE5 17 0.0055 + bond_coeff @bond:n3-os harmonic 160.59 1.441 # SOURCE1_SOURCE5 84 0.0191 + bond_coeff @bond:n3-p2 harmonic 275.64 1.670 # SOUECE3 1 + bond_coeff @bond:n3-p3 harmonic 229.90 1.730 # SOURCE1 40 + bond_coeff @bond:n3-p4 harmonic 253.83 1.697 # SOURCE1 88 + bond_coeff @bond:n3-p5 harmonic 275.98 1.670 # SOURCE1_SOURCE5 680 0.0109 + bond_coeff @bond:n3-py harmonic 256.22 1.694 # SOURCE4_SOURCE5 16 0.0080 + bond_coeff @bond:n3-s harmonic 228.53 1.792 # SOURCE3 3 0.0178 + bond_coeff @bond:n3-s4 harmonic 254.85 1.754 # SOURCE3_SOURCE5 15 0.0416 + bond_coeff @bond:n3-s6 harmonic 326.04 1.672 # SOURCE1_SOURCE5 243 0.0144 + bond_coeff @bond:n3-sh harmonic 266.66 1.739 # SOURCE3 3 0.0154 + bond_coeff @bond:n3-ss harmonic 279.14 1.724 # SOURCE3_SOURCE5 25 0.0197 + bond_coeff @bond:n3-sy harmonic 303.10 1.696 # SOURCE4_SOURCE5 511 0.0083 + bond_coeff @bond:n4-n4 harmonic 188.86 1.484 # SOURCE3 4 0.0089 + bond_coeff @bond:n4-na harmonic 224.44 1.435 # SOURCE3 9 0.0390 + bond_coeff @bond:n4-nh harmonic 201.09 1.466 # SOURCE3 5 0.0108 + bond_coeff @bond:n4-no harmonic 191.50 1.480 # SOUECE3 1 + bond_coeff @bond:n4-o harmonic 215.08 1.361 # SOURCE3 3 0.0041 + bond_coeff @bond:n4-oh harmonic 186.01 1.400 # SOURCE3 3 0.0115 + bond_coeff @bond:n4-os harmonic 172.30 1.421 # SOURCE3 5 0.0249 + bond_coeff @bond:n4-p2 harmonic 126.91 1.942 # SOURCE3 10 0.0643 + bond_coeff @bond:n4-p3 harmonic 149.95 1.880 # SOURCE3 5 0.0146 + bond_coeff @bond:n4-p4 harmonic 128.26 1.938 # SOURCE3 1 + bond_coeff @bond:n4-p5 harmonic 172.23 1.830 # SOURCE3 5 0.0087 + bond_coeff @bond:n4-py harmonic 141.24 1.902 # SOURCE3 4 + bond_coeff @bond:n4-s harmonic 204.02 1.832 # SOURCE3 3 0.0004 + bond_coeff @bond:n4-s4 harmonic 139.73 1.972 # SOURCE3 3 0.0198 + bond_coeff @bond:n4-s6 harmonic 162.90 1.914 # SOURCE3 5 0.0432 + bond_coeff @bond:n4-sh harmonic 216.47 1.811 # SOURCE3 3 0.0027 + bond_coeff @bond:n4-ss harmonic 215.86 1.812 # SOURCE3 5 0.0064 + bond_coeff @bond:na-na harmonic 253.88 1.401 # SOURCE1 40 + bond_coeff @bond:na-nb harmonic 310.48 1.347 # SOURCE4_SOURCE5 26 0.0093 + bond_coeff @bond:na-nc harmonic 300.49 1.356 # SOURCE3_SOURCE5 899 0.0083 + bond_coeff @bond:na-nd harmonic 302.44 1.354 # SOURCE3_SOURCE5 362 0.0113 + bond_coeff @bond:na-nh harmonic 254.81 1.400 # SOURCE1_SOURCE5 20 0.0066 + bond_coeff @bond:na-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 16 0.0192 + bond_coeff @bond:na-o harmonic 347.95 1.239 # SOURCE1_SOURCE5 93 0.0208 + bond_coeff @bond:na-oh harmonic 191.21 1.393 # SOURCE3_SOURCE5 18 0.0144 + bond_coeff @bond:na-os harmonic 158.65 1.444 # SOURCE3 45 0.0423 + bond_coeff @bond:na-p2 harmonic 217.35 1.749 # SOURCE3 11 0.0192 + bond_coeff @bond:na-p3 harmonic 209.23 1.762 # SOURCE3 8 0.0113 + bond_coeff @bond:na-p4 harmonic 386.12 1.564 # SOURCE3 5 0.2161 + bond_coeff @bond:na-p5 harmonic 240.43 1.715 # SOURCE3 11 0.0238 + bond_coeff @bond:na-pc harmonic 228.54 1.732 # SOURCE3 81 0.0207 + bond_coeff @bond:na-pd harmonic 228.54 1.732 # SOURCE3 81 + bond_coeff @bond:na-py harmonic 242.60 1.712 # SOURCE3 2 + bond_coeff @bond:na-s harmonic 247.08 1.765 # SOURCE3 8 0.0095 + bond_coeff @bond:na-s4 harmonic 227.88 1.793 # SOURCE3 10 0.0421 + bond_coeff @bond:na-s6 harmonic 279.89 1.723 # SOURCE3_SOURCE5 15 0.0153 + bond_coeff @bond:na-sh harmonic 281.31 1.721 # SOURCE3 9 0.0113 + bond_coeff @bond:na-ss harmonic 271.85 1.732 # SOURCE3_SOURCE5 50 0.0325 + bond_coeff @bond:na-sy harmonic 276.32 1.727 # SOURCE3 1 + bond_coeff @bond:nb-nb harmonic 327.23 1.333 # SOURCE1_SOURCE5 98 0.0106 + bond_coeff @bond:nb-pb harmonic 358.21 1.587 # SOURCE1 162 0.0091 + bond_coeff @bond:nc-nc harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 + bond_coeff @bond:nc-nd harmonic 374.73 1.299 # SOURCE3_SOURCE5 185 0.0074 + bond_coeff @bond:nc-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 + bond_coeff @bond:nc-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 + bond_coeff @bond:nc-sy harmonic 473.81 1.555 # SOURCE3 2 + bond_coeff @bond:nd-nd harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 + bond_coeff @bond:nd-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 + bond_coeff @bond:nd-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 + bond_coeff @bond:nd-sy harmonic 473.81 1.555 # SOURCE3 2 + bond_coeff @bond:ne-ne harmonic 235.02 1.422 # SOURCE3_SOURCE5 47 0.0776 + bond_coeff @bond:ne-nf harmonic 432.27 1.263 # SOURCE4_SOURCE5 78 0.0037 + bond_coeff @bond:ne-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 55 0.0223 + bond_coeff @bond:ne-p2 harmonic 387.40 1.563 # SOURCE3 14 0.1325 + bond_coeff @bond:ne-pe harmonic 242.60 1.712 # SOURCE3 28 0.1076 + bond_coeff @bond:ne-px harmonic 250.02 1.702 # SOURCE3 11 0.0883 + bond_coeff @bond:ne-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 94 0.0111 + bond_coeff @bond:ne-s harmonic 503.04 1.537 # SOURCE3 22 0.1708 + bond_coeff @bond:ne-sx harmonic 200.62 1.838 # SOURCE3 7 0.1060 + bond_coeff @bond:ne-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 49 0.0285 + bond_coeff @bond:nf-nf harmonic 235.02 1.422 # SOURCE3_SOURCE5 28 0.0146 + bond_coeff @bond:nf-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 15 0.0138 + bond_coeff @bond:nf-p2 harmonic 387.40 1.563 # SOURCE3 14 + bond_coeff @bond:nf-pf harmonic 242.60 1.712 # SOURCE3 28 + bond_coeff @bond:nf-px harmonic 250.02 1.702 # SOURCE3 11 + bond_coeff @bond:nf-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 84 0.0113 + bond_coeff @bond:nf-s harmonic 503.04 1.537 # SOURCE3 22 + bond_coeff @bond:nf-sx harmonic 200.62 1.838 # SOURCE3 7 + bond_coeff @bond:nf-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 42 0.0197 + bond_coeff @bond:nh-nh harmonic 252.77 1.402 # SOURCE1_SOURCE5 8 0.0109 + bond_coeff @bond:nh-no harmonic 267.93 1.386 # SOURCE4_SOURCE5 22 0.0046 + bond_coeff @bond:nh-o harmonic 316.06 1.263 # SOURCE3_SOURCE5 18 0.0143 + bond_coeff @bond:nh-oh harmonic 175.33 1.416 # SOURCE4_SOURCE5 63 0.0072 + bond_coeff @bond:nh-os harmonic 175.90 1.415 # SOURCE4_SOURCE5 26 0.0063 + bond_coeff @bond:nh-p2 harmonic 268.13 1.679 # SOURCE3 17 0.0872 + bond_coeff @bond:nh-p3 harmonic 229.90 1.730 # SOURCE3 3 0.0016 + bond_coeff @bond:nh-p4 harmonic 247.02 1.706 # SOURCE3 3 0.0008 + bond_coeff @bond:nh-p5 harmonic 274.79 1.671 # SOURCE3 3 0.0007 + bond_coeff @bond:nh-s harmonic 233.85 1.784 # SOURCE3 3 0.0076 + bond_coeff @bond:nh-s4 harmonic 258.92 1.749 # SOURCE3 3 0.0203 + bond_coeff @bond:nh-s6 harmonic 301.91 1.698 # SOURCE4_SOURCE5 93 0.0076 + bond_coeff @bond:nh-sh harmonic 292.49 1.708 # SOURCE3 1 + bond_coeff @bond:nh-ss harmonic 291.53 1.709 # SOURCE1_SOURCE5 58 0.0020 + bond_coeff @bond:nh-sy harmonic 287.18 1.714 # SOURCE4_SOURCE5 239 0.0099 + bond_coeff @bond:n-n1 harmonic 319.16 1.340 # SOUECE3 1 + bond_coeff @bond:n-n2 harmonic 295.31 1.360 # SOURCE3_SOURCE5 272 0.0114 + bond_coeff @bond:n-n3 harmonic 250.92 1.404 # SOURCE3_SOURCE5 87 0.0076 + bond_coeff @bond:n-n4 harmonic 226.87 1.432 # SOURCE3 5 0.0098 + bond_coeff @bond:n-n harmonic 250.83 1.404 # SOURCE3_SOURCE5 47 0.0125 + bond_coeff @bond:n-na harmonic 248.27 1.407 # SOURCE3_SOURCE5 56 0.0060 + bond_coeff @bond:n-nc harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 + bond_coeff @bond:n-nd harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 + bond_coeff @bond:n-nh harmonic 253.32 1.402 # SOURCE4_SOURCE5 51 0.0075 + bond_coeff @bond:n-no harmonic 208.29 1.456 # SOURCE3 4 0.0327 + bond_coeff @bond:n-o harmonic 342.80 1.243 # SOURCE3_SOURCE5 16 0.0255 + bond_coeff @bond:n-oh harmonic 181.83 1.406 # SOURCE3_SOURCE5 119 0.0062 + bond_coeff @bond:no-no harmonic 65.41 1.824 # SOURCE3 1 + bond_coeff @bond:no-o harmonic 367.95 1.226 # SOURCE1_SOURCE5 4403 0.0099 + bond_coeff @bond:no-oh harmonic 181.96 1.406 # SOURCE2 1 + bond_coeff @bond:no-os harmonic 172.24 1.421 # SOURCE4_SOURCE5 138 0.0070 + bond_coeff @bond:no-p2 harmonic 224.52 1.738 # SOURCE3 10 0.2231 + bond_coeff @bond:no-p3 harmonic 165.61 1.844 # SOURCE3 3 0.0005 + bond_coeff @bond:no-p4 harmonic 154.11 1.870 # SOURCE3 3 0.0006 + bond_coeff @bond:no-p5 harmonic 170.31 1.834 # SOURCE3 4 0.0020 + bond_coeff @bond:no-s harmonic 264.31 1.742 # SOURCE3 2 + bond_coeff @bond:n-os harmonic 180.04 1.409 # SOURCE4_SOURCE5 73 0.0121 + bond_coeff @bond:no-s4 harmonic 131.30 1.996 # SOURCE3 3 0.0313 + bond_coeff @bond:no-s6 harmonic 138.28 1.976 # SOURCE3 3 0.0520 + bond_coeff @bond:no-sh harmonic 220.82 1.804 # SOURCE3 1 + bond_coeff @bond:no-ss harmonic 206.32 1.828 # SOURCE3 3 0.0244 + bond_coeff @bond:n-p2 harmonic 227.87 1.733 # SOURCE3 8 0.0217 + bond_coeff @bond:n-p3 harmonic 204.42 1.770 # SOURCE3 9 0.0118 + bond_coeff @bond:n-p4 harmonic 227.19 1.734 # SOURCE3 1 + bond_coeff @bond:n-p5 harmonic 238.92 1.717 # SOURCE4_SOURCE5 25 0.0133 + bond_coeff @bond:n-pc harmonic 223.19 1.740 # SOURCE3 3 0.0010 + bond_coeff @bond:n-pd harmonic 223.19 1.740 # SOURCE3 3 + bond_coeff @bond:n-s harmonic 245.64 1.767 # SOURCE3 3 0.0011 + bond_coeff @bond:n-s4 harmonic 244.86 1.768 # SOURCE3_SOURCE5 9 0.0163 + bond_coeff @bond:n-s6 harmonic 283.34 1.719 # SOURCE4_SOURCE5 45 0.0154 + bond_coeff @bond:n-sh harmonic 275.50 1.728 # SOURCE3 4 0.0128 + bond_coeff @bond:n-ss harmonic 277.23 1.726 # SOURCE3_SOURCE5 22 0.0103 + bond_coeff @bond:n-sy harmonic 285.29 1.716 # SOURCE4_SOURCE5 126 0.0086 + bond_coeff @bond:oh-oh harmonic 123.13 1.469 # SOURCE3 1 + bond_coeff @bond:oh-os harmonic 129.12 1.456 # SOURCE4_SOURCE5 49 0.0046 + bond_coeff @bond:oh-p2 harmonic 329.87 1.630 # SOURCE3 8 0.0916 + bond_coeff @bond:oh-p3 harmonic 285.03 1.677 # SOURCE3 3 0.0148 + bond_coeff @bond:oh-p4 harmonic 318.66 1.641 # SOURCE3 4 0.0092 + bond_coeff @bond:oh-p5 harmonic 346.03 1.615 # SOURCE3_SOURCE5 1121 0.0129 + bond_coeff @bond:oh-py harmonic 344.61 1.616 # SOURCE3_SOURCE5 112 0.0110 + bond_coeff @bond:oh-s harmonic 219.79 1.812 # SOURCE3 2 + bond_coeff @bond:oh-s4 harmonic 309.00 1.696 # SOURCE4_SOURCE5 29 0.0100 + bond_coeff @bond:oh-s6 harmonic 373.26 1.635 # SOURCE3_SOURCE5 193 0.0162 + bond_coeff @bond:oh-sh harmonic 312.59 1.692 # SOURCE3 2 0.0003 + bond_coeff @bond:oh-ss harmonic 316.41 1.688 # SOURCE3_SOURCE5 12 0.0167 + bond_coeff @bond:oh-sy harmonic 356.03 1.650 # SOURCE4_SOURCE5 123 0.0037 + bond_coeff @bond:o-o harmonic 141.39 1.430 # SOURCE3 2 0.0500 + bond_coeff @bond:o-oh harmonic 104.37 1.517 # SOURCE3 2 + bond_coeff @bond:o-os harmonic 109.10 1.504 # SOURCE3 3 0.0117 + bond_coeff @bond:o-p2 harmonic 492.04 1.508 # SOURCE3 17 0.0306 + bond_coeff @bond:o-p3 harmonic 480.47 1.515 # SOURCE3 35 0.0297 + bond_coeff @bond:o-p4 harmonic 498.98 1.504 # SOURCE3_SOURCE5 60 0.0565 + bond_coeff @bond:o-p5 harmonic 529.55 1.487 # SOURCE1_SOURCE5 1318 0.0133 + bond_coeff @bond:o-pe harmonic 470.81 1.521 # SOURCE3 20 0.0171 + bond_coeff @bond:o-pf harmonic 470.81 1.521 # SOURCE3 20 + bond_coeff @bond:o-px harmonic 499.66 1.504 # SOURCE3_SOURCE5 45 0.0136 + bond_coeff @bond:o-py harmonic 527.91 1.488 # SOURCE3_SOURCE5 119 0.0072 + bond_coeff @bond:o-s harmonic 226.13 1.802 # SOURCE3 2 + bond_coeff @bond:o-s2 harmonic 417.99 1.599 # SOURCE3 3 0.0707 + bond_coeff @bond:o-s4 harmonic 572.26 1.504 # SOURCE1_SOURCE5 137 0.0127 + bond_coeff @bond:o-s6 harmonic 683.03 1.453 # SOURCE1_SOURCE5 2456 0.0105 + bond_coeff @bond:o-sh harmonic 410.02 1.605 # SOURCE3 2 + bond_coeff @bond:os-os harmonic 124.74 1.465 # SOURCE1_SOURCE5 69 0.0090 + bond_coeff @bond:os-p2 harmonic 396.10 1.573 # SOURCE1 16 + bond_coeff @bond:os-p3 harmonic 287.31 1.674 # SOURCE3_SOURCE5 22 0.0105 + bond_coeff @bond:os-p4 harmonic 323.70 1.636 # SOURCE3 4 0.0057 + bond_coeff @bond:os-p5 harmonic 346.25 1.615 # SOURCE1_SOURCE5 1200 0.0218 + bond_coeff @bond:os-py harmonic 342.10 1.619 # SOURCE3_SOURCE5 68 0.0106 + bond_coeff @bond:os-s harmonic 227.43 1.800 # SOURCE3 3 0.0052 + bond_coeff @bond:o-ss harmonic 567.21 1.507 # SOURCE3_SOURCE5 22 0.0235 + bond_coeff @bond:os-s4 harmonic 312.40 1.692 # SOURCE3_SOURCE5 25 0.0189 + bond_coeff @bond:os-s6 harmonic 387.79 1.623 # SOURCE1_SOURCE5 242 0.0147 + bond_coeff @bond:os-sh harmonic 333.31 1.671 # SOURCE3 3 0.0106 + bond_coeff @bond:os-ss harmonic 301.43 1.704 # SOURCE3 9 0.0277 + bond_coeff @bond:os-sy harmonic 306.02 1.699 # SOURCE3 1 + bond_coeff @bond:o-sx harmonic 555.55 1.513 # SOURCE3_SOURCE5 136 0.0072 + bond_coeff @bond:o-sy harmonic 653.16 1.466 # SOURCE3_SOURCE5 2007 0.0061 + bond_coeff @bond:p2-p2 harmonic 307.63 1.786 # SOURCE3 25 0.3488 + bond_coeff @bond:p2-p3 harmonic 118.00 2.152 # SOURCE3 9 0.1777 + bond_coeff @bond:p2-p4 harmonic 110.68 2.179 # SOUECE3 1 + bond_coeff @bond:p2-p5 harmonic 110.42 2.180 # SOUECE3 1 + bond_coeff @bond:p2-pe harmonic 244.92 1.867 # SOURCE3 16 0.3571 + bond_coeff @bond:p2-pf harmonic 244.92 1.867 # SOURCE3 16 + bond_coeff @bond:p2-s harmonic 375.05 1.772 # SOURCE3 26 0.3014 + bond_coeff @bond:p2-s4 harmonic 126.27 2.190 # SOUECE3 1 + bond_coeff @bond:p2-s6 harmonic 129.28 2.180 # SOUECE3 1 + bond_coeff @bond:p2-sh harmonic 217.02 1.971 # SOURCE3 10 0.2829 + bond_coeff @bond:p2-ss harmonic 219.87 1.966 # SOURCE3 10 0.2739 + bond_coeff @bond:p3-p3 harmonic 101.97 2.214 # SOURCE1 41 + bond_coeff @bond:p3-p4 harmonic 101.50 2.216 # SOURCE3 3 0.0011 + bond_coeff @bond:p3-p5 harmonic 102.21 2.213 # SOURCE3 9 0.0265 + bond_coeff @bond:p3-s harmonic 168.70 2.070 # SOUECE3 1 + bond_coeff @bond:p3-s4 harmonic 161.75 2.087 # SOURCE3 8 0.2235 + bond_coeff @bond:p3-s6 harmonic 165.79 2.077 # SOURCE3 11 0.1420 + bond_coeff @bond:p3-sh harmonic 144.95 2.132 # SOURCE3 3 0.0078 + bond_coeff @bond:p3-ss harmonic 148.86 2.121 # SOURCE3 3 0.0059 + bond_coeff @bond:p4-p4 harmonic 157.68 2.034 # SOURCE1 1 + bond_coeff @bond:p4-p5 harmonic 96.70 2.237 # SOUECE3 1 + bond_coeff @bond:p4-s harmonic 140.16 2.146 # SOURCE3 5 0.0601 + bond_coeff @bond:p4-s4 harmonic 109.64 2.251 # SOUECE3 1 + bond_coeff @bond:p4-s6 harmonic 105.24 2.269 # SOUECE3 1 + bond_coeff @bond:p4-sh harmonic 151.04 2.115 # SOURCE3 4 0.0008 + bond_coeff @bond:p4-ss harmonic 155.14 2.104 # SOURCE3 4 0.0044 + bond_coeff @bond:p5-p5 harmonic 149.95 2.054 # SOURCE1 1 + bond_coeff @bond:p5-s harmonic 239.16 1.934 # SOURCE1_SOURCE5 173 0.0138 + bond_coeff @bond:p5-s4 harmonic 181.84 2.040 # SOUECE3 1 + bond_coeff @bond:p5-s6 harmonic 181.84 2.040 # SOUECE3 1 + bond_coeff @bond:p5-sh harmonic 163.76 2.082 # SOURCE3 3 0.0035 + bond_coeff @bond:p5-ss harmonic 150.09 2.118 # SOURCE4_SOURCE5 70 0.0117 + bond_coeff @bond:pe-pe harmonic 136.46 2.092 # SOURCE3 7 0.1369 + bond_coeff @bond:pe-pf harmonic 149.57 2.055 # SOURCE3 1 + bond_coeff @bond:pe-px harmonic 169.76 2.005 # SOURCE3 12 0.2609 + bond_coeff @bond:pe-py harmonic 161.32 2.025 # SOURCE3 12 0.2617 + bond_coeff @bond:pe-s harmonic 390.65 1.758 # SOURCE3 31 0.3197 + bond_coeff @bond:pe-sx harmonic 133.00 2.168 # SOURCE3 9 0.1743 + bond_coeff @bond:pe-sy harmonic 119.67 2.213 # SOURCE3 6 0.0127 + bond_coeff @bond:pf-pf harmonic 136.46 2.092 # SOURCE3 7 + bond_coeff @bond:pf-px harmonic 169.76 2.005 # SOURCE3 12 + bond_coeff @bond:pf-py harmonic 161.32 2.025 # SOURCE3 12 + bond_coeff @bond:pf-s harmonic 390.65 1.758 # SOURCE3 31 + bond_coeff @bond:pf-sx harmonic 133.00 2.168 # SOURCE3 9 + bond_coeff @bond:pf-sy harmonic 119.67 2.213 # SOURCE3 6 + bond_coeff @bond:px-py harmonic 105.60 2.199 # SOURCE3 5 0.0238 + bond_coeff @bond:px-sx harmonic 111.92 2.242 # SOURCE3 3 0.0119 + bond_coeff @bond:px-sy harmonic 110.14 2.249 # SOURCE3 3 0.0272 + bond_coeff @bond:py-py harmonic 108.87 2.186 # SOURCE3 8 0.0132 + bond_coeff @bond:py-sx harmonic 107.66 2.259 # SOURCE3 7 0.0603 + bond_coeff @bond:py-sy harmonic 128.67 2.182 # SOURCE3 5 0.0047 + bond_coeff @bond:s4-s4 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s4-s6 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s4-sh harmonic 196.89 2.168 # SOURCE3 3 0.0227 + bond_coeff @bond:s4-ss harmonic 197.83 2.166 # SOURCE3 5 0.0247 + bond_coeff @bond:s6-s6 harmonic 243.62 2.080 # SOUECE3 1 + bond_coeff @bond:s6-sh harmonic 227.44 2.108 # SOURCE3 3 0.0144 + bond_coeff @bond:s6-ss harmonic 221.98 2.118 # SOURCE3 5 0.0209 + bond_coeff @bond:sh-sh harmonic 257.31 2.058 # SOURCE2 1 + bond_coeff @bond:sh-ss harmonic 251.60 2.067 # SOURCE3 3 0.0029 + bond_coeff @bond:s-s harmonic 276.08 2.030 # SOURCE3 1 + bond_coeff @bond:s-s2 harmonic 391.11 1.897 # SOURCE1 5 + bond_coeff @bond:s-s4 harmonic 246.05 2.076 # SOURCE3 4 0.0345 + bond_coeff @bond:s-s6 harmonic 270.56 2.038 # SOURCE3 3 0.0311 + bond_coeff @bond:s-sh harmonic 226.34 2.110 # SOURCE3 2 + bond_coeff @bond:s-ss harmonic 238.28 2.089 # SOURCE3 1 + bond_coeff @bond:ss-ss harmonic 248.01 2.073 # SOURCE1_SOURCE5 457 0.0074 + bond_coeff @bond:sx-sx harmonic 119.03 2.391 # SOURCE3 3 0.0185 + bond_coeff @bond:sx-sy harmonic 160.84 2.255 # SOURCE3 5 0.0737 + bond_coeff @bond:sy-sy harmonic 162.69 2.250 # SOURCE3 3 0.0289 + bond_coeff @bond:br-cd harmonic 172.53 1.885 # SOURCE4_SOURCE5 89 0.0082 + bond_coeff @bond:c1-cf harmonic 518.69 1.315 # SOURCE4 6 + bond_coeff @bond:cd-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 46 0.0041 + bond_coeff @bond:cd-n4 harmonic 236.72 1.493 # SOURCE4 7 + bond_coeff @bond:cd-nf harmonic 356.61 1.379 # SOURCE4_SOURCE5 52 0.0115 + bond_coeff @bond:cd-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 253 0.0081 + bond_coeff @bond:cd-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 14 0.0031 + bond_coeff @bond:cd-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 28 0.0024 + bond_coeff @bond:cc-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 11 0.0006 + bond_coeff @bond:cf-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 66 0.0129 + bond_coeff @bond:cf-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 26 0.0077 + bond_coeff @bond:cf-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 36 0.0052 + bond_coeff @bond:cf-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 6 0.0049 + bond_coeff @bond:cf-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 46 0.0106 + bond_coeff @bond:cq-na harmonic 349.52 1.384 # SOURCE4 7 + bond_coeff @bond:cq-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 120 0.0071 + bond_coeff @bond:cl-py harmonic 152.76 2.045 # SOURCE5 45 0.0072 + bond_coeff @bond:f-py harmonic 456.16 1.577 # SOURCE5 25 0.0035 + bond_coeff @bond:py-s harmonic 215.89 1.973 # SOURCE5 17 0.0159 + bond_coeff @bond:cy-nh harmonic 251.08 1.476 # SOURCE5 16 0.0050 + bond_coeff @bond:cy-hx harmonic 386.49 1.091 # SOURCE5 13 0.0007 + bond_coeff @bond:br-ce harmonic 163.42 1.905 # SOURCE5 12 0.0099 + bond_coeff @bond:cc-i harmonic 110.60 2.120 # SOURCE5 11 0.0086 + bond_coeff @bond:cy-n4 harmonic 214.44 1.522 # SOURCE5 11 0.0076 + bond_coeff @bond:cy-p3 harmonic 146.83 1.908 # SOURCE5 10 0.0056 + bond_coeff @bond:cy-na harmonic 279.03 1.446 # SOURCE5 8 0.0049 + bond_coeff @bond:cx-n4 harmonic 234.29 1.496 # SOURCE5 9 0.0009 + bond_coeff @bond:ne-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 + bond_coeff @bond:cv-ss harmonic 228.75 1.761 # SOURCE5 8 0.0086 + bond_coeff @bond:cy-no harmonic 216.62 1.519 # SOURCE5 7 0.0035 + bond_coeff @bond:ce-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 + bond_coeff @bond:cd-i harmonic 111.95 2.115 # SOURCE5 7 0.0138 + bond_coeff @bond:cy-s4 harmonic 149.47 1.913 # SOURCE5 5 0.0068 + bond_coeff @bond:n2-sy harmonic 491.42 1.544 # SOURCE5 7 0.0042 + bond_coeff @bond:cc-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 + bond_coeff @bond:i-s2 harmonic 48.08 2.883 # SOURCE5 5 0.0165 + bond_coeff @bond:br-cy harmonic 144.56 1.951 # SOURCE5 5 0.0056 + bond_coeff @bond:br-cf harmonic 163.42 1.905 # SOURCE5 12 0.0099 + bond_coeff @bond:nf-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 + bond_coeff @bond:cf-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 + bond_coeff @bond:cd-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 + bond_coeff @bond:ss-sy harmonic 177.36 2.212 # SOURCE5 4 0.0105 + bond_coeff @bond:h5-ce harmonic 390.52 1.089 # SOURCE5 4 0.0006 + bond_coeff @bond:h5-cf harmonic 390.52 1.089 # SOURCE5 4 0.0006 + bond_coeff @bond:ce-s4 harmonic 226.75 1.764 # SOURCE5 4 0.0087 + bond_coeff @bond:cf-s4 harmonic 226.69 1.764 # SOURCE5 4 0.0087 + bond_coeff @bond:cy-py harmonic 136.02 1.937 # SOURCE5 4 0.0000 + bond_coeff @bond:cd-o harmonic 649.55 1.219 # SOURCE5 4 0.0015 + bond_coeff @bond:ne-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 + bond_coeff @bond:nf-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 + bond_coeff @bond:ce-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 + bond_coeff @bond:cf-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 + } # (end of bond_coeffs) + + write_once("Data Bonds By Type") { + @bond:ow-hw @atom:ow @atom:hw + @bond:hw-hw @atom:hw @atom:hw + @bond:br-br @atom:br @atom:br + @bond:br-c1 @atom:br @atom:c1 + @bond:br-c2 @atom:br @atom:c2 + @bond:br-c @atom:br @atom:c + @bond:br-c3 @atom:br @atom:c3 + @bond:br-ca @atom:br @atom:ca + @bond:br-cc @atom:br @atom:cc + @bond:br-cx @atom:br @atom:cx + @bond:br-n1 @atom:br @atom:n1 + @bond:br-n2 @atom:br @atom:n2 + @bond:br-n @atom:br @atom:n + @bond:br-n3 @atom:br @atom:n3 + @bond:br-n4 @atom:br @atom:n4 + @bond:br-na @atom:br @atom:na + @bond:br-nh @atom:br @atom:nh + @bond:br-no @atom:br @atom:no + @bond:br-o @atom:br @atom:o + @bond:br-oh @atom:br @atom:oh + @bond:br-os @atom:br @atom:os + @bond:br-p2 @atom:br @atom:p2 + @bond:br-p3 @atom:br @atom:p3 + @bond:br-p4 @atom:br @atom:p4 + @bond:br-p5 @atom:br @atom:p5 + @bond:br-s @atom:br @atom:s + @bond:br-s4 @atom:br @atom:s4 + @bond:br-s6 @atom:br @atom:s6 + @bond:br-sh @atom:br @atom:sh + @bond:br-ss @atom:br @atom:ss + @bond:c1-c1 @atom:c1 @atom:c1 + @bond:c1-c2 @atom:c1 @atom:c2 + @bond:c1-c3 @atom:c1 @atom:c3 + @bond:c1-ca @atom:c1 @atom:ca + @bond:c1-ce @atom:c1 @atom:ce + @bond:c1-cg @atom:c1 @atom:cg + @bond:c1-ch @atom:c1 @atom:ch + @bond:c1-cl @atom:c1 @atom:cl + @bond:c1-cx @atom:c1 @atom:cx + @bond:c1-f @atom:c1 @atom:f + @bond:c1-ha @atom:c1 @atom:ha + @bond:c1-hc @atom:c1 @atom:hc + @bond:c1-i @atom:c1 @atom:i + @bond:c1-n1 @atom:c1 @atom:n1 + @bond:c1-n2 @atom:c1 @atom:n2 + @bond:c1-n3 @atom:c1 @atom:n3 + @bond:c1-n4 @atom:c1 @atom:n4 + @bond:c1-n @atom:c1 @atom:n + @bond:c1-na @atom:c1 @atom:na + @bond:c1-ne @atom:c1 @atom:ne + @bond:c1-nf @atom:c1 @atom:nf + @bond:c1-nh @atom:c1 @atom:nh + @bond:c1-no @atom:c1 @atom:no + @bond:c1-o @atom:c1 @atom:o + @bond:c1-oh @atom:c1 @atom:oh + @bond:c1-os @atom:c1 @atom:os + @bond:c1-p2 @atom:c1 @atom:p2 + @bond:c1-p3 @atom:c1 @atom:p3 + @bond:c1-p4 @atom:c1 @atom:p4 + @bond:c1-p5 @atom:c1 @atom:p5 + @bond:c1-s2 @atom:c1 @atom:s2 + @bond:c1-s @atom:c1 @atom:s + @bond:c1-s4 @atom:c1 @atom:s4 + @bond:c1-s6 @atom:c1 @atom:s6 + @bond:c1-sh @atom:c1 @atom:sh + @bond:c1-ss @atom:c1 @atom:ss + @bond:c2-c2 @atom:c2 @atom:c2 + @bond:c2-c3 @atom:c2 @atom:c3 + @bond:c2-ca @atom:c2 @atom:ca + @bond:c2-cc @atom:c2 @atom:cc + @bond:c2-cd @atom:c2 @atom:cd + @bond:c2-ce @atom:c2 @atom:ce + @bond:c2-cf @atom:c2 @atom:cf + @bond:c2-cl @atom:c2 @atom:cl + @bond:c2-cu @atom:c2 @atom:cu + @bond:c2-cx @atom:c2 @atom:cx + @bond:c2-cy @atom:c2 @atom:cy + @bond:c2-f @atom:c2 @atom:f + @bond:c2-h4 @atom:c2 @atom:h4 + @bond:c2-h5 @atom:c2 @atom:h5 + @bond:c2-ha @atom:c2 @atom:ha + @bond:c2-hc @atom:c2 @atom:hc + @bond:c2-hx @atom:c2 @atom:hx + @bond:c2-i @atom:c2 @atom:i + @bond:c2-n1 @atom:c2 @atom:n1 + @bond:c2-n2 @atom:c2 @atom:n2 + @bond:c2-n3 @atom:c2 @atom:n3 + @bond:c2-n @atom:c2 @atom:n + @bond:c2-n4 @atom:c2 @atom:n4 + @bond:c2-na @atom:c2 @atom:na + @bond:c2-nc @atom:c2 @atom:nc + @bond:c2-nd @atom:c2 @atom:nd + @bond:c2-ne @atom:c2 @atom:ne + @bond:c2-nf @atom:c2 @atom:nf + @bond:c2-nh @atom:c2 @atom:nh + @bond:c2-no @atom:c2 @atom:no + @bond:c2-o @atom:c2 @atom:o + @bond:c2-oh @atom:c2 @atom:oh + @bond:c2-os @atom:c2 @atom:os + @bond:c2-p2 @atom:c2 @atom:p2 + @bond:c2-p3 @atom:c2 @atom:p3 + @bond:c2-p4 @atom:c2 @atom:p4 + @bond:c2-p5 @atom:c2 @atom:p5 + @bond:c2-pe @atom:c2 @atom:pe + @bond:c2-pf @atom:c2 @atom:pf + @bond:c2-s2 @atom:c2 @atom:s2 + @bond:c2-s @atom:c2 @atom:s + @bond:c2-s4 @atom:c2 @atom:s4 + @bond:c2-s6 @atom:c2 @atom:s6 + @bond:c2-sh @atom:c2 @atom:sh + @bond:c2-ss @atom:c2 @atom:ss + @bond:c3-c3 @atom:c3 @atom:c3 + @bond:c3-ca @atom:c3 @atom:ca + @bond:c3-cc @atom:c3 @atom:cc + @bond:c3-cd @atom:c3 @atom:cd + @bond:c3-ce @atom:c3 @atom:ce + @bond:c3-cf @atom:c3 @atom:cf + @bond:c3-cl @atom:c3 @atom:cl + @bond:c3-cu @atom:c3 @atom:cu + @bond:c3-cv @atom:c3 @atom:cv + @bond:c3-cx @atom:c3 @atom:cx + @bond:c3-cy @atom:c3 @atom:cy + @bond:c3-f @atom:c3 @atom:f + @bond:c3-h1 @atom:c3 @atom:h1 + @bond:c3-h2 @atom:c3 @atom:h2 + @bond:c3-h3 @atom:c3 @atom:h3 + @bond:c3-hc @atom:c3 @atom:hc + @bond:c3-hx @atom:c3 @atom:hx + @bond:c3-i @atom:c3 @atom:i + @bond:c3-n1 @atom:c3 @atom:n1 + @bond:c3-n2 @atom:c3 @atom:n2 + @bond:c3-n @atom:c3 @atom:n + @bond:c3-n3 @atom:c3 @atom:n3 + @bond:c3-n4 @atom:c3 @atom:n4 + @bond:c3-na @atom:c3 @atom:na + @bond:c3-nc @atom:c3 @atom:nc + @bond:c3-nd @atom:c3 @atom:nd + @bond:c3-nh @atom:c3 @atom:nh + @bond:c3-no @atom:c3 @atom:no + @bond:c3-o @atom:c3 @atom:o + @bond:c3-oh @atom:c3 @atom:oh + @bond:c3-os @atom:c3 @atom:os + @bond:c3-p2 @atom:c3 @atom:p2 + @bond:c3-p3 @atom:c3 @atom:p3 + @bond:c3-p4 @atom:c3 @atom:p4 + @bond:c3-p5 @atom:c3 @atom:p5 + @bond:c3-px @atom:c3 @atom:px + @bond:c3-py @atom:c3 @atom:py + @bond:c3-s @atom:c3 @atom:s + @bond:c3-s4 @atom:c3 @atom:s4 + @bond:c3-s6 @atom:c3 @atom:s6 + @bond:c3-sh @atom:c3 @atom:sh + @bond:c3-ss @atom:c3 @atom:ss + @bond:c3-sx @atom:c3 @atom:sx + @bond:c3-sy @atom:c3 @atom:sy + @bond:ca-ca @atom:ca @atom:ca + @bond:ca-cc @atom:ca @atom:cc + @bond:ca-cd @atom:ca @atom:cd + @bond:ca-ce @atom:ca @atom:ce + @bond:ca-cf @atom:ca @atom:cf + @bond:ca-cg @atom:ca @atom:cg + @bond:ca-ch @atom:ca @atom:ch + @bond:ca-cl @atom:ca @atom:cl + @bond:ca-cp @atom:ca @atom:cp + @bond:ca-cq @atom:ca @atom:cq + @bond:ca-cx @atom:ca @atom:cx + @bond:ca-cy @atom:ca @atom:cy + @bond:ca-f @atom:ca @atom:f + @bond:ca-h4 @atom:ca @atom:h4 + @bond:ca-h5 @atom:ca @atom:h5 + @bond:ca-ha @atom:ca @atom:ha + @bond:ca-i @atom:ca @atom:i + @bond:ca-n1 @atom:ca @atom:n1 + @bond:ca-n2 @atom:ca @atom:n2 + @bond:ca-n @atom:ca @atom:n + @bond:ca-n4 @atom:ca @atom:n4 + @bond:ca-na @atom:ca @atom:na + @bond:ca-nb @atom:ca @atom:nb + @bond:ca-nc @atom:ca @atom:nc + @bond:ca-nd @atom:ca @atom:nd + @bond:ca-ne @atom:ca @atom:ne + @bond:ca-nf @atom:ca @atom:nf + @bond:ca-nh @atom:ca @atom:nh + @bond:ca-no @atom:ca @atom:no + @bond:ca-o @atom:ca @atom:o + @bond:ca-oh @atom:ca @atom:oh + @bond:ca-os @atom:ca @atom:os + @bond:ca-p2 @atom:ca @atom:p2 + @bond:ca-p3 @atom:ca @atom:p3 + @bond:ca-p4 @atom:ca @atom:p4 + @bond:ca-p5 @atom:ca @atom:p5 + @bond:ca-pe @atom:ca @atom:pe + @bond:ca-pf @atom:ca @atom:pf + @bond:ca-px @atom:ca @atom:px + @bond:ca-py @atom:ca @atom:py + @bond:ca-s @atom:ca @atom:s + @bond:ca-s4 @atom:ca @atom:s4 + @bond:ca-s6 @atom:ca @atom:s6 + @bond:ca-sh @atom:ca @atom:sh + @bond:ca-ss @atom:ca @atom:ss + @bond:ca-sx @atom:ca @atom:sx + @bond:ca-sy @atom:ca @atom:sy + @bond:c-c1 @atom:c @atom:c1 + @bond:c-c2 @atom:c @atom:c2 + @bond:c-c @atom:c @atom:c + @bond:c-c3 @atom:c @atom:c3 + @bond:c-ca @atom:c @atom:ca + @bond:c-cc @atom:c @atom:cc + @bond:cc-cc @atom:cc @atom:cc + @bond:cc-cd @atom:cc @atom:cd + @bond:cc-ce @atom:cc @atom:ce + @bond:cc-cf @atom:cc @atom:cf + @bond:cc-cg @atom:cc @atom:cg + @bond:cc-ch @atom:cc @atom:ch + @bond:cc-cl @atom:cc @atom:cl + @bond:cc-cx @atom:cc @atom:cx + @bond:c-cd @atom:c @atom:cd + @bond:c-ce @atom:c @atom:ce + @bond:c-cf @atom:c @atom:cf + @bond:cc-f @atom:cc @atom:f + @bond:c-cg @atom:c @atom:cg + @bond:c-ch @atom:c @atom:ch + @bond:cc-h4 @atom:cc @atom:h4 + @bond:cc-h5 @atom:cc @atom:h5 + @bond:cc-ha @atom:cc @atom:ha + @bond:c-cl @atom:c @atom:cl + @bond:cc-n2 @atom:cc @atom:n2 + @bond:cc-n @atom:cc @atom:n + @bond:cc-n4 @atom:cc @atom:n4 + @bond:cc-na @atom:cc @atom:na + @bond:cc-nc @atom:cc @atom:nc + @bond:cc-nd @atom:cc @atom:nd + @bond:cc-ne @atom:cc @atom:ne + @bond:cc-nf @atom:cc @atom:nf + @bond:cc-nh @atom:cc @atom:nh + @bond:cc-no @atom:cc @atom:no + @bond:cc-oh @atom:cc @atom:oh + @bond:cc-os @atom:cc @atom:os + @bond:cc-pd @atom:cc @atom:pd + @bond:cc-sh @atom:cc @atom:sh + @bond:cc-ss @atom:cc @atom:ss + @bond:cc-sx @atom:cc @atom:sx + @bond:cc-sy @atom:cc @atom:sy + @bond:c-cu @atom:c @atom:cu + @bond:c-cx @atom:c @atom:cx + @bond:c-cy @atom:c @atom:cy + @bond:cd-cd @atom:cd @atom:cd + @bond:cd-ce @atom:cd @atom:ce + @bond:cd-cf @atom:cd @atom:cf + @bond:cd-cg @atom:cd @atom:cg + @bond:cd-ch @atom:cd @atom:ch + @bond:cd-cl @atom:cd @atom:cl + @bond:cd-cx @atom:cd @atom:cx + @bond:cd-cy @atom:cd @atom:cy + @bond:cd-h4 @atom:cd @atom:h4 + @bond:cd-h5 @atom:cd @atom:h5 + @bond:cd-ha @atom:cd @atom:ha + @bond:cd-n2 @atom:cd @atom:n2 + @bond:cd-n @atom:cd @atom:n + @bond:cd-na @atom:cd @atom:na + @bond:cd-nc @atom:cd @atom:nc + @bond:cd-nd @atom:cd @atom:nd + @bond:cd-ne @atom:cd @atom:ne + @bond:cd-nh @atom:cd @atom:nh + @bond:cd-oh @atom:cd @atom:oh + @bond:cd-os @atom:cd @atom:os + @bond:cd-pc @atom:cd @atom:pc + @bond:cd-ss @atom:cd @atom:ss + @bond:cd-sy @atom:cd @atom:sy + @bond:ce-ce @atom:ce @atom:ce + @bond:ce-cf @atom:ce @atom:cf + @bond:ce-cg @atom:ce @atom:cg + @bond:ce-ch @atom:ce @atom:ch + @bond:ce-cl @atom:ce @atom:cl + @bond:ce-cx @atom:ce @atom:cx + @bond:ce-cy @atom:ce @atom:cy + @bond:ce-h4 @atom:ce @atom:h4 + @bond:ce-ha @atom:ce @atom:ha + @bond:ce-n1 @atom:ce @atom:n1 + @bond:ce-n2 @atom:ce @atom:n2 + @bond:ce-n @atom:ce @atom:n + @bond:ce-na @atom:ce @atom:na + @bond:ce-ne @atom:ce @atom:ne + @bond:ce-nf @atom:ce @atom:nf + @bond:ce-nh @atom:ce @atom:nh + @bond:ce-oh @atom:ce @atom:oh + @bond:ce-os @atom:ce @atom:os + @bond:ce-p2 @atom:ce @atom:p2 + @bond:ce-pe @atom:ce @atom:pe + @bond:ce-px @atom:ce @atom:px + @bond:ce-py @atom:ce @atom:py + @bond:ce-s @atom:ce @atom:s + @bond:ce-ss @atom:ce @atom:ss + @bond:ce-sx @atom:ce @atom:sx + @bond:ce-sy @atom:ce @atom:sy + @bond:c-f @atom:c @atom:f + @bond:cf-cf @atom:cf @atom:cf + @bond:cf-cg @atom:cf @atom:cg + @bond:cf-ch @atom:cf @atom:ch + @bond:cf-h4 @atom:cf @atom:h4 + @bond:cf-ha @atom:cf @atom:ha + @bond:cf-n1 @atom:cf @atom:n1 + @bond:cf-n2 @atom:cf @atom:n2 + @bond:cf-n @atom:cf @atom:n + @bond:cf-ne @atom:cf @atom:ne + @bond:cf-nf @atom:cf @atom:nf + @bond:cf-nh @atom:cf @atom:nh + @bond:cf-oh @atom:cf @atom:oh + @bond:cf-os @atom:cf @atom:os + @bond:cf-p2 @atom:cf @atom:p2 + @bond:cf-pf @atom:cf @atom:pf + @bond:cf-px @atom:cf @atom:px + @bond:cf-py @atom:cf @atom:py + @bond:cf-s @atom:cf @atom:s + @bond:cf-sx @atom:cf @atom:sx + @bond:cf-sy @atom:cf @atom:sy + @bond:cg-cg @atom:cg @atom:cg + @bond:cg-ch @atom:cg @atom:ch + @bond:cg-n1 @atom:cg @atom:n1 + @bond:cg-ne @atom:cg @atom:ne + @bond:cg-pe @atom:cg @atom:pe + @bond:c-h4 @atom:c @atom:h4 + @bond:c-h5 @atom:c @atom:h5 + @bond:c-ha @atom:c @atom:ha + @bond:ch-ch @atom:ch @atom:ch + @bond:ch-n1 @atom:ch @atom:n1 + @bond:ch-nf @atom:ch @atom:nf + @bond:ch-pf @atom:ch @atom:pf + @bond:c-i @atom:c @atom:i + @bond:cl-cl @atom:cl @atom:cl + @bond:cl-cx @atom:cl @atom:cx + @bond:cl-cy @atom:cl @atom:cy + @bond:cl-n1 @atom:cl @atom:n1 + @bond:cl-n2 @atom:cl @atom:n2 + @bond:cl-n3 @atom:cl @atom:n3 + @bond:cl-n @atom:cl @atom:n + @bond:cl-n4 @atom:cl @atom:n4 + @bond:cl-na @atom:cl @atom:na + @bond:cl-nh @atom:cl @atom:nh + @bond:cl-no @atom:cl @atom:no + @bond:cl-o @atom:cl @atom:o + @bond:cl-oh @atom:cl @atom:oh + @bond:cl-os @atom:cl @atom:os + @bond:cl-p2 @atom:cl @atom:p2 + @bond:cl-p3 @atom:cl @atom:p3 + @bond:cl-p4 @atom:cl @atom:p4 + @bond:cl-p5 @atom:cl @atom:p5 + @bond:cl-pb @atom:cl @atom:pb + @bond:cl-s @atom:cl @atom:s + @bond:cl-s2 @atom:cl @atom:s2 + @bond:cl-s4 @atom:cl @atom:s4 + @bond:cl-s6 @atom:cl @atom:s6 + @bond:cl-sh @atom:cl @atom:sh + @bond:cl-ss @atom:cl @atom:ss + @bond:cl-sx @atom:cl @atom:sx + @bond:cl-sy @atom:cl @atom:sy + @bond:c-n2 @atom:c @atom:n2 + @bond:c-n4 @atom:c @atom:n4 + @bond:c-n @atom:c @atom:n + @bond:c-nc @atom:c @atom:nc + @bond:c-nd @atom:c @atom:nd + @bond:c-ne @atom:c @atom:ne + @bond:c-nf @atom:c @atom:nf + @bond:c-no @atom:c @atom:no + @bond:c-o @atom:c @atom:o + @bond:c-oh @atom:c @atom:oh + @bond:c-os @atom:c @atom:os + @bond:c-p2 @atom:c @atom:p2 + @bond:c-p3 @atom:c @atom:p3 + @bond:c-p4 @atom:c @atom:p4 + @bond:c-p5 @atom:c @atom:p5 + @bond:cp-cp @atom:cp @atom:cp + @bond:cp-cq @atom:cp @atom:cq + @bond:c-pe @atom:c @atom:pe + @bond:c-pf @atom:c @atom:pf + @bond:cp-na @atom:cp @atom:na + @bond:cp-nb @atom:cp @atom:nb + @bond:c-px @atom:c @atom:px + @bond:c-py @atom:c @atom:py + @bond:cq-cq @atom:cq @atom:cq + @bond:c-s @atom:c @atom:s + @bond:c-s4 @atom:c @atom:s4 + @bond:c-s6 @atom:c @atom:s6 + @bond:c-sh @atom:c @atom:sh + @bond:c-ss @atom:c @atom:ss + @bond:c-sx @atom:c @atom:sx + @bond:c-sy @atom:c @atom:sy + @bond:cu-cu @atom:cu @atom:cu + @bond:cu-cx @atom:cu @atom:cx + @bond:cu-ha @atom:cu @atom:ha + @bond:cv-cv @atom:cv @atom:cv + @bond:cv-cy @atom:cv @atom:cy + @bond:cv-ha @atom:cv @atom:ha + @bond:cx-cv @atom:cx @atom:cv + @bond:cx-cx @atom:cx @atom:cx + @bond:cx-cy @atom:cx @atom:cy + @bond:cx-f @atom:cx @atom:f + @bond:cx-h1 @atom:cx @atom:h1 + @bond:cx-h2 @atom:cx @atom:h2 + @bond:cx-hc @atom:cx @atom:hc + @bond:cx-hx @atom:cx @atom:hx + @bond:cx-n2 @atom:cx @atom:n2 + @bond:cx-n3 @atom:cx @atom:n3 + @bond:cx-n @atom:cx @atom:n + @bond:cx-na @atom:cx @atom:na + @bond:cx-nh @atom:cx @atom:nh + @bond:cx-oh @atom:cx @atom:oh + @bond:cx-os @atom:cx @atom:os + @bond:cx-p3 @atom:cx @atom:p3 + @bond:cx-s4 @atom:cx @atom:s4 + @bond:cx-s6 @atom:cx @atom:s6 + @bond:cx-ss @atom:cx @atom:ss + @bond:cy-cy @atom:cy @atom:cy + @bond:cy-f @atom:cy @atom:f + @bond:cy-h1 @atom:cy @atom:h1 + @bond:cy-h2 @atom:cy @atom:h2 + @bond:cy-hc @atom:cy @atom:hc + @bond:cy-n @atom:cy @atom:n + @bond:cy-n3 @atom:cy @atom:n3 + @bond:cy-oh @atom:cy @atom:oh + @bond:cy-os @atom:cy @atom:os + @bond:cy-s6 @atom:cy @atom:s6 + @bond:cy-ss @atom:cy @atom:ss + @bond:cz-nh @atom:cz @atom:nh + @bond:f-n1 @atom:f @atom:n1 + @bond:f-n2 @atom:f @atom:n2 + @bond:f-n3 @atom:f @atom:n3 + @bond:f-n @atom:f @atom:n + @bond:f-n4 @atom:f @atom:n4 + @bond:f-na @atom:f @atom:na + @bond:f-nh @atom:f @atom:nh + @bond:f-no @atom:f @atom:no + @bond:f-o @atom:f @atom:o + @bond:f-oh @atom:f @atom:oh + @bond:f-os @atom:f @atom:os + @bond:f-p2 @atom:f @atom:p2 + @bond:f-p3 @atom:f @atom:p3 + @bond:f-p4 @atom:f @atom:p4 + @bond:f-p5 @atom:f @atom:p5 + @bond:f-s2 @atom:f @atom:s2 + @bond:f-s @atom:f @atom:s + @bond:f-s4 @atom:f @atom:s4 + @bond:f-s6 @atom:f @atom:s6 + @bond:f-sh @atom:f @atom:sh + @bond:f-ss @atom:f @atom:ss + @bond:hn-n1 @atom:hn @atom:n1 + @bond:hn-n2 @atom:hn @atom:n2 + @bond:hn-n3 @atom:hn @atom:n3 + @bond:hn-n @atom:hn @atom:n + @bond:hn-n4 @atom:hn @atom:n4 + @bond:hn-na @atom:hn @atom:na + @bond:hn-nh @atom:hn @atom:nh + @bond:hn-no @atom:hn @atom:no + @bond:ho-o @atom:ho @atom:o + @bond:ho-oh @atom:ho @atom:oh + @bond:hp-p2 @atom:hp @atom:p2 + @bond:hp-p3 @atom:hp @atom:p3 + @bond:hp-p4 @atom:hp @atom:p4 + @bond:hp-p5 @atom:hp @atom:p5 + @bond:hs-s @atom:hs @atom:s + @bond:hs-s4 @atom:hs @atom:s4 + @bond:hs-s6 @atom:hs @atom:s6 + @bond:hs-sh @atom:hs @atom:sh + @bond:i-i @atom:i @atom:i + @bond:i-n1 @atom:i @atom:n1 + @bond:i-n2 @atom:i @atom:n2 + @bond:i-n @atom:i @atom:n + @bond:i-n3 @atom:i @atom:n3 + @bond:i-n4 @atom:i @atom:n4 + @bond:i-na @atom:i @atom:na + @bond:i-nh @atom:i @atom:nh + @bond:i-no @atom:i @atom:no + @bond:i-o @atom:i @atom:o + @bond:i-oh @atom:i @atom:oh + @bond:i-os @atom:i @atom:os + @bond:i-p2 @atom:i @atom:p2 + @bond:i-p3 @atom:i @atom:p3 + @bond:i-p4 @atom:i @atom:p4 + @bond:i-p5 @atom:i @atom:p5 + @bond:i-s @atom:i @atom:s + @bond:i-s4 @atom:i @atom:s4 + @bond:i-s6 @atom:i @atom:s6 + @bond:i-sh @atom:i @atom:sh + @bond:i-ss @atom:i @atom:ss + @bond:n1-n1 @atom:n1 @atom:n1 + @bond:n1-n2 @atom:n1 @atom:n2 + @bond:n1-n3 @atom:n1 @atom:n3 + @bond:n1-n4 @atom:n1 @atom:n4 + @bond:n1-na @atom:n1 @atom:na + @bond:n1-nc @atom:n1 @atom:nc + @bond:n1-nd @atom:n1 @atom:nd + @bond:n1-ne @atom:n1 @atom:ne + @bond:n1-nf @atom:n1 @atom:nf + @bond:n1-nh @atom:n1 @atom:nh + @bond:n1-no @atom:n1 @atom:no + @bond:n1-o @atom:n1 @atom:o + @bond:n1-oh @atom:n1 @atom:oh + @bond:n1-os @atom:n1 @atom:os + @bond:n1-p2 @atom:n1 @atom:p2 + @bond:n1-p3 @atom:n1 @atom:p3 + @bond:n1-p4 @atom:n1 @atom:p4 + @bond:n1-p5 @atom:n1 @atom:p5 + @bond:n1-s2 @atom:n1 @atom:s2 + @bond:n1-s @atom:n1 @atom:s + @bond:n1-s4 @atom:n1 @atom:s4 + @bond:n1-s6 @atom:n1 @atom:s6 + @bond:n1-sh @atom:n1 @atom:sh + @bond:n1-ss @atom:n1 @atom:ss + @bond:n2-n2 @atom:n2 @atom:n2 + @bond:n2-n3 @atom:n2 @atom:n3 + @bond:n2-n4 @atom:n2 @atom:n4 + @bond:n2-na @atom:n2 @atom:na + @bond:n2-nc @atom:n2 @atom:nc + @bond:n2-nd @atom:n2 @atom:nd + @bond:n2-ne @atom:n2 @atom:ne + @bond:n2-nf @atom:n2 @atom:nf + @bond:n2-nh @atom:n2 @atom:nh + @bond:n2-no @atom:n2 @atom:no + @bond:n2-o @atom:n2 @atom:o + @bond:n2-oh @atom:n2 @atom:oh + @bond:n2-os @atom:n2 @atom:os + @bond:n2-p2 @atom:n2 @atom:p2 + @bond:n2-p3 @atom:n2 @atom:p3 + @bond:n2-p4 @atom:n2 @atom:p4 + @bond:n2-p5 @atom:n2 @atom:p5 + @bond:n2-pe @atom:n2 @atom:pe + @bond:n2-pf @atom:n2 @atom:pf + @bond:n2-s2 @atom:n2 @atom:s2 + @bond:n2-s4 @atom:n2 @atom:s4 + @bond:n2-s @atom:n2 @atom:s + @bond:n2-s6 @atom:n2 @atom:s6 + @bond:n2-sh @atom:n2 @atom:sh + @bond:n2-ss @atom:n2 @atom:ss + @bond:n3-n3 @atom:n3 @atom:n3 + @bond:n3-n4 @atom:n3 @atom:n4 + @bond:n3-na @atom:n3 @atom:na + @bond:n3-nh @atom:n3 @atom:nh + @bond:n3-no @atom:n3 @atom:no + @bond:n3-o @atom:n3 @atom:o + @bond:n3-oh @atom:n3 @atom:oh + @bond:n3-os @atom:n3 @atom:os + @bond:n3-p2 @atom:n3 @atom:p2 + @bond:n3-p3 @atom:n3 @atom:p3 + @bond:n3-p4 @atom:n3 @atom:p4 + @bond:n3-p5 @atom:n3 @atom:p5 + @bond:n3-py @atom:n3 @atom:py + @bond:n3-s @atom:n3 @atom:s + @bond:n3-s4 @atom:n3 @atom:s4 + @bond:n3-s6 @atom:n3 @atom:s6 + @bond:n3-sh @atom:n3 @atom:sh + @bond:n3-ss @atom:n3 @atom:ss + @bond:n3-sy @atom:n3 @atom:sy + @bond:n4-n4 @atom:n4 @atom:n4 + @bond:n4-na @atom:n4 @atom:na + @bond:n4-nh @atom:n4 @atom:nh + @bond:n4-no @atom:n4 @atom:no + @bond:n4-o @atom:n4 @atom:o + @bond:n4-oh @atom:n4 @atom:oh + @bond:n4-os @atom:n4 @atom:os + @bond:n4-p2 @atom:n4 @atom:p2 + @bond:n4-p3 @atom:n4 @atom:p3 + @bond:n4-p4 @atom:n4 @atom:p4 + @bond:n4-p5 @atom:n4 @atom:p5 + @bond:n4-py @atom:n4 @atom:py + @bond:n4-s @atom:n4 @atom:s + @bond:n4-s4 @atom:n4 @atom:s4 + @bond:n4-s6 @atom:n4 @atom:s6 + @bond:n4-sh @atom:n4 @atom:sh + @bond:n4-ss @atom:n4 @atom:ss + @bond:na-na @atom:na @atom:na + @bond:na-nb @atom:na @atom:nb + @bond:na-nc @atom:na @atom:nc + @bond:na-nd @atom:na @atom:nd + @bond:na-nh @atom:na @atom:nh + @bond:na-no @atom:na @atom:no + @bond:na-o @atom:na @atom:o + @bond:na-oh @atom:na @atom:oh + @bond:na-os @atom:na @atom:os + @bond:na-p2 @atom:na @atom:p2 + @bond:na-p3 @atom:na @atom:p3 + @bond:na-p4 @atom:na @atom:p4 + @bond:na-p5 @atom:na @atom:p5 + @bond:na-pc @atom:na @atom:pc + @bond:na-pd @atom:na @atom:pd + @bond:na-py @atom:na @atom:py + @bond:na-s @atom:na @atom:s + @bond:na-s4 @atom:na @atom:s4 + @bond:na-s6 @atom:na @atom:s6 + @bond:na-sh @atom:na @atom:sh + @bond:na-ss @atom:na @atom:ss + @bond:na-sy @atom:na @atom:sy + @bond:nb-nb @atom:nb @atom:nb + @bond:nb-pb @atom:nb @atom:pb + @bond:nc-nc @atom:nc @atom:nc + @bond:nc-nd @atom:nc @atom:nd + @bond:nc-os @atom:nc @atom:os + @bond:nc-ss @atom:nc @atom:ss + @bond:nc-sy @atom:nc @atom:sy + @bond:nd-nd @atom:nd @atom:nd + @bond:nd-os @atom:nd @atom:os + @bond:nd-ss @atom:nd @atom:ss + @bond:nd-sy @atom:nd @atom:sy + @bond:ne-ne @atom:ne @atom:ne + @bond:ne-nf @atom:ne @atom:nf + @bond:ne-o @atom:ne @atom:o + @bond:ne-p2 @atom:ne @atom:p2 + @bond:ne-pe @atom:ne @atom:pe + @bond:ne-px @atom:ne @atom:px + @bond:ne-py @atom:ne @atom:py + @bond:ne-s @atom:ne @atom:s + @bond:ne-sx @atom:ne @atom:sx + @bond:ne-sy @atom:ne @atom:sy + @bond:nf-nf @atom:nf @atom:nf + @bond:nf-o @atom:nf @atom:o + @bond:nf-p2 @atom:nf @atom:p2 + @bond:nf-pf @atom:nf @atom:pf + @bond:nf-px @atom:nf @atom:px + @bond:nf-py @atom:nf @atom:py + @bond:nf-s @atom:nf @atom:s + @bond:nf-sx @atom:nf @atom:sx + @bond:nf-sy @atom:nf @atom:sy + @bond:nh-nh @atom:nh @atom:nh + @bond:nh-no @atom:nh @atom:no + @bond:nh-o @atom:nh @atom:o + @bond:nh-oh @atom:nh @atom:oh + @bond:nh-os @atom:nh @atom:os + @bond:nh-p2 @atom:nh @atom:p2 + @bond:nh-p3 @atom:nh @atom:p3 + @bond:nh-p4 @atom:nh @atom:p4 + @bond:nh-p5 @atom:nh @atom:p5 + @bond:nh-s @atom:nh @atom:s + @bond:nh-s4 @atom:nh @atom:s4 + @bond:nh-s6 @atom:nh @atom:s6 + @bond:nh-sh @atom:nh @atom:sh + @bond:nh-ss @atom:nh @atom:ss + @bond:nh-sy @atom:nh @atom:sy + @bond:n-n1 @atom:n @atom:n1 + @bond:n-n2 @atom:n @atom:n2 + @bond:n-n3 @atom:n @atom:n3 + @bond:n-n4 @atom:n @atom:n4 + @bond:n-n @atom:n @atom:n + @bond:n-na @atom:n @atom:na + @bond:n-nc @atom:n @atom:nc + @bond:n-nd @atom:n @atom:nd + @bond:n-nh @atom:n @atom:nh + @bond:n-no @atom:n @atom:no + @bond:n-o @atom:n @atom:o + @bond:n-oh @atom:n @atom:oh + @bond:no-no @atom:no @atom:no + @bond:no-o @atom:no @atom:o + @bond:no-oh @atom:no @atom:oh + @bond:no-os @atom:no @atom:os + @bond:no-p2 @atom:no @atom:p2 + @bond:no-p3 @atom:no @atom:p3 + @bond:no-p4 @atom:no @atom:p4 + @bond:no-p5 @atom:no @atom:p5 + @bond:no-s @atom:no @atom:s + @bond:n-os @atom:n @atom:os + @bond:no-s4 @atom:no @atom:s4 + @bond:no-s6 @atom:no @atom:s6 + @bond:no-sh @atom:no @atom:sh + @bond:no-ss @atom:no @atom:ss + @bond:n-p2 @atom:n @atom:p2 + @bond:n-p3 @atom:n @atom:p3 + @bond:n-p4 @atom:n @atom:p4 + @bond:n-p5 @atom:n @atom:p5 + @bond:n-pc @atom:n @atom:pc + @bond:n-pd @atom:n @atom:pd + @bond:n-s @atom:n @atom:s + @bond:n-s4 @atom:n @atom:s4 + @bond:n-s6 @atom:n @atom:s6 + @bond:n-sh @atom:n @atom:sh + @bond:n-ss @atom:n @atom:ss + @bond:n-sy @atom:n @atom:sy + @bond:oh-oh @atom:oh @atom:oh + @bond:oh-os @atom:oh @atom:os + @bond:oh-p2 @atom:oh @atom:p2 + @bond:oh-p3 @atom:oh @atom:p3 + @bond:oh-p4 @atom:oh @atom:p4 + @bond:oh-p5 @atom:oh @atom:p5 + @bond:oh-py @atom:oh @atom:py + @bond:oh-s @atom:oh @atom:s + @bond:oh-s4 @atom:oh @atom:s4 + @bond:oh-s6 @atom:oh @atom:s6 + @bond:oh-sh @atom:oh @atom:sh + @bond:oh-ss @atom:oh @atom:ss + @bond:oh-sy @atom:oh @atom:sy + @bond:o-o @atom:o @atom:o + @bond:o-oh @atom:o @atom:oh + @bond:o-os @atom:o @atom:os + @bond:o-p2 @atom:o @atom:p2 + @bond:o-p3 @atom:o @atom:p3 + @bond:o-p4 @atom:o @atom:p4 + @bond:o-p5 @atom:o @atom:p5 + @bond:o-pe @atom:o @atom:pe + @bond:o-pf @atom:o @atom:pf + @bond:o-px @atom:o @atom:px + @bond:o-py @atom:o @atom:py + @bond:o-s @atom:o @atom:s + @bond:o-s2 @atom:o @atom:s2 + @bond:o-s4 @atom:o @atom:s4 + @bond:o-s6 @atom:o @atom:s6 + @bond:o-sh @atom:o @atom:sh + @bond:os-os @atom:os @atom:os + @bond:os-p2 @atom:os @atom:p2 + @bond:os-p3 @atom:os @atom:p3 + @bond:os-p4 @atom:os @atom:p4 + @bond:os-p5 @atom:os @atom:p5 + @bond:os-py @atom:os @atom:py + @bond:os-s @atom:os @atom:s + @bond:o-ss @atom:o @atom:ss + @bond:os-s4 @atom:os @atom:s4 + @bond:os-s6 @atom:os @atom:s6 + @bond:os-sh @atom:os @atom:sh + @bond:os-ss @atom:os @atom:ss + @bond:os-sy @atom:os @atom:sy + @bond:o-sx @atom:o @atom:sx + @bond:o-sy @atom:o @atom:sy + @bond:p2-p2 @atom:p2 @atom:p2 + @bond:p2-p3 @atom:p2 @atom:p3 + @bond:p2-p4 @atom:p2 @atom:p4 + @bond:p2-p5 @atom:p2 @atom:p5 + @bond:p2-pe @atom:p2 @atom:pe + @bond:p2-pf @atom:p2 @atom:pf + @bond:p2-s @atom:p2 @atom:s + @bond:p2-s4 @atom:p2 @atom:s4 + @bond:p2-s6 @atom:p2 @atom:s6 + @bond:p2-sh @atom:p2 @atom:sh + @bond:p2-ss @atom:p2 @atom:ss + @bond:p3-p3 @atom:p3 @atom:p3 + @bond:p3-p4 @atom:p3 @atom:p4 + @bond:p3-p5 @atom:p3 @atom:p5 + @bond:p3-s @atom:p3 @atom:s + @bond:p3-s4 @atom:p3 @atom:s4 + @bond:p3-s6 @atom:p3 @atom:s6 + @bond:p3-sh @atom:p3 @atom:sh + @bond:p3-ss @atom:p3 @atom:ss + @bond:p4-p4 @atom:p4 @atom:p4 + @bond:p4-p5 @atom:p4 @atom:p5 + @bond:p4-s @atom:p4 @atom:s + @bond:p4-s4 @atom:p4 @atom:s4 + @bond:p4-s6 @atom:p4 @atom:s6 + @bond:p4-sh @atom:p4 @atom:sh + @bond:p4-ss @atom:p4 @atom:ss + @bond:p5-p5 @atom:p5 @atom:p5 + @bond:p5-s @atom:p5 @atom:s + @bond:p5-s4 @atom:p5 @atom:s4 + @bond:p5-s6 @atom:p5 @atom:s6 + @bond:p5-sh @atom:p5 @atom:sh + @bond:p5-ss @atom:p5 @atom:ss + @bond:pe-pe @atom:pe @atom:pe + @bond:pe-pf @atom:pe @atom:pf + @bond:pe-px @atom:pe @atom:px + @bond:pe-py @atom:pe @atom:py + @bond:pe-s @atom:pe @atom:s + @bond:pe-sx @atom:pe @atom:sx + @bond:pe-sy @atom:pe @atom:sy + @bond:pf-pf @atom:pf @atom:pf + @bond:pf-px @atom:pf @atom:px + @bond:pf-py @atom:pf @atom:py + @bond:pf-s @atom:pf @atom:s + @bond:pf-sx @atom:pf @atom:sx + @bond:pf-sy @atom:pf @atom:sy + @bond:px-py @atom:px @atom:py + @bond:px-sx @atom:px @atom:sx + @bond:px-sy @atom:px @atom:sy + @bond:py-py @atom:py @atom:py + @bond:py-sx @atom:py @atom:sx + @bond:py-sy @atom:py @atom:sy + @bond:s4-s4 @atom:s4 @atom:s4 + @bond:s4-s6 @atom:s4 @atom:s6 + @bond:s4-sh @atom:s4 @atom:sh + @bond:s4-ss @atom:s4 @atom:ss + @bond:s6-s6 @atom:s6 @atom:s6 + @bond:s6-sh @atom:s6 @atom:sh + @bond:s6-ss @atom:s6 @atom:ss + @bond:sh-sh @atom:sh @atom:sh + @bond:sh-ss @atom:sh @atom:ss + @bond:s-s @atom:s @atom:s + @bond:s-s2 @atom:s @atom:s2 + @bond:s-s4 @atom:s @atom:s4 + @bond:s-s6 @atom:s @atom:s6 + @bond:s-sh @atom:s @atom:sh + @bond:s-ss @atom:s @atom:ss + @bond:ss-ss @atom:ss @atom:ss + @bond:sx-sx @atom:sx @atom:sx + @bond:sx-sy @atom:sx @atom:sy + @bond:sy-sy @atom:sy @atom:sy + @bond:br-cd @atom:br @atom:cd + @bond:c1-cf @atom:c1 @atom:cf + @bond:cd-f @atom:cd @atom:f + @bond:cd-n4 @atom:cd @atom:n4 + @bond:cd-nf @atom:cd @atom:nf + @bond:cd-no @atom:cd @atom:no + @bond:cd-sh @atom:cd @atom:sh + @bond:cd-sx @atom:cd @atom:sx + @bond:cc-cy @atom:cc @atom:cy + @bond:cf-cl @atom:cf @atom:cl + @bond:cf-cx @atom:cf @atom:cx + @bond:cf-cy @atom:cf @atom:cy + @bond:cf-na @atom:cf @atom:na + @bond:cf-ss @atom:cf @atom:ss + @bond:cq-na @atom:cq @atom:na + @bond:cq-nb @atom:cq @atom:nb + @bond:cl-py @atom:cl @atom:py + @bond:f-py @atom:f @atom:py + @bond:py-s @atom:py @atom:s + @bond:cy-nh @atom:cy @atom:nh + @bond:cy-hx @atom:cy @atom:hx + @bond:br-ce @atom:br @atom:ce + @bond:cc-i @atom:cc @atom:i + @bond:cy-n4 @atom:cy @atom:n4 + @bond:cy-p3 @atom:cy @atom:p3 + @bond:cy-na @atom:cy @atom:na + @bond:cx-n4 @atom:cx @atom:n4 + @bond:ne-s4 @atom:ne @atom:s4 + @bond:cv-ss @atom:cv @atom:ss + @bond:cy-no @atom:cy @atom:no + @bond:ce-cv @atom:ce @atom:cv + @bond:cd-i @atom:cd @atom:i + @bond:cy-s4 @atom:cy @atom:s4 + @bond:n2-sy @atom:n2 @atom:sy + @bond:cc-s6 @atom:cc @atom:s6 + @bond:i-s2 @atom:i @atom:s2 + @bond:br-cy @atom:br @atom:cy + @bond:br-cf @atom:br @atom:cf + @bond:nf-s4 @atom:nf @atom:s4 + @bond:cf-cv @atom:cf @atom:cv + @bond:cd-s6 @atom:cd @atom:s6 + @bond:ss-sy @atom:ss @atom:sy + @bond:h5-ce @atom:h5 @atom:ce + @bond:h5-cf @atom:h5 @atom:cf + @bond:ce-s4 @atom:ce @atom:s4 + @bond:cf-s4 @atom:cf @atom:s4 + @bond:cy-py @atom:cy @atom:py + @bond:cd-o @atom:cd @atom:o + @bond:ne-s6 @atom:ne @atom:s6 + @bond:nf-s6 @atom:nf @atom:s6 + @bond:ce-no @atom:ce @atom:no + @bond:cf-no @atom:cf @atom:no + } # (end of Bonds By Type) + + write_once("In Settings") { + angle_coeff @angle:hw-ow-hw harmonic 43.276 104.520 # AMBER 1 TIP3P_water + angle_coeff @angle:hw-hw-ow harmonic 0.000 127.740 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) + angle_coeff @angle:br-c1-br harmonic 58.432 180.000 # Guess 0 + angle_coeff @angle:br-c1-c1 harmonic 56.125 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-c1 harmonic 65.529 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-c2 harmonic 62.451 180.000 # SOURCE3 2 + angle_coeff @angle:c1-c1-c3 harmonic 57.975 178.510 # SOURCE4_SOURCE5 618 0.7369 + angle_coeff @angle:c1-c1-ca harmonic 58.535 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-cl harmonic 63.947 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-f harmonic 80.686 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ha harmonic 44.782 179.110 # SOURCE3_SOURCE5 219 0.5885 + angle_coeff @angle:c1-c1-hc harmonic 44.772 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-i harmonic 52.986 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n1 harmonic 83.562 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n2 harmonic 82.100 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n3 harmonic 76.721 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-n4 harmonic 74.244 179.560 # SOURCE3 3 0.3096 + angle_coeff @angle:c1-c1-n harmonic 77.977 177.180 # SOURCE3 1 + angle_coeff @angle:c1-c1-na harmonic 76.884 176.750 # SOURCE3 8 2.9328 + angle_coeff @angle:c1-c1-nh harmonic 77.069 179.270 # SOURCE3 3 0.2357 + angle_coeff @angle:c1-c1-no harmonic 74.597 180.000 # SOURCE3 3 + angle_coeff @angle:c1-c1-o harmonic 82.936 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-oh harmonic 78.242 176.650 # SOURCE3 1 + angle_coeff @angle:c1-c1-os harmonic 78.471 176.930 # SOURCE3_SOURCE5 5 1.1927 + angle_coeff @angle:c1-c1-p2 harmonic 68.155 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p3 harmonic 69.444 169.630 # SOURCE3 2 + angle_coeff @angle:c1-c1-p4 harmonic 67.414 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-p5 harmonic 69.535 176.170 # SOURCE3 2 + angle_coeff @angle:c1-c1-s4 harmonic 55.785 167.470 # SOURCE3 2 + angle_coeff @angle:c1-c1-s6 harmonic 55.388 174.380 # SOURCE3 2 + angle_coeff @angle:c1-c1-s harmonic 58.129 179.970 # SOURCE3 1 + angle_coeff @angle:c1-c1-sh harmonic 55.773 180.000 # SOURCE3 1 + angle_coeff @angle:c1-c1-ss harmonic 56.169 175.600 # SOURCE3_SOURCE5 19 1.3679 + angle_coeff @angle:c2-c1-c2 harmonic 60.185 179.370 # SOURCE3_SOURCE5 14 0.3391 + angle_coeff @angle:c2-c1-ce harmonic 60.047 179.050 # SOURCE4_SOURCE5 15 0.4210 + angle_coeff @angle:c2-c1-n1 harmonic 79.308 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-c1-o harmonic 78.963 179.500 # SOURCE2 1 + angle_coeff @angle:c2-c1-s2 harmonic 58.516 172.980 # SOURCE3 1 + angle_coeff @angle:c3-c1-c3 harmonic 53.523 180.000 # Guess 0 + angle_coeff @angle:c3-c1-cg harmonic 57.770 178.430 # SOURCE4_SOURCE5 134 0.5502 + angle_coeff @angle:c3-c1-n1 harmonic 73.216 178.580 # SOURCE4_SOURCE5 245 0.5409 + angle_coeff @angle:ca-c1-ca harmonic 54.530 180.000 # Guess 0 + angle_coeff @angle:c-c1-c1 harmonic 57.944 180.000 # SOURCE3 1 + angle_coeff @angle:cg-c1-ha harmonic 44.392 178.830 # SOURCE3_SOURCE5 60 1.1251 + angle_coeff @angle:ch-c1-ha harmonic 44.307 178.830 # SOURCE3_SOURCE5 38 0.3321 + angle_coeff @angle:cl-c1-cl harmonic 70.163 180.000 # Guess 0 + angle_coeff @angle:f-c1-f harmonic 99.768 180.000 # Guess 0 + angle_coeff @angle:i-c1-i harmonic 58.397 180.000 # Guess 0 + angle_coeff @angle:n1-c1-n1 harmonic 141.802 102.010 # SOURCE3 1 + angle_coeff @angle:n1-c1-n3 harmonic 98.388 176.010 # SOURCE2_SOURCE5 5 0.1498 + angle_coeff @angle:n1-c1-nh harmonic 98.195 177.650 # SOURCE4_SOURCE5 18 0.7845 + angle_coeff @angle:n1-c1-os harmonic 99.150 178.590 # SOURCE3 1 + angle_coeff @angle:n1-c1-p3 harmonic 86.562 171.200 # SOURCE2 1 + angle_coeff @angle:n1-c1-ss harmonic 70.134 177.470 # SOURCE3_SOURCE5 15 0.7211 + angle_coeff @angle:n2-c1-n2 harmonic 102.862 180.000 # Guess 0 + angle_coeff @angle:n2-c1-o harmonic 106.076 172.730 # SOURCE3_SOURCE5 10 0.3647 + angle_coeff @angle:n2-c1-s harmonic 73.638 175.910 # SOURCE4_SOURCE5 29 0.2046 + angle_coeff @angle:n3-c1-n3 harmonic 91.381 180.000 # Guess 0 + angle_coeff @angle:n4-c1-n4 harmonic 86.899 180.000 # Guess 0 + angle_coeff @angle:na-c1-na harmonic 90.408 180.000 # Guess 0 + angle_coeff @angle:ne-c1-o harmonic 105.956 172.330 # SOURCE3 1 + angle_coeff @angle:ne-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 23 0.2168 + angle_coeff @angle:nf-c1-o harmonic 105.956 172.330 # SOURCE3 1 + angle_coeff @angle:nh-c1-nh harmonic 91.735 180.000 # Guess 0 + angle_coeff @angle:n-c1-n harmonic 92.583 180.000 # Guess 0 + angle_coeff @angle:no-c1-no harmonic 87.641 180.000 # Guess 0 + angle_coeff @angle:oh-c1-oh harmonic 92.863 180.000 # Guess 0 + angle_coeff @angle:o-c1-o harmonic 105.029 180.000 # Guess 0 + angle_coeff @angle:os-c1-os harmonic 93.419 180.000 # Guess 0 + angle_coeff @angle:p2-c1-p2 harmonic 85.393 180.000 # Guess 0 + angle_coeff @angle:p3-c1-p3 harmonic 84.439 180.000 # Guess 0 + angle_coeff @angle:p4-c1-p4 harmonic 84.439 180.000 # Guess 0 + angle_coeff @angle:p5-c1-p5 harmonic 86.221 180.000 # Guess 0 + angle_coeff @angle:s2-c1-s2 harmonic 57.538 180.000 # Guess 0 + angle_coeff @angle:s4-c1-s4 harmonic 52.562 180.000 # Guess 0 + angle_coeff @angle:s6-c1-s6 harmonic 53.295 180.000 # Guess 0 + angle_coeff @angle:sh-c1-sh harmonic 54.627 180.000 # Guess 0 + angle_coeff @angle:s-c1-s harmonic 57.244 180.000 # Guess 0 + angle_coeff @angle:ss-c1-ss harmonic 54.310 180.000 # Guess 0 + angle_coeff @angle:br-c2-br harmonic 68.999 115.060 # SOURCE3 1 + angle_coeff @angle:br-c2-c2 harmonic 64.458 121.030 # SOURCE4_SOURCE5 18 0.8426 + angle_coeff @angle:br-c2-c3 harmonic 64.834 115.320 # SOURCE4_SOURCE5 18 0.6855 + angle_coeff @angle:br-c2-ce harmonic 64.279 121.530 # SOURCE4_SOURCE5 18 0.7036 + angle_coeff @angle:br-c2-h4 harmonic 42.846 113.730 # SOURCE4_SOURCE5 17 0.5888 + angle_coeff @angle:br-c2-ha harmonic 42.937 113.280 # SOURCE3 1 + angle_coeff @angle:c1-c2-c1 harmonic 74.593 116.770 # SOURCE3 1 + angle_coeff @angle:c1-c2-c2 harmonic 72.319 121.620 # SOURCE3 1 + angle_coeff @angle:c1-c2-c3 harmonic 66.250 124.900 # SOURCE4_SOURCE5 44 0.7045 + angle_coeff @angle:c1-c2-f harmonic 90.501 124.900 # SOURCE2 1 + angle_coeff @angle:c1-c2-ha harmonic 51.141 120.420 # SOURCE3_SOURCE5 30 0.4602 + angle_coeff @angle:c2-c2-c2 harmonic 71.539 121.810 # SOURCE3 10 0.3843 + angle_coeff @angle:c2-c2-c3 harmonic 66.132 123.630 # SOURCE3_SOURCE5 4623 2.2803 + angle_coeff @angle:c2-c2-ca harmonic 71.595 117.000 # SOURCE3 1 + angle_coeff @angle:c2-c2-cc harmonic 72.240 117.210 # SOURCE3 2 0.3418 + angle_coeff @angle:c2-c2-cd harmonic 72.240 117.210 # SOURCE3 2 + angle_coeff @angle:c2-c2-cl harmonic 72.331 123.110 # SOURCE4_SOURCE5 103 1.0574 + angle_coeff @angle:c2-c2-cx harmonic 66.489 124.950 # SOURCE4_SOURCE5 51 1.8521 + angle_coeff @angle:c2-c2-cy harmonic 67.939 117.180 # SOURCE2_SOURCE5 11 1.7549 + angle_coeff @angle:c2-c2-f harmonic 90.338 122.870 # SOURCE4_SOURCE5 37 0.6494 + angle_coeff @angle:c2-c2-h4 harmonic 49.914 122.670 # SOURCE4_SOURCE5 266 1.3387 + angle_coeff @angle:c2-c2-ha harmonic 50.363 120.430 # SOURCE3_SOURCE5 3764 1.3300 + angle_coeff @angle:c2-c2-hc harmonic 50.527 119.700 # SOURCE3 1 + angle_coeff @angle:c2-c2-hx harmonic 49.204 126.450 # SOURCE3 3 0.0219 + angle_coeff @angle:c2-c2-i harmonic 59.321 121.030 # SOURCE3 2 + angle_coeff @angle:c2-c2-n1 harmonic 90.093 122.980 # HF/6-31G* 1 + angle_coeff @angle:c2-c2-n2 harmonic 89.778 126.010 # SOURCE3 1 + angle_coeff @angle:c2-c2-n3 harmonic 88.404 124.550 # SOURCE3 1 + angle_coeff @angle:c2-c2-n4 harmonic 83.421 121.520 # SOURCE3 5 1.2656 + angle_coeff @angle:c2-c2-n harmonic 86.693 123.670 # SOURCE4_SOURCE5 48 1.8326 + angle_coeff @angle:c2-c2-na harmonic 87.232 121.940 # SOURCE3_SOURCE5 35 5.4059 + angle_coeff @angle:c2-c2-nh harmonic 86.653 124.990 # SOURCE3 7 0.9929 + angle_coeff @angle:c2-c2-no harmonic 85.060 123.460 # SOURCE4_SOURCE5 26 1.6311 + angle_coeff @angle:c2-c2-o harmonic 89.793 130.890 # SOURCE3 2 0.0201 + angle_coeff @angle:c2-c2-oh harmonic 89.312 122.170 # SOURCE4_SOURCE5 18 1.1206 + angle_coeff @angle:c2-c2-os harmonic 88.706 121.870 # SOURCE4_SOURCE5 114 1.6810 + angle_coeff @angle:c2-c2-p2 harmonic 88.516 115.100 # SOURCE3 1 + angle_coeff @angle:c2-c2-p3 harmonic 78.573 124.830 # SOURCE3 5 2.1222 + angle_coeff @angle:c2-c2-p4 harmonic 80.685 119.760 # SOURCE3 1 + angle_coeff @angle:c2-c2-p5 harmonic 77.141 125.970 # SOURCE3 1 + angle_coeff @angle:c2-c2-s4 harmonic 64.747 119.840 # SOURCE3 1 + angle_coeff @angle:c2-c2-s6 harmonic 64.702 120.010 # SOURCE3 1 + angle_coeff @angle:c2-c2-s harmonic 63.092 129.370 # SOURCE3 2 + angle_coeff @angle:c2-c2-sh harmonic 62.559 125.700 # SOURCE3 3 1.3390 + angle_coeff @angle:c2-c2-ss harmonic 64.815 122.350 # SOURCE4_SOURCE5 54 2.2017 + angle_coeff @angle:c3-c2-c3 harmonic 64.898 115.650 # SOURCE3_SOURCE5 1743 1.5647 + angle_coeff @angle:c3-c2-cc harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 + angle_coeff @angle:c3-c2-cd harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 + angle_coeff @angle:c3-c2-ce harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 + angle_coeff @angle:c3-c2-cf harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 + angle_coeff @angle:c3-c2-h4 harmonic 45.760 119.020 # SOURCE4_SOURCE5 63 1.6077 + angle_coeff @angle:c3-c2-ha harmonic 46.411 115.680 # SOURCE3_SOURCE5 3991 1.1961 + angle_coeff @angle:c3-c2-hc harmonic 45.572 120.000 # SOURCE3 1 + angle_coeff @angle:c3-c2-n2 harmonic 83.960 123.430 # SOURCE4_SOURCE5 388 2.3609 + angle_coeff @angle:c3-c2-n harmonic 84.414 114.800 # SOURCE4 12 1.8112 + angle_coeff @angle:c3-c2-na harmonic 83.495 117.200 # SOURCE3_SOURCE5 5 0.8937 + angle_coeff @angle:c3-c2-ne harmonic 84.706 120.710 # SOURCE3_SOURCE5 11 0.9157 + angle_coeff @angle:c3-c2-nf harmonic 84.706 120.710 # SOURCE3_SOURCE5 7 1.3134 + angle_coeff @angle:c3-c2-nh harmonic 84.195 116.210 # SOURCE3_SOURCE5 339 2.4814 + angle_coeff @angle:c3-c2-o harmonic 85.206 122.820 # SOURCE4_SOURCE5 12 1.1220 + angle_coeff @angle:c3-c2-oh harmonic 85.711 115.160 # SOURCE4_SOURCE5 90 2.0675 + angle_coeff @angle:c3-c2-os harmonic 86.117 112.800 # SOURCE4_SOURCE5 148 2.4217 + angle_coeff @angle:c3-c2-p2 harmonic 82.609 122.740 # SOURCE3 2 + angle_coeff @angle:c3-c2-s harmonic 64.740 115.440 # SOURCE3 2 0.0115 + angle_coeff @angle:c3-c2-ss harmonic 63.539 119.660 # SOURCE4_SOURCE5 137 2.1299 + angle_coeff @angle:ca-c2-ca harmonic 70.080 117.880 # SOURCE3 1 + angle_coeff @angle:ca-c2-hc harmonic 48.375 123.300 # SOURCE3 1 + angle_coeff @angle:c-c2-c2 harmonic 69.891 120.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c3 harmonic 65.889 119.700 # SOURCE3 1 + angle_coeff @angle:c-c2-c harmonic 68.722 118.880 # SOURCE3 1 + angle_coeff @angle:cc-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 23 0.5829 + angle_coeff @angle:cc-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 + angle_coeff @angle:cc-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 27 1.0384 + angle_coeff @angle:cc-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 12 0.0560 + angle_coeff @angle:cd-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 + angle_coeff @angle:ce-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 41 0.8440 + angle_coeff @angle:ce-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 220 1.5462 + angle_coeff @angle:ce-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2139 1.1520 + angle_coeff @angle:ce-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 12 1.9766 + angle_coeff @angle:ce-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 243 2.3407 + angle_coeff @angle:ce-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 10 0.9817 + angle_coeff @angle:ce-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 14 0.7592 + angle_coeff @angle:ce-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 104 1.7734 + angle_coeff @angle:ce-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 149 2.3406 + angle_coeff @angle:cf-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2017 1.1895 + angle_coeff @angle:c-c2-ha harmonic 48.160 121.330 # SOURCE3 4 0.2462 + angle_coeff @angle:c-c2-hc harmonic 48.494 119.700 # SOURCE3 1 + angle_coeff @angle:cl-c2-cl harmonic 82.957 114.340 # SOURCE4_SOURCE5 29 0.6417 + angle_coeff @angle:cl-c2-h4 harmonic 49.503 113.540 # SOURCE4_SOURCE5 33 0.7337 + angle_coeff @angle:cl-c2-ha harmonic 49.579 113.200 # SOURCE3 1 + angle_coeff @angle:cx-c2-ha harmonic 47.006 116.150 # SOURCE4_SOURCE5 64 0.8729 + angle_coeff @angle:f-c2-f harmonic 120.199 111.640 # SOURCE2_SOURCE5 12 0.8567 + angle_coeff @angle:f-c2-ha harmonic 66.780 110.000 # SOURCE2 1 + angle_coeff @angle:h4-c2-n2 harmonic 64.810 120.990 # SOURCE4_SOURCE5 77 1.9305 + angle_coeff @angle:h4-c2-n harmonic 62.621 113.440 # SOURCE4_SOURCE5 78 1.0580 + angle_coeff @angle:h4-c2-na harmonic 62.675 112.970 # SOURCE4_SOURCE5 27 0.6876 + angle_coeff @angle:h4-c2-ne harmonic 64.858 119.510 # SOURCE4_SOURCE5 52 1.6395 + angle_coeff @angle:h4-c2-nh harmonic 62.613 115.080 # SOURCE4_SOURCE5 109 1.1974 + angle_coeff @angle:h4-c2-no harmonic 60.883 113.380 # SOURCE4_SOURCE5 20 0.1373 + angle_coeff @angle:h4-c2-os harmonic 63.989 113.730 # SOURCE3_SOURCE5 89 1.3113 + angle_coeff @angle:h4-c2-ss harmonic 43.595 116.670 # SOURCE3_SOURCE5 49 1.4612 + angle_coeff @angle:h5-c2-n2 harmonic 64.543 121.700 # SOURCE4_SOURCE5 71 2.1538 + angle_coeff @angle:h5-c2-na harmonic 59.208 126.390 # SOURCE3 4 0.3299 + angle_coeff @angle:h5-c2-ne harmonic 64.691 119.850 # SOURCE4_SOURCE5 44 1.3576 + angle_coeff @angle:h5-c2-nh harmonic 62.882 113.910 # SOURCE4_SOURCE5 119 0.8516 + angle_coeff @angle:ha-c2-ha harmonic 37.684 116.900 # SOURCE3_SOURCE5 1456 0.6313 + angle_coeff @angle:ha-c2-n1 harmonic 63.987 120.760 # SOURCE3 8 0.6632 + angle_coeff @angle:ha-c2-n2 harmonic 64.911 120.540 # SOURCE3 92 1.4571 + angle_coeff @angle:ha-c2-n3 harmonic 64.744 113.540 # SOURCE3 1 + angle_coeff @angle:ha-c2-n harmonic 62.620 113.400 # SOURCE3 4 1.2182 + angle_coeff @angle:ha-c2-na harmonic 62.816 112.420 # SOURCE3 8 0.6507 + angle_coeff @angle:ha-c2-ne harmonic 64.391 121.180 # SOURCE3 68 0.6824 + angle_coeff @angle:ha-c2-nf harmonic 64.391 121.180 # SOURCE3 68 + angle_coeff @angle:ha-c2-nh harmonic 62.169 116.680 # SOURCE3 13 2.5734 + angle_coeff @angle:ha-c2-no harmonic 61.209 112.140 # SOURCE3 2 0.0264 + angle_coeff @angle:ha-c2-o harmonic 67.875 117.230 # SOURCE3 2 0.0201 + angle_coeff @angle:ha-c2-oh harmonic 64.058 116.180 # SOURCE3 2 + angle_coeff @angle:ha-c2-os harmonic 64.269 112.690 # SOURCE3 13 2.5851 + angle_coeff @angle:ha-c2-p2 harmonic 57.111 121.480 # SOURCE3 122 0.4329 + angle_coeff @angle:ha-c2-p3 harmonic 53.276 114.310 # SOURCE3 3 + angle_coeff @angle:ha-c2-p4 harmonic 52.849 117.860 # SOURCE3 1 + angle_coeff @angle:ha-c2-p5 harmonic 51.984 116.000 # SOURCE3_SOURCE5 6 0.1220 + angle_coeff @angle:ha-c2-pe harmonic 56.443 121.400 # SOURCE3_SOURCE5 119 0.8904 + angle_coeff @angle:ha-c2-pf harmonic 56.443 121.400 # SOURCE3_SOURCE5 15 1.6416 + angle_coeff @angle:ha-c2-s2 harmonic 46.632 118.740 # SOURCE3 2 + angle_coeff @angle:ha-c2-s4 harmonic 43.223 115.300 # SOURCE3 2 + angle_coeff @angle:ha-c2-s harmonic 43.832 115.700 # SOURCE3 2 + angle_coeff @angle:ha-c2-s6 harmonic 42.982 116.600 # SOURCE3 2 + angle_coeff @angle:ha-c2-sh harmonic 43.327 111.740 # SOURCE3 1 + angle_coeff @angle:ha-c2-ss harmonic 43.588 116.720 # SOURCE3 7 2.7543 + angle_coeff @angle:hc-c2-hc harmonic 37.394 118.920 # SOURCE3 1 + angle_coeff @angle:hc-c2-n2 harmonic 64.965 120.400 # SOURCE3 1 + angle_coeff @angle:hc-c2-n harmonic 62.454 114.040 # SOURCE3 1 + angle_coeff @angle:hc-c2-na harmonic 61.038 119.100 # SOURCE3 1 + angle_coeff @angle:hc-c2-nh harmonic 63.084 113.360 # SOURCE3 1 + angle_coeff @angle:hc-c2-no harmonic 61.222 112.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-oh harmonic 64.060 116.220 # SOURCE3 1 + angle_coeff @angle:hc-c2-os harmonic 63.327 116.110 # SOURCE3 1 + angle_coeff @angle:hc-c2-p3 harmonic 52.613 117.190 # SOURCE3 1 + angle_coeff @angle:hc-c2-p5 harmonic 51.195 119.580 # SOURCE3 1 + angle_coeff @angle:hc-c2-s4 harmonic 43.068 116.120 # SOURCE3 1 + angle_coeff @angle:hc-c2-s6 harmonic 43.193 115.450 # SOURCE3 1 + angle_coeff @angle:hc-c2-sh harmonic 42.589 115.630 # SOURCE3 1 + angle_coeff @angle:hc-c2-ss harmonic 43.793 115.620 # SOURCE3 1 + angle_coeff @angle:hx-c2-n4 harmonic 58.717 113.030 # SOURCE3 3 0.3873 + angle_coeff @angle:i-c2-i harmonic 66.122 117.940 # SOURCE3 1 + angle_coeff @angle:n1-c2-n1 harmonic 113.528 124.150 # HF/6-31G* 1 + angle_coeff @angle:n2-c2-n2 harmonic 120.816 113.820 # SOURCE3 1 + angle_coeff @angle:n2-c2-n4 harmonic 109.745 112.970 # SOURCE4_SOURCE5 13 0.4034 + angle_coeff @angle:n2-c2-na harmonic 110.312 123.620 # SOURCE3 1 + angle_coeff @angle:n2-c2-nh harmonic 110.708 124.270 # SOURCE3 12 2.4114 + angle_coeff @angle:n2-c2-oh harmonic 114.021 122.080 # SOURCE3 1 + angle_coeff @angle:n2-c2-os harmonic 114.100 119.780 # SOURCE4_SOURCE5 55 1.3881 + angle_coeff @angle:n2-c2-ss harmonic 79.299 129.770 # SOURCE3 1 + angle_coeff @angle:n3-c2-n3 harmonic 113.269 118.470 # SOURCE3 1 + angle_coeff @angle:n4-c2-n4 harmonic 102.331 113.930 # SOURCE3 1 + angle_coeff @angle:n4-c2-ss harmonic 80.666 116.270 # SOURCE4_SOURCE5 14 2.4226 + angle_coeff @angle:na-c2-na harmonic 112.735 109.330 # SOURCE3 3 3.0187 + angle_coeff @angle:ne-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 + angle_coeff @angle:ne-c2-os harmonic 114.213 118.760 # SOURCE4 5 0.3382 + angle_coeff @angle:ne-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 32 2.1160 + angle_coeff @angle:nf-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 + angle_coeff @angle:nh-c2-nh harmonic 112.122 112.820 # SOURCE4_SOURCE5 689 1.9577 + angle_coeff @angle:nh-c2-oh harmonic 111.944 117.110 # SOURCE4_SOURCE5 15 0.8639 + angle_coeff @angle:nh-c2-os harmonic 112.490 114.300 # SOURCE4_SOURCE5 50 1.3395 + angle_coeff @angle:nh-c2-ss harmonic 84.343 111.550 # SOURCE4 37 1.1778 + angle_coeff @angle:n-c2-n2 harmonic 110.772 122.820 # SOURCE3_SOURCE5 46 2.2661 + angle_coeff @angle:n-c2-n harmonic 110.943 113.230 # SOURCE3 1 + angle_coeff @angle:n-c2-na harmonic 114.893 105.420 # SOURCE3 1 + angle_coeff @angle:n-c2-ne harmonic 109.323 125.340 # SOURCE4_SOURCE5 25 1.6082 + angle_coeff @angle:n-c2-nh harmonic 113.384 109.350 # SOURCE4_SOURCE5 61 1.6924 + angle_coeff @angle:no-c2-no harmonic 106.896 113.900 # SOURCE3 1 + angle_coeff @angle:n-c2-ss harmonic 84.310 111.190 # SOURCE4_SOURCE5 24 0.6195 + angle_coeff @angle:oh-c2-oh harmonic 115.431 114.330 # SOURCE3 1 + angle_coeff @angle:o-c2-o harmonic 122.282 121.690 # SOURCE3 1 + angle_coeff @angle:o-c2-oh harmonic 116.614 121.230 # SOURCE4_SOURCE5 12 0.0958 + angle_coeff @angle:o-c2-s harmonic 80.412 127.680 # SOURCE3 2 0.0547 + angle_coeff @angle:os-c2-os harmonic 113.284 115.050 # SOURCE3_SOURCE5 6 1.2203 + angle_coeff @angle:p2-c2-p2 harmonic 106.670 129.800 # SOURCE3 1 + angle_coeff @angle:p3-c2-p3 harmonic 102.865 115.540 # SOURCE3 1 + angle_coeff @angle:p5-c2-p5 harmonic 98.628 121.850 # SOURCE3 1 + angle_coeff @angle:s4-c2-s4 harmonic 63.778 120.320 # SOURCE3 1 + angle_coeff @angle:s4-c2-s6 harmonic 63.877 119.950 # SOURCE3 1 + angle_coeff @angle:s6-c2-s6 harmonic 63.871 119.970 # SOURCE3 1 + angle_coeff @angle:sh-c2-sh harmonic 65.736 110.480 # SOURCE3 1 + angle_coeff @angle:sh-c2-ss harmonic 64.466 117.820 # SOURCE3 1 + angle_coeff @angle:s-c2-s harmonic 64.374 121.670 # SOURCE3 1 + angle_coeff @angle:ss-c2-ss harmonic 65.740 116.400 # SOURCE3_SOURCE5 22 2.3993 + angle_coeff @angle:br-c3-br harmonic 67.612 109.740 # SOURCE4_SOURCE5 24 0.9971 + angle_coeff @angle:br-c3-c1 harmonic 63.834 111.800 # SOURCE2 3 0.2160 + angle_coeff @angle:br-c3-c3 harmonic 63.860 110.010 # SOURCE3_SOURCE5 216 1.1568 + angle_coeff @angle:br-c3-c harmonic 64.284 108.920 # SOURCE4_SOURCE5 35 2.3703 + angle_coeff @angle:br-c3-h1 harmonic 42.433 105.070 # SOURCE3_SOURCE5 175 0.8275 + angle_coeff @angle:br-c3-h2 harmonic 42.082 106.800 # SOURCE4_SOURCE5 25 0.8044 + angle_coeff @angle:br-c3-hc harmonic 42.147 106.500 # SOURCE3 1 + angle_coeff @angle:c1-c3-c1 harmonic 68.433 110.110 # SOURCE2_SOURCE5 11 0.3454 + angle_coeff @angle:c1-c3-c2 harmonic 67.184 110.920 # SOURCE4_SOURCE5 35 0.5903 + angle_coeff @angle:c1-c3-c3 harmonic 66.276 111.710 # SOURCE4_SOURCE5 624 1.1320 + angle_coeff @angle:c1-c3-ca harmonic 67.047 110.890 # SOURCE4_SOURCE5 78 1.1306 + angle_coeff @angle:c1-c3-cc harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 + angle_coeff @angle:c1-c3-cd harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 + angle_coeff @angle:c1-c3-cl harmonic 72.363 110.630 # SOURCE2 3 1.2257 + angle_coeff @angle:c1-c3-h1 harmonic 48.917 109.240 # SOURCE4_SOURCE5 436 0.5758 + angle_coeff @angle:c1-c3-hc harmonic 48.879 109.410 # SOURCE3_SOURCE5 495 0.5104 + angle_coeff @angle:c1-c3-hx harmonic 48.339 112.040 # SOURCE4_SOURCE5 52 0.3815 + angle_coeff @angle:c1-c3-n3 harmonic 84.763 112.730 # SOURCE4_SOURCE5 99 0.7675 + angle_coeff @angle:c1-c3-n4 harmonic 83.658 112.060 # SOURCE4_SOURCE5 25 0.5395 + angle_coeff @angle:c1-c3-n harmonic 84.975 112.380 # SOURCE4_SOURCE5 55 0.9540 + angle_coeff @angle:c1-c3-nh harmonic 84.843 112.570 # SOURCE4_SOURCE5 21 0.9525 + angle_coeff @angle:c1-c3-oh harmonic 87.220 109.440 # SOURCE4_SOURCE5 127 0.9878 + angle_coeff @angle:c1-c3-os harmonic 87.159 109.000 # SOURCE4_SOURCE5 87 0.9531 + angle_coeff @angle:c2-c3-c2 harmonic 65.947 112.000 # SOURCE4_SOURCE5 453 0.8153 + angle_coeff @angle:c2-c3-c3 harmonic 65.459 111.560 # SOURCE4_SOURCE5 9345 1.7373 + angle_coeff @angle:c2-c3-ca harmonic 65.670 112.490 # SOURCE4_SOURCE5 475 1.6791 + angle_coeff @angle:c2-c3-cc harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 + angle_coeff @angle:c2-c3-cd harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 + angle_coeff @angle:c2-c3-ce harmonic 65.863 111.810 # CORR_SOURCE5 85 1.8411 + angle_coeff @angle:c2-c3-cf harmonic 65.867 111.810 # CORR_SOURCE5 85 1.8411 + angle_coeff @angle:c2-c3-cl harmonic 71.864 110.510 # SOURCE4_SOURCE5 60 1.4762 + angle_coeff @angle:c2-c3-cx harmonic 65.673 112.270 # SOURCE4_SOURCE5 76 1.2985 + angle_coeff @angle:c2-c3-cy harmonic 68.713 101.630 # SOURCE4_SOURCE5 164 1.0542 + angle_coeff @angle:c2-c3-f harmonic 88.392 110.760 # SOURCE4_SOURCE5 69 0.5776 + angle_coeff @angle:c2-c3-h1 harmonic 47.561 109.960 # SOURCE3_SOURCE5 2169 0.9645 + angle_coeff @angle:c2-c3-h2 harmonic 47.195 111.690 # SOURCE4_SOURCE5 49 0.9061 + angle_coeff @angle:c2-c3-hc harmonic 47.475 110.360 # SOURCE3_SOURCE5 11033 0.8531 + angle_coeff @angle:c2-c3-hx harmonic 47.293 111.340 # SOURCE4_SOURCE5 56 0.8089 + angle_coeff @angle:c2-c3-n2 harmonic 85.005 108.720 # SOURCE4_SOURCE5 36 1.3485 + angle_coeff @angle:c2-c3-n3 harmonic 84.006 111.420 # SOURCE4_SOURCE5 447 1.5436 + angle_coeff @angle:c2-c3-n harmonic 84.129 111.290 # SOURCE4_SOURCE5 180 1.8899 + angle_coeff @angle:c2-c3-na harmonic 83.365 113.270 # SOURCE4_SOURCE5 78 1.2929 + angle_coeff @angle:c2-c3-nh harmonic 84.408 110.410 # SOURCE4_SOURCE5 134 1.7670 + angle_coeff @angle:c2-c3-oh harmonic 85.495 110.350 # SOURCE4_SOURCE5 793 1.4429 + angle_coeff @angle:c2-c3-os harmonic 85.982 108.560 # SOURCE4_SOURCE5 763 1.7474 + angle_coeff @angle:c2-c3-s4 harmonic 63.867 109.890 # SOURCE4_SOURCE5 19 0.8365 + angle_coeff @angle:c2-c3-ss harmonic 65.117 104.970 # SOURCE3 2 2.2248 + angle_coeff @angle:c3-c3-c3 harmonic 64.888 111.510 # SOURCE3_SOURCE5 61999 1.8007 + angle_coeff @angle:c3-c3-ca harmonic 65.183 112.070 # SOURCE4_SOURCE5 11982 1.5875 + angle_coeff @angle:c3-c3-cc harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 + angle_coeff @angle:c3-c3-cd harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 + angle_coeff @angle:c3-c3-ce harmonic 65.514 110.920 # CORR_SOURCE5 1159 1.8552 + angle_coeff @angle:c3-c3-cf harmonic 65.518 110.920 # CORR_SOURCE5 1159 1.8552 + angle_coeff @angle:c3-c3-cl harmonic 71.515 110.410 # SOURCE3_SOURCE5 824 0.9824 + angle_coeff @angle:c3-c3-cx harmonic 65.198 111.820 # SOURCE4 179 2.4814 + angle_coeff @angle:c3-c3-cy harmonic 64.751 112.390 # SOURCE3_SOURCE5 322 1.3623 + angle_coeff @angle:c3-c3-f harmonic 87.947 109.240 # SOURCE3_SOURCE5 785 1.1106 + angle_coeff @angle:c3-c3-h1 harmonic 46.868 109.560 # SOURCE3_SOURCE5 55294 0.8125 + angle_coeff @angle:c3-c3-h2 harmonic 46.730 110.220 # SOURCE3_SOURCE5 1083 0.9457 + angle_coeff @angle:c3-c3-hc harmonic 46.816 109.800 # SOURCE3_SOURCE5 179054 0.7972 + angle_coeff @angle:c3-c3-hx harmonic 46.677 110.560 # SOURCE3_SOURCE5 1758 0.9658 + angle_coeff @angle:c3-c3-i harmonic 60.771 111.150 # SOURCE3_SOURCE5 48 1.3033 + angle_coeff @angle:c3-c3-n1 harmonic 84.875 108.980 # SOURCE4_SOURCE5 20 0.8416 + angle_coeff @angle:c3-c3-n2 harmonic 84.123 108.800 # SOURCE3_SOURCE5 665 2.1214 + angle_coeff @angle:c3-c3-n3 harmonic 83.305 111.040 # SOURCE3_SOURCE5 12086 1.5519 + angle_coeff @angle:c3-c3-n4 harmonic 80.976 114.210 # SOURCE4_SOURCE5 1537 2.4293 + angle_coeff @angle:c3-c3-n harmonic 83.161 111.610 # SOURCE3_SOURCE5 3543 1.6672 + angle_coeff @angle:c3-c3-na harmonic 82.668 112.880 # SOURCE4_SOURCE5 1677 1.4742 + angle_coeff @angle:c3-c3-nh harmonic 83.541 110.460 # SOURCE4_SOURCE5 3983 1.4189 + angle_coeff @angle:c3-c3-no harmonic 82.142 109.410 # SOURCE4_SOURCE5 111 1.3831 + angle_coeff @angle:c3-c3-o harmonic 85.929 113.010 # SOURCE4_SOURCE5 31 1.2728 + angle_coeff @angle:c3-c3-oh harmonic 84.642 110.190 # SOURCE3_SOURCE5 10188 1.4761 + angle_coeff @angle:c3-c3-os harmonic 85.306 107.970 # SOURCE3_SOURCE5 11384 1.3754 + angle_coeff @angle:c3-c3-p3 harmonic 79.425 113.360 # SOURCE4_SOURCE5 47 0.9033 + angle_coeff @angle:c3-c3-p5 harmonic 80.490 112.020 # SOURCE4_SOURCE5 346 1.5599 + angle_coeff @angle:c3-c3-s4 harmonic 63.481 110.120 # SOURCE4_SOURCE5 117 0.9869 + angle_coeff @angle:c3-c3-s6 harmonic 64.024 110.220 # SOURCE4_SOURCE5 420 1.6420 + angle_coeff @angle:c3-c3-sh harmonic 62.313 113.130 # SOURCE4_SOURCE5 226 1.3868 + angle_coeff @angle:c3-c3-ss harmonic 63.222 110.270 # SOURCE3_SOURCE5 1315 1.5441 + angle_coeff @angle:c3-c3-sy harmonic 64.081 109.920 # SOURCE4_SOURCE5 62 0.8825 + angle_coeff @angle:ca-c3-ca harmonic 65.611 112.240 # SOURCE4_SOURCE5 1062 1.7394 + angle_coeff @angle:ca-c3-cc harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 + angle_coeff @angle:ca-c3-cd harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 + angle_coeff @angle:ca-c3-ce harmonic 65.614 112.210 # SOURCE4_SOURCE5 144 1.2359 + angle_coeff @angle:ca-c3-cl harmonic 71.631 110.980 # SOURCE4_SOURCE5 62 0.7657 + angle_coeff @angle:ca-c3-cx harmonic 65.472 112.510 # SOURCE4_SOURCE5 24 2.0281 + angle_coeff @angle:ca-c3-f harmonic 87.765 111.770 # SOURCE4_SOURCE5 1080 0.3344 + angle_coeff @angle:ca-c3-h1 harmonic 47.477 109.560 # SOURCE3_SOURCE5 3349 0.8812 + angle_coeff @angle:ca-c3-h2 harmonic 47.451 109.700 # SOURCE4_SOURCE5 86 1.1507 + angle_coeff @angle:ca-c3-hc harmonic 47.281 110.470 # SOURCE3_SOURCE5 13973 0.8325 + angle_coeff @angle:ca-c3-hx harmonic 47.099 111.450 # SOURCE4_SOURCE5 113 0.5046 + angle_coeff @angle:ca-c3-n2 harmonic 83.424 112.390 # SOURCE4_SOURCE5 58 1.2061 + angle_coeff @angle:ca-c3-n3 harmonic 83.546 112.160 # SOURCE4_SOURCE5 1125 1.2435 + angle_coeff @angle:ca-c3-n4 harmonic 81.721 113.800 # SOURCE4_SOURCE5 79 2.4049 + angle_coeff @angle:ca-c3-n harmonic 83.537 112.380 # SOURCE4_SOURCE5 512 1.5411 + angle_coeff @angle:ca-c3-na harmonic 83.330 112.870 # SOURCE4_SOURCE5 240 1.5673 + angle_coeff @angle:ca-c3-nc harmonic 85.966 106.510 # SOURCE3 1 + angle_coeff @angle:ca-c3-nd harmonic 85.966 106.510 # SOURCE3 1 + angle_coeff @angle:ca-c3-nh harmonic 83.853 111.390 # SOURCE4_SOURCE5 349 0.9955 + angle_coeff @angle:ca-c3-oh harmonic 85.192 110.620 # SOURCE4_SOURCE5 1007 1.2078 + angle_coeff @angle:ca-c3-os harmonic 85.631 108.950 # SOURCE4_SOURCE5 1123 1.1238 + angle_coeff @angle:ca-c3-p5 harmonic 80.237 113.600 # SOURCE4_SOURCE5 41 1.4171 + angle_coeff @angle:ca-c3-s6 harmonic 63.909 111.540 # SOURCE4_SOURCE5 38 1.2112 + angle_coeff @angle:ca-c3-ss harmonic 63.252 111.020 # SOURCE4_SOURCE5 226 1.6105 + angle_coeff @angle:ca-c3-sx harmonic 63.255 110.780 # SOURCE4_SOURCE5 40 0.6145 + angle_coeff @angle:c-c3-c1 harmonic 66.399 112.380 # SOURCE4_SOURCE5 32 1.1114 + angle_coeff @angle:c-c3-c2 harmonic 65.824 111.330 # SOURCE4_SOURCE5 282 2.0882 + angle_coeff @angle:c-c3-c3 harmonic 65.307 111.040 # SOURCE3_SOURCE5 8161 1.7693 + angle_coeff @angle:c-c3-c harmonic 65.424 111.630 # SOURCE4_SOURCE5 409 2.2030 + angle_coeff @angle:c-c3-ca harmonic 65.788 111.010 # SOURCE4_SOURCE5 1282 1.7239 + angle_coeff @angle:c-c3-cc harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 + angle_coeff @angle:cc-c3-cc harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 + angle_coeff @angle:cc-c3-cd harmonic 66.037 112.890 # SOURCE3_SOURCE5 10 1.0674 + angle_coeff @angle:cc-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 12 1.5999 + angle_coeff @angle:c-c3-cd harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 + angle_coeff @angle:c-c3-ce harmonic 65.523 111.890 # SOURCE4_SOURCE5 75 1.6968 + angle_coeff @angle:cc-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 + angle_coeff @angle:cc-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 + angle_coeff @angle:cc-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 + angle_coeff @angle:cc-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 19 0.7303 + angle_coeff @angle:c-c3-cl harmonic 71.700 110.410 # SOURCE4_SOURCE5 146 1.5057 + angle_coeff @angle:cc-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 32 0.5465 + angle_coeff @angle:cc-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 + angle_coeff @angle:cc-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 12 1.1723 + angle_coeff @angle:cc-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 + angle_coeff @angle:cc-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 18 0.7152 + angle_coeff @angle:cc-c3-nc harmonic 86.190 107.040 # SOURCE3 2 + angle_coeff @angle:cc-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 + angle_coeff @angle:cc-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 + angle_coeff @angle:cc-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 + angle_coeff @angle:cc-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 12 0.7766 + angle_coeff @angle:cc-c3-sh harmonic 62.454 114.020 # SOURCE3 1 + angle_coeff @angle:cc-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 + angle_coeff @angle:c-c3-cx harmonic 65.687 111.150 # SOURCE4_SOURCE5 48 1.8520 + angle_coeff @angle:cd-c3-cd harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 + angle_coeff @angle:cd-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 + angle_coeff @angle:cd-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 + angle_coeff @angle:cd-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 + angle_coeff @angle:cd-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 + angle_coeff @angle:cd-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 + angle_coeff @angle:cd-c3-nd harmonic 86.190 107.040 # SOURCE3 2 + angle_coeff @angle:cd-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 + angle_coeff @angle:cd-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 + angle_coeff @angle:cd-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 + angle_coeff @angle:cd-c3-sh harmonic 62.454 114.020 # SOURCE3 1 + angle_coeff @angle:cd-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 + angle_coeff @angle:ce-c3-ce harmonic 65.825 111.470 # SOURCE4_SOURCE5 53 0.5207 + angle_coeff @angle:ce-c3-cy harmonic 68.161 102.860 # CORR_SOURCE5 72 0.2321 + angle_coeff @angle:ce-c3-h1 harmonic 47.473 109.540 # CORR_SOURCE5 252 0.8257 + angle_coeff @angle:ce-c3-hc harmonic 47.247 110.590 # SOURCE3_SOURCE5 2438 0.7216 + angle_coeff @angle:ce-c3-n3 harmonic 83.687 111.760 # CORR_SOURCE5 83 0.9878 + angle_coeff @angle:ce-c3-n harmonic 84.343 110.220 # SOURCE4_SOURCE5 16 1.1101 + angle_coeff @angle:ce-c3-oh harmonic 84.964 111.190 # SOURCE4_SOURCE5 74 1.5577 + angle_coeff @angle:ce-c3-os harmonic 85.406 109.500 # SOURCE4_SOURCE5 71 1.9041 + angle_coeff @angle:ce-c3-ss harmonic 63.335 110.720 # SOURCE4_SOURCE5 19 1.8179 + angle_coeff @angle:c-c3-f harmonic 88.148 110.000 # SOURCE4_SOURCE5 101 0.9951 + angle_coeff @angle:cf-c3-cy harmonic 68.165 102.860 # CORR_SOURCE5 72 0.2321 + angle_coeff @angle:cf-c3-h1 harmonic 47.479 109.540 # CORR_SOURCE5 252 0.8257 + angle_coeff @angle:cf-c3-hc harmonic 47.253 110.590 # SOURCE3_SOURCE5 2411 0.7279 + angle_coeff @angle:cf-c3-n3 harmonic 83.693 111.760 # CORR_SOURCE5 83 0.9878 + angle_coeff @angle:c-c3-h1 harmonic 47.531 108.220 # SOURCE3_SOURCE5 3484 0.9857 + angle_coeff @angle:c-c3-h2 harmonic 47.215 109.690 # SOURCE4_SOURCE5 100 1.0452 + angle_coeff @angle:c-c3-hc harmonic 47.411 108.770 # SOURCE3_SOURCE5 11750 0.9577 + angle_coeff @angle:c-c3-hx harmonic 47.419 108.850 # SOURCE4_SOURCE5 172 0.8753 + angle_coeff @angle:cl-c3-cl harmonic 81.372 109.330 # SOURCE2_SOURCE5 325 0.5772 + angle_coeff @angle:cl-c3-f harmonic 94.073 109.110 # SOURCE4_SOURCE5 57 0.3048 + angle_coeff @angle:cl-c3-h1 harmonic 48.859 106.780 # SOURCE3_SOURCE5 860 0.4999 + angle_coeff @angle:cl-c3-h2 harmonic 48.808 106.990 # SOURCE4_SOURCE5 147 0.6435 + angle_coeff @angle:cl-c3-hc harmonic 48.661 107.650 # SOURCE2 2 2.2500 + angle_coeff @angle:cl-c3-os harmonic 91.033 110.860 # SOURCE4_SOURCE5 26 1.1129 + angle_coeff @angle:cl-c3-ss harmonic 71.130 112.530 # SOURCE4_SOURCE5 39 1.6937 + angle_coeff @angle:c-c3-n2 harmonic 84.195 109.670 # SOURCE4_SOURCE5 157 1.3668 + angle_coeff @angle:c-c3-n3 harmonic 83.673 111.140 # SOURCE4_SOURCE5 1652 1.6694 + angle_coeff @angle:c-c3-n4 harmonic 82.611 110.730 # SOURCE4_SOURCE5 103 1.8311 + angle_coeff @angle:c-c3-n harmonic 84.540 109.060 # SOURCE3_SOURCE5 905 1.7615 + angle_coeff @angle:c-c3-na harmonic 83.584 111.500 # SOURCE4_SOURCE5 87 1.4027 + angle_coeff @angle:c-c3-nh harmonic 84.373 109.350 # SOURCE4_SOURCE5 106 1.8043 + angle_coeff @angle:c-c3-oh harmonic 85.627 108.790 # SOURCE4_SOURCE5 824 1.3178 + angle_coeff @angle:c-c3-os harmonic 85.254 109.210 # SOURCE3_SOURCE5 429 1.7229 + angle_coeff @angle:c-c3-p5 harmonic 81.107 110.850 # SOURCE4_SOURCE5 32 1.9944 + angle_coeff @angle:c-c3-s6 harmonic 64.058 110.670 # SOURCE4_SOURCE5 14 2.0336 + angle_coeff @angle:c-c3-sh harmonic 63.714 108.720 # SOURCE4_SOURCE5 31 0.7714 + angle_coeff @angle:c-c3-ss harmonic 63.788 108.840 # SOURCE3_SOURCE5 149 1.5563 + angle_coeff @angle:cx-c3-cx harmonic 65.100 113.590 # SOURCE4_SOURCE5 27 1.6971 + angle_coeff @angle:cx-c3-h1 harmonic 47.373 109.680 # SOURCE4_SOURCE5 611 0.9276 + angle_coeff @angle:cx-c3-hc harmonic 47.265 110.180 # SOURCE4_SOURCE5 1366 0.9055 + angle_coeff @angle:cx-c3-hx harmonic 46.751 112.740 # SOURCE4_SOURCE5 30 0.2036 + angle_coeff @angle:cx-c3-n3 harmonic 83.086 113.180 # SOURCE4_SOURCE5 97 1.4360 + angle_coeff @angle:cx-c3-n4 harmonic 86.467 101.460 # SOURCE4_SOURCE5 26 0.1569 + angle_coeff @angle:cx-c3-n harmonic 83.435 112.430 # SOURCE4_SOURCE5 68 0.9548 + angle_coeff @angle:cx-c3-oh harmonic 85.349 109.980 # SOURCE4_SOURCE5 145 1.5821 + angle_coeff @angle:cx-c3-os harmonic 85.968 107.870 # SOURCE4_SOURCE5 126 1.4698 + angle_coeff @angle:cy-c3-h1 harmonic 47.300 108.280 # SOURCE4_SOURCE5 415 1.0438 + angle_coeff @angle:cy-c3-hc harmonic 46.770 110.750 # SOURCE3_SOURCE5 539 0.9100 + angle_coeff @angle:cy-c3-n3 harmonic 82.598 113.410 # SOURCE4_SOURCE5 17 1.2266 + angle_coeff @angle:cy-c3-oh harmonic 84.330 111.490 # SOURCE4_SOURCE5 347 0.5753 + angle_coeff @angle:cy-c3-os harmonic 85.847 107.070 # SOURCE4_SOURCE5 16 1.1669 + angle_coeff @angle:f-c3-f harmonic 121.555 107.360 # SOURCE2_SOURCE5 1178 0.5429 + angle_coeff @angle:f-c3-h1 harmonic 66.869 107.900 # SOURCE3_SOURCE5 181 0.5803 + angle_coeff @angle:f-c3-h2 harmonic 66.607 108.790 # SOURCE3_SOURCE5 66 0.6474 + angle_coeff @angle:f-c3-h3 harmonic 66.233 110.080 # SOURCE4_SOURCE5 45 0.6178 + angle_coeff @angle:f-c3-hc harmonic 66.555 108.920 # SOURCE2 5 3.0534 + angle_coeff @angle:f-c3-n2 harmonic 112.898 110.400 # SOURCE2 3 2.6470 + angle_coeff @angle:f-c3-os harmonic 114.397 110.580 # SOURCE4_SOURCE5 114 1.2792 + angle_coeff @angle:f-c3-p5 harmonic 107.070 107.610 # SOURCE4_SOURCE5 35 1.1282 + angle_coeff @angle:f-c3-s6 harmonic 83.906 109.680 # SOURCE4_SOURCE5 57 0.4273 + angle_coeff @angle:f-c3-ss harmonic 81.883 111.750 # SOURCE4_SOURCE5 38 1.8571 + angle_coeff @angle:h1-c3-h1 harmonic 38.802 108.460 # SOURCE3_SOURCE5 50971 0.8222 + angle_coeff @angle:h1-c3-n1 harmonic 62.841 107.990 # HF/6-31G*_SOURCE5 7 0.3554 + angle_coeff @angle:h1-c3-n2 harmonic 61.133 109.810 # SOURCE3_SOURCE5 957 1.0346 + angle_coeff @angle:h1-c3-n3 harmonic 61.163 109.880 # SOURCE3_SOURCE5 20428 1.2681 + angle_coeff @angle:h1-c3-n harmonic 61.544 108.880 # SOURCE3_SOURCE5 6816 1.0842 + angle_coeff @angle:h1-c3-na harmonic 61.536 108.780 # SOURCE3_SOURCE5 2896 0.9339 + angle_coeff @angle:h1-c3-nc harmonic 61.844 108.570 # SOURCE3 6 0.0764 + angle_coeff @angle:h1-c3-nd harmonic 61.844 108.570 # SOURCE3 6 + angle_coeff @angle:h1-c3-nh harmonic 61.213 109.790 # SOURCE3_SOURCE5 6106 1.0471 + angle_coeff @angle:h1-c3-no harmonic 59.962 105.470 # SOURCE4_SOURCE5 73 0.6459 + angle_coeff @angle:h1-c3-o harmonic 64.637 116.450 # SOURCE3_SOURCE5 25 1.4798 + angle_coeff @angle:h1-c3-oh harmonic 62.540 110.260 # SOURCE3_SOURCE5 7971 1.1355 + angle_coeff @angle:h1-c3-os harmonic 62.377 109.780 # SOURCE3_SOURCE5 19982 1.1092 + angle_coeff @angle:h1-c3-p5 harmonic 54.608 108.270 # SOURCE4_SOURCE5 222 1.1376 + angle_coeff @angle:h1-c3-s4 harmonic 42.850 107.920 # SOURCE3_SOURCE5 496 0.6942 + angle_coeff @angle:h1-c3-s harmonic 41.631 112.370 # SOURCE3_SOURCE5 14 0.4580 + angle_coeff @angle:h1-c3-s6 harmonic 43.600 107.150 # SOURCE3_SOURCE5 1022 0.8992 + angle_coeff @angle:h1-c3-sh harmonic 42.420 108.420 # SOURCE3_SOURCE5 259 1.4350 + angle_coeff @angle:h1-c3-ss harmonic 42.463 108.760 # SOURCE3_SOURCE5 3369 1.0506 + angle_coeff @angle:h1-c3-sx harmonic 42.605 107.700 # SOURCE3_SOURCE5 201 0.7977 + angle_coeff @angle:h1-c3-sy harmonic 43.421 107.880 # SOURCE3_SOURCE5 377 1.1089 + angle_coeff @angle:h2-c3-h2 harmonic 38.523 110.200 # SOURCE3_SOURCE5 677 0.8586 + angle_coeff @angle:h2-c3-i harmonic 39.064 104.990 # SOURCE3 2 + angle_coeff @angle:h2-c3-n2 harmonic 61.031 110.200 # SOURCE3_SOURCE5 69 0.8494 + angle_coeff @angle:h2-c3-n3 harmonic 61.318 109.350 # SOURCE4_SOURCE5 660 0.9086 + angle_coeff @angle:h2-c3-n harmonic 62.008 107.280 # SOURCE4_SOURCE5 692 1.3634 + angle_coeff @angle:h2-c3-na harmonic 61.963 107.310 # SOURCE3_SOURCE5 428 0.9670 + angle_coeff @angle:h2-c3-nc harmonic 61.596 109.470 # SOURCE3 10 0.3133 + angle_coeff @angle:h2-c3-nd harmonic 61.596 109.470 # SOURCE3 10 + angle_coeff @angle:h2-c3-nh harmonic 61.159 110.010 # SOURCE4_SOURCE5 274 1.1061 + angle_coeff @angle:h2-c3-no harmonic 59.186 108.270 # SOURCE3_SOURCE5 13 0.4528 + angle_coeff @angle:h2-c3-o harmonic 66.832 108.970 # SOURCE3 4 + angle_coeff @angle:h2-c3-oh harmonic 62.785 109.430 # SOURCE3_SOURCE5 258 1.6998 + angle_coeff @angle:h2-c3-os harmonic 62.442 109.580 # SOURCE3_SOURCE5 2823 0.6377 + angle_coeff @angle:h2-c3-s4 harmonic 42.969 107.310 # SOURCE3_SOURCE5 29 0.3344 + angle_coeff @angle:h2-c3-s harmonic 42.709 106.750 # SOURCE3 4 + angle_coeff @angle:h2-c3-s6 harmonic 43.728 106.510 # SOURCE4_SOURCE5 67 1.0466 + angle_coeff @angle:h2-c3-sh harmonic 42.525 107.870 # SOURCE3 6 0.4376 + angle_coeff @angle:h2-c3-ss harmonic 42.544 108.330 # SOURCE3_SOURCE5 279 1.1804 + angle_coeff @angle:h3-c3-n3 harmonic 61.502 108.730 # SOURCE4_SOURCE5 32 1.8953 + angle_coeff @angle:h3-c3-nc harmonic 61.634 109.370 # SOURCE3 1 + angle_coeff @angle:h3-c3-nd harmonic 61.634 109.370 # SOURCE3 1 + angle_coeff @angle:h3-c3-nh harmonic 61.116 110.200 # SOURCE4_SOURCE5 11 1.4222 + angle_coeff @angle:h3-c3-os harmonic 61.911 111.510 # SOURCE4_SOURCE5 44 1.4444 + angle_coeff @angle:h3-c3-ss harmonic 42.391 109.090 # SOURCE4_SOURCE5 19 0.8547 + angle_coeff @angle:hc-c3-hc harmonic 38.960 107.580 # SOURCE3_SOURCE5 92717 0.5328 + angle_coeff @angle:hc-c3-i harmonic 39.071 104.990 # SOURCE3 1 + angle_coeff @angle:hc-c3-n2 harmonic 61.220 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-n3 harmonic 61.186 109.800 # SOURCE2 5 2.0070 + angle_coeff @angle:hc-c3-n4 harmonic 60.071 107.900 # SOURCE3 1 + angle_coeff @angle:hc-c3-n harmonic 61.369 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-na harmonic 61.334 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-nh harmonic 60.731 111.540 # SOURCE3 1 + angle_coeff @angle:hc-c3-no harmonic 59.477 107.200 # SOURCE2 1 + angle_coeff @angle:hc-c3-oh harmonic 62.756 109.500 # SOURCE3 1 + angle_coeff @angle:hc-c3-os harmonic 62.686 108.700 # SOURCE2 13 2.3739 + angle_coeff @angle:hc-c3-p2 harmonic 53.633 110.180 # SOURCE3 25 0.4057 + angle_coeff @angle:hc-c3-p3 harmonic 53.601 109.890 # SOURCE3_SOURCE5 528 0.6740 + angle_coeff @angle:hc-c3-p4 harmonic 54.339 109.450 # SOURCE3_SOURCE5 128 0.4042 + angle_coeff @angle:hc-c3-p5 harmonic 54.567 108.430 # SOURCE3_SOURCE5 513 1.0539 + angle_coeff @angle:hc-c3-px harmonic 54.606 109.700 # SOURCE3_SOURCE5 103 0.3664 + angle_coeff @angle:hc-c3-py harmonic 54.373 109.180 # SOURCE3_SOURCE5 74 0.4506 + angle_coeff @angle:hc-c3-s4 harmonic 42.934 107.500 # SOURCE2 1 + angle_coeff @angle:hc-c3-s6 harmonic 43.388 108.200 # SOURCE3 1 + angle_coeff @angle:hc-c3-sh harmonic 42.529 107.870 # SOURCE2 3 2.0981 + angle_coeff @angle:hc-c3-ss harmonic 42.463 108.760 # SOURCE2 3 1.6891 + angle_coeff @angle:hx-c3-hx harmonic 38.782 109.750 # SOURCE3_SOURCE5 5075 0.8234 + angle_coeff @angle:hx-c3-n4 harmonic 60.076 108.010 # SOURCE3_SOURCE5 6129 1.3658 + angle_coeff @angle:i-c3-i harmonic 66.247 113.120 # SOURCE3 1 + angle_coeff @angle:n1-c3-n1 harmonic 112.470 105.070 # HF/6-31G* 1 + angle_coeff @angle:n2-c3-n2 harmonic 107.595 109.680 # SOURCE3_SOURCE5 6 0.6095 + angle_coeff @angle:n2-c3-nh harmonic 106.900 111.270 # SOURCE4_SOURCE5 19 0.9194 + angle_coeff @angle:n2-c3-oh harmonic 108.058 111.890 # SOURCE4_SOURCE5 31 0.2948 + angle_coeff @angle:n2-c3-os harmonic 108.177 111.040 # SOURCE4_SOURCE5 16 1.7109 + angle_coeff @angle:n3-c3-n3 harmonic 106.945 111.230 # SOURCE4_SOURCE5 123 1.3731 + angle_coeff @angle:n3-c3-nc harmonic 106.282 113.290 # SOURCE3 1 + angle_coeff @angle:n3-c3-nd harmonic 106.282 113.290 # SOURCE3 1 + angle_coeff @angle:n3-c3-nh harmonic 107.270 110.610 # SOURCE4_SOURCE5 58 1.2027 + angle_coeff @angle:n3-c3-oh harmonic 108.693 110.700 # SOURCE4_SOURCE5 52 0.9667 + angle_coeff @angle:n3-c3-os harmonic 109.486 108.510 # SOURCE4_SOURCE5 53 1.7879 + angle_coeff @angle:n3-c3-p5 harmonic 103.225 109.410 # SOURCE4_SOURCE5 26 1.5078 + angle_coeff @angle:n3-c3-ss harmonic 81.202 107.380 # SOURCE4_SOURCE5 50 1.6843 + angle_coeff @angle:n4-c3-n4 harmonic 102.708 113.320 # SOURCE3 1 + angle_coeff @angle:na-c3-na harmonic 106.005 113.490 # SOURCE3 1 + angle_coeff @angle:na-c3-os harmonic 109.296 109.030 # SOURCE4_SOURCE5 495 0.5894 + angle_coeff @angle:nc-c3-nc harmonic 107.885 110.610 # SOURCE3 1 + angle_coeff @angle:nc-c3-nh harmonic 106.714 112.430 # SOURCE3 1 + angle_coeff @angle:nc-c3-os harmonic 106.495 115.410 # SOURCE3 3 1.0288 + angle_coeff @angle:nd-c3-nd harmonic 107.885 110.610 # SOURCE3 1 + angle_coeff @angle:nd-c3-nh harmonic 106.714 112.430 # SOURCE3 1 + angle_coeff @angle:nd-c3-os harmonic 106.495 115.410 # SOURCE3 3 + angle_coeff @angle:nh-c3-nh harmonic 109.672 105.870 # SOURCE3 1 + angle_coeff @angle:nh-c3-oh harmonic 107.958 112.270 # SOURCE4_SOURCE5 43 0.9258 + angle_coeff @angle:nh-c3-os harmonic 109.202 109.130 # SOURCE4_SOURCE5 47 1.3529 + angle_coeff @angle:nh-c3-p5 harmonic 101.809 112.500 # SOURCE4 5 1.7371 + angle_coeff @angle:nh-c3-ss harmonic 80.602 109.010 # SOURCE4_SOURCE5 19 2.2237 + angle_coeff @angle:n-c3-n2 harmonic 106.958 111.310 # SOURCE4_SOURCE5 12 1.5991 + angle_coeff @angle:n-c3-n3 harmonic 107.105 111.110 # SOURCE4_SOURCE5 37 1.6907 + angle_coeff @angle:n-c3-n harmonic 106.473 112.650 # SOURCE3_SOURCE5 30 2.1166 + angle_coeff @angle:n-c3-nh harmonic 108.332 108.660 # SOURCE4_SOURCE5 26 1.9779 + angle_coeff @angle:n-c3-oh harmonic 107.902 112.560 # SOURCE4_SOURCE5 75 1.1310 + angle_coeff @angle:no-c3-no harmonic 105.051 105.180 # SOURCE4_SOURCE5 23 1.9192 + angle_coeff @angle:n-c3-os harmonic 109.285 109.130 # SOURCE4_SOURCE5 432 0.8256 + angle_coeff @angle:n-c3-p5 harmonic 102.749 110.520 # SOURCE4_SOURCE5 12 1.2739 + angle_coeff @angle:oh-c3-oh harmonic 110.720 109.900 # SOURCE4_SOURCE5 20 1.5118 + angle_coeff @angle:oh-c3-os harmonic 110.658 109.380 # SOURCE4_SOURCE5 280 1.2270 + angle_coeff @angle:oh-c3-p5 harmonic 104.174 108.680 # SOURCE4_SOURCE5 77 1.3087 + angle_coeff @angle:oh-c3-sh harmonic 78.616 115.460 # SOURCE3 1 + angle_coeff @angle:o-c3-o harmonic 113.472 122.300 # SOURCE3 1 + angle_coeff @angle:os-c3-os harmonic 110.893 108.290 # SOURCE3_SOURCE5 723 1.0283 + angle_coeff @angle:os-c3-p5 harmonic 104.392 107.990 # SOURCE4_SOURCE5 63 2.0205 + angle_coeff @angle:os-c3-ss harmonic 81.130 108.590 # SOURCE4_SOURCE5 54 1.6231 + angle_coeff @angle:p2-c3-p2 harmonic 104.003 110.480 # SOURCE3 1 + angle_coeff @angle:p3-c3-p3 harmonic 103.975 110.160 # SOURCE3 1 + angle_coeff @angle:p5-c3-p5 harmonic 105.046 110.130 # SOURCE4 33 2.4116 + angle_coeff @angle:p5-c3-ss harmonic 81.364 111.480 # SOURCE4_SOURCE5 12 1.9291 + angle_coeff @angle:s4-c3-s4 harmonic 63.477 112.290 # SOURCE3 2 1.2724 + angle_coeff @angle:s4-c3-s6 harmonic 63.526 113.520 # SOURCE3 1 + angle_coeff @angle:s6-c3-s6 harmonic 64.593 111.220 # SOURCE3_SOURCE5 6 1.7567 + angle_coeff @angle:sh-c3-sh harmonic 61.944 116.260 # SOURCE3 1 + angle_coeff @angle:sh-c3-ss harmonic 63.545 110.730 # SOURCE3 1 + angle_coeff @angle:s-c3-s harmonic 60.088 123.350 # SOURCE3 1 + angle_coeff @angle:ss-c3-ss harmonic 63.417 111.440 # SOURCE4_SOURCE5 66 1.6272 + angle_coeff @angle:br-ca-br harmonic 67.710 117.600 # SOURCE3 1 + angle_coeff @angle:br-ca-ca harmonic 64.160 119.300 # SOURCE3_SOURCE5 640 0.4898 + angle_coeff @angle:c1-ca-c1 harmonic 66.786 120.000 # SOURCE3 1 + angle_coeff @angle:c1-ca-ca harmonic 67.736 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-c2 harmonic 69.458 120.000 # SOURCE3 1 + angle_coeff @angle:c2-ca-ca harmonic 68.938 120.600 # SOURCE3 1 + angle_coeff @angle:c3-ca-c2 harmonic 66.051 120.000 # SOURCE3 1 + angle_coeff @angle:c3-ca-c3 harmonic 64.318 116.800 # SOURCE3 1 + angle_coeff @angle:c3-ca-ca harmonic 65.583 120.770 # SOURCE3_SOURCE5 23865 1.2220 + angle_coeff @angle:c3-ca-cp harmonic 65.482 120.630 # CORR 120 + angle_coeff @angle:c3-ca-cq harmonic 65.482 120.630 # CORR 120 + angle_coeff @angle:c3-ca-na harmonic 83.171 118.720 # SOURCE4_SOURCE5 145 1.1124 + angle_coeff @angle:c3-ca-nb harmonic 84.916 116.680 # SOURCE4_SOURCE5 1062 0.9093 + angle_coeff @angle:ca-ca-ca harmonic 68.767 120.020 # SOURCE3_SOURCE5 108055 0.7701 + angle_coeff @angle:ca-ca-cc harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 + angle_coeff @angle:ca-ca-cd harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 + angle_coeff @angle:ca-ca-ce harmonic 66.584 120.820 # SOURCE3_SOURCE5 3962 1.5682 + angle_coeff @angle:ca-ca-cf harmonic 66.584 120.820 # SOURCE3_SOURCE5 3948 1.5732 + angle_coeff @angle:ca-ca-cg harmonic 67.841 120.270 # SOURCE3_SOURCE5 453 0.4194 + angle_coeff @angle:ca-ca-ch harmonic 67.841 120.270 # SOURCE3_SOURCE5 447 0.4218 + angle_coeff @angle:ca-ca-cl harmonic 72.112 119.390 # SOURCE4_SOURCE5 6669 0.5363 + angle_coeff @angle:ca-ca-cp harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 + angle_coeff @angle:ca-ca-cq harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 + angle_coeff @angle:ca-ca-cx harmonic 66.227 120.830 # SOURCE4 71 1.3062 + angle_coeff @angle:ca-ca-cy harmonic 65.564 120.860 # SOURCE4 17 2.0287 + angle_coeff @angle:ca-ca-f harmonic 89.261 118.960 # SOURCE4_SOURCE5 2636 0.3804 + angle_coeff @angle:ca-ca-h4 harmonic 48.561 120.340 # SOURCE3_SOURCE5 2590 0.5568 + angle_coeff @angle:ca-ca-ha harmonic 48.680 119.880 # SOURCE3_SOURCE5 126779 0.4424 + angle_coeff @angle:ca-ca-i harmonic 61.098 119.110 # SOURCE3_SOURCE5 123 0.9416 + angle_coeff @angle:ca-ca-n1 harmonic 88.104 119.780 # HF/6-31G*_SOURCE5 14 0.4655 + angle_coeff @angle:ca-ca-n2 harmonic 89.100 119.570 # SOURCE3 1 + angle_coeff @angle:ca-ca-n4 harmonic 83.650 119.310 # SOURCE3_SOURCE5 63 1.4960 + angle_coeff @angle:ca-ca-n harmonic 85.629 120.190 # SOURCE3_SOURCE5 3041 2.2480 + angle_coeff @angle:ca-ca-na harmonic 87.167 118.340 # SOURCE3 54 3.6168 + angle_coeff @angle:ca-ca-nb harmonic 86.849 122.940 # SOURCE3_SOURCE5 5507 1.1495 + angle_coeff @angle:ca-ca-nc harmonic 87.635 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-nd harmonic 87.635 119.720 # SOURCE3 22 3.3994 + angle_coeff @angle:ca-ca-ne harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 + angle_coeff @angle:ca-ca-nf harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 + angle_coeff @angle:ca-ca-nh harmonic 86.163 120.950 # SOURCE3_SOURCE5 4970 1.2168 + angle_coeff @angle:ca-ca-no harmonic 84.250 119.010 # SOURCE3_SOURCE5 854 0.7071 + angle_coeff @angle:ca-ca-o harmonic 89.534 123.260 # SOURCE4_SOURCE5 35 1.2620 + angle_coeff @angle:ca-ca-oh harmonic 87.211 119.900 # SOURCE3_SOURCE5 6384 1.7827 + angle_coeff @angle:ca-ca-os harmonic 87.289 119.200 # SOURCE3 52 0.5240 + angle_coeff @angle:ca-ca-p2 harmonic 81.329 114.360 # SOURCE3 1 + angle_coeff @angle:ca-ca-p3 harmonic 79.908 120.010 # SOURCE3_SOURCE5 24 1.1566 + angle_coeff @angle:ca-ca-p4 harmonic 80.525 120.300 # SOURCE3 1 + angle_coeff @angle:ca-ca-p5 harmonic 80.938 120.240 # SOURCE4_SOURCE5 15 0.0746 + angle_coeff @angle:ca-ca-pe harmonic 79.643 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-pf harmonic 79.643 120.450 # SOURCE3 20 0.2719 + angle_coeff @angle:ca-ca-px harmonic 79.761 120.530 # SOURCE3 10 0.4509 + angle_coeff @angle:ca-ca-py harmonic 80.172 120.250 # SOURCE3_SOURCE5 75 1.5353 + angle_coeff @angle:ca-ca-s4 harmonic 63.561 119.150 # SOURCE3 1 + angle_coeff @angle:ca-ca-s6 harmonic 63.822 120.430 # SOURCE4_SOURCE5 89 1.1843 + angle_coeff @angle:ca-ca-s harmonic 64.056 122.550 # SOURCE3 4 + angle_coeff @angle:ca-ca-sh harmonic 63.072 121.780 # SOURCE4_SOURCE5 54 1.3490 + angle_coeff @angle:ca-ca-ss harmonic 63.530 120.060 # SOURCE3_SOURCE5 1341 2.1632 + angle_coeff @angle:ca-ca-sx harmonic 62.473 119.280 # SOURCE3_SOURCE5 140 1.1919 + angle_coeff @angle:ca-ca-sy harmonic 63.407 119.420 # SOURCE3_SOURCE5 1489 0.7572 + angle_coeff @angle:c-ca-c3 harmonic 64.497 118.060 # SOURCE3 1 + angle_coeff @angle:c-ca-c harmonic 64.519 120.000 # SOURCE3 1 + angle_coeff @angle:c-ca-ca harmonic 66.351 120.330 # SOURCE3_SOURCE5 8320 1.9221 + angle_coeff @angle:cc-ca-cp harmonic 66.010 124.300 # SOURCE4_SOURCE5 20 0.6423 + angle_coeff @angle:cc-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 + angle_coeff @angle:cd-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 + angle_coeff @angle:ce-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 38 0.5659 + angle_coeff @angle:ce-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 + angle_coeff @angle:cf-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 + angle_coeff @angle:cg-ca-cp harmonic 67.320 121.530 # SOURCE4_SOURCE5 24 0.1831 + angle_coeff @angle:c-ca-ha harmonic 46.900 115.900 # SOURCE3 1 + angle_coeff @angle:cl-ca-cl harmonic 80.510 118.720 # SOURCE3 1 + angle_coeff @angle:cl-ca-cp harmonic 71.726 120.390 # SOURCE4_SOURCE5 52 0.5449 + angle_coeff @angle:cl-ca-nb harmonic 92.329 116.180 # SOURCE4_SOURCE5 152 0.5909 + angle_coeff @angle:c-ca-nb harmonic 85.429 117.780 # SOURCE4_SOURCE5 262 1.1507 + angle_coeff @angle:c-ca-nc harmonic 80.781 130.800 # SOURCE3 1 + angle_coeff @angle:c-ca-nd harmonic 80.781 130.800 # SOURCE3 1 + angle_coeff @angle:cp-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 46 0.2425 + angle_coeff @angle:cp-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 62 0.4243 + angle_coeff @angle:cp-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 + angle_coeff @angle:cp-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 514 0.5055 + angle_coeff @angle:cp-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 129 0.8391 + angle_coeff @angle:cp-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 30 0.5872 + angle_coeff @angle:cp-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 41 1.3658 + angle_coeff @angle:cp-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 24 1.8180 + angle_coeff @angle:cp-ca-sy harmonic 65.646 111.180 # CORR 4 + angle_coeff @angle:cq-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 + angle_coeff @angle:cq-ca-sy harmonic 65.646 111.180 # CORR 4 + angle_coeff @angle:f-ca-f harmonic 116.252 117.500 # SOURCE3 1 + angle_coeff @angle:f-ca-nb harmonic 116.437 114.670 # SOURCE4_SOURCE5 42 0.4295 + angle_coeff @angle:h4-ca-n harmonic 61.444 116.020 # SOURCE3 1 + angle_coeff @angle:h4-ca-na harmonic 62.367 116.320 # SOURCE3_SOURCE5 394 0.4031 + angle_coeff @angle:h4-ca-nb harmonic 64.066 116.030 # SOURCE3_SOURCE5 2217 0.2861 + angle_coeff @angle:h4-ca-nc harmonic 62.978 118.360 # SOURCE3 1 + angle_coeff @angle:h4-ca-nd harmonic 62.978 118.360 # SOURCE3 1 + angle_coeff @angle:h4-ca-os harmonic 64.330 111.150 # SOURCE3 1 + angle_coeff @angle:h4-ca-ss harmonic 42.528 116.190 # SOURCE3 1 + angle_coeff @angle:h5-ca-nb harmonic 64.141 115.820 # SOURCE3_SOURCE5 618 0.3893 + angle_coeff @angle:h5-ca-nc harmonic 62.019 122.110 # SOURCE3 1 + angle_coeff @angle:h5-ca-nd harmonic 62.019 122.110 # SOURCE3 1 + angle_coeff @angle:ha-ca-n2 harmonic 65.427 116.000 # SOURCE2 1 + angle_coeff @angle:ha-ca-p2 harmonic 51.256 122.560 # SOURCE3 1 + angle_coeff @angle:i-ca-i harmonic 67.026 119.280 # SOURCE3 1 + angle_coeff @angle:n1-ca-n1 harmonic 114.391 117.030 # HF/6-31G* 1 + angle_coeff @angle:n2-ca-n2 harmonic 115.741 120.000 # SOURCE3 1 + angle_coeff @angle:n2-ca-na harmonic 112.235 119.600 # SOURCE3 1 + angle_coeff @angle:n4-ca-n4 harmonic 102.984 116.820 # SOURCE3 1 + angle_coeff @angle:na-ca-na harmonic 115.064 107.620 # SOURCE4_SOURCE5 11 0.8382 + angle_coeff @angle:na-ca-nb harmonic 107.575 127.090 # SOURCE4_SOURCE5 708 1.9791 + angle_coeff @angle:na-ca-nh harmonic 109.505 118.660 # SOURCE4_SOURCE5 73 0.9977 + angle_coeff @angle:nb-ca-nb harmonic 109.369 127.260 # SOURCE4_SOURCE5 1586 1.1854 + angle_coeff @angle:nb-ca-nc harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 + angle_coeff @angle:nb-ca-nd harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 + angle_coeff @angle:nb-ca-nh harmonic 112.063 116.940 # SOURCE4_SOURCE5 2042 0.7868 + angle_coeff @angle:nb-ca-oh harmonic 112.676 117.680 # SOURCE4_SOURCE5 182 0.7979 + angle_coeff @angle:nb-ca-os harmonic 111.458 119.720 # SOURCE4_SOURCE5 194 0.7211 + angle_coeff @angle:nb-ca-sh harmonic 80.990 117.610 # SOURCE4_SOURCE5 35 1.3741 + angle_coeff @angle:nb-ca-ss harmonic 80.595 118.800 # SOURCE4_SOURCE5 111 1.8247 + angle_coeff @angle:nc-ca-nc harmonic 107.717 128.740 # SOURCE3 1 + angle_coeff @angle:nc-ca-nh harmonic 110.670 118.860 # SOURCE3 1 + angle_coeff @angle:nd-ca-nd harmonic 107.717 128.740 # SOURCE3 1 + angle_coeff @angle:nd-ca-nh harmonic 110.670 118.860 # SOURCE3 1 + angle_coeff @angle:nh-ca-nh harmonic 108.376 120.980 # SOURCE3 1 + angle_coeff @angle:n-ca-nc harmonic 107.316 123.860 # SOURCE3 1 + angle_coeff @angle:n-ca-nd harmonic 107.316 123.860 # SOURCE3 1 + angle_coeff @angle:n-ca-nh harmonic 109.547 116.160 # SOURCE3 1 + angle_coeff @angle:no-ca-no harmonic 103.915 117.140 # SOURCE3 1 + angle_coeff @angle:oh-ca-oh harmonic 110.589 120.000 # SOURCE3 1 + angle_coeff @angle:o-ca-o harmonic 118.708 126.820 # SOURCE3 1 + angle_coeff @angle:os-ca-os harmonic 113.107 113.730 # SOURCE3 1 + angle_coeff @angle:p2-ca-p2 harmonic 100.107 121.200 # SOURCE3 1 + angle_coeff @angle:p3-ca-p3 harmonic 100.783 121.460 # SOURCE3 1 + angle_coeff @angle:p5-ca-p5 harmonic 103.117 120.000 # SOURCE3 1 + angle_coeff @angle:s4-ca-s4 harmonic 66.946 105.810 # SOURCE3 1 + angle_coeff @angle:s6-ca-s6 harmonic 67.745 105.810 # SOURCE3 1 + angle_coeff @angle:sh-ca-sh harmonic 63.051 120.240 # SOURCE3 1 + angle_coeff @angle:s-ca-s harmonic 63.293 125.140 # SOURCE3 1 + angle_coeff @angle:ss-ca-ss harmonic 64.440 115.150 # SOURCE3 1 + angle_coeff @angle:br-c-br harmonic 67.692 113.100 # SOURCE3 1 + angle_coeff @angle:br-c-c3 harmonic 64.598 110.740 # SOURCE3 1 + angle_coeff @angle:br-c-o harmonic 78.490 121.460 # SOURCE3 5 1.6264 + angle_coeff @angle:c1-c-c1 harmonic 67.194 115.320 # SOURCE3 1 + angle_coeff @angle:c1-c-o harmonic 87.628 122.340 # SOURCE3 1 + angle_coeff @angle:c2-c-c2 harmonic 69.337 116.780 # SOURCE3 1 + angle_coeff @angle:c2-c-ha harmonic 49.151 115.950 # SOURCE3 1 + angle_coeff @angle:c2-c-o harmonic 91.182 119.120 # SOURCE3 2 + angle_coeff @angle:c2-c-s harmonic 66.780 119.160 # SOURCE3 2 + angle_coeff @angle:c3-c-c3 harmonic 64.041 116.500 # SOURCE3_SOURCE5 720 1.3034 + angle_coeff @angle:c3-c-ca harmonic 64.216 118.400 # SOURCE4_SOURCE5 749 1.4991 + angle_coeff @angle:c3-c-cc harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 + angle_coeff @angle:c3-c-cd harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 + angle_coeff @angle:c3-c-ce harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 + angle_coeff @angle:c3-c-cf harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 + angle_coeff @angle:c3-c-cg harmonic 65.958 115.000 # SOURCE2 1 + angle_coeff @angle:c3-c-ch harmonic 65.958 115.000 # SOURCE2 1 + angle_coeff @angle:c3-c-cl harmonic 71.237 111.990 # SOURCE3 2 0.0125 + angle_coeff @angle:c3-c-f harmonic 88.418 110.700 # SOURCE2 1 + angle_coeff @angle:c3-c-h4 harmonic 46.112 114.640 # SOURCE4_SOURCE5 193 0.4989 + angle_coeff @angle:c3-c-ha harmonic 46.047 115.220 # SOURCE3 15 0.3181 + angle_coeff @angle:c3-c-i harmonic 60.388 112.940 # SOURCE3 1 + angle_coeff @angle:c3-c-n2 harmonic 83.534 114.530 # SOURCE3 1 + angle_coeff @angle:c3-c-n4 harmonic 81.106 112.260 # SOURCE3 2 + angle_coeff @angle:c3-c-n harmonic 84.266 115.180 # SOURCE3_SOURCE5 2997 1.3885 + angle_coeff @angle:c3-c-ne harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 + angle_coeff @angle:c3-c-nf harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 + angle_coeff @angle:c3-c-o harmonic 84.552 123.200 # SOURCE3_SOURCE5 10083 1.8011 + angle_coeff @angle:c3-c-oh harmonic 85.803 112.730 # SOURCE3_SOURCE5 1989 1.3796 + angle_coeff @angle:c3-c-os harmonic 86.419 110.720 # SOURCE3_SOURCE5 1786 0.9391 + angle_coeff @angle:c3-c-p3 harmonic 77.773 116.420 # SOURCE3 3 0.1291 + angle_coeff @angle:c3-c-p5 harmonic 76.995 118.900 # SOURCE3 1 + angle_coeff @angle:c3-c-pe harmonic 77.418 114.850 # SOURCE3 1 + angle_coeff @angle:c3-c-pf harmonic 77.418 114.850 # SOURCE3 1 + angle_coeff @angle:c3-c-px harmonic 77.387 115.600 # SOURCE3 1 + angle_coeff @angle:c3-c-py harmonic 77.698 118.160 # SOURCE3 3 1.0735 + angle_coeff @angle:c3-c-s4 harmonic 61.352 114.790 # SOURCE3 1 + angle_coeff @angle:c3-c-s6 harmonic 61.371 114.720 # SOURCE3 1 + angle_coeff @angle:c3-c-s harmonic 63.941 123.150 # SOURCE3_SOURCE5 66 1.3121 + angle_coeff @angle:c3-c-sh harmonic 63.752 112.650 # SOURCE3_SOURCE5 9 1.5127 + angle_coeff @angle:c3-c-ss harmonic 63.438 113.510 # SOURCE3_SOURCE5 65 0.9334 + angle_coeff @angle:c3-c-sx harmonic 61.201 113.970 # SOURCE3 3 0.0610 + angle_coeff @angle:c3-c-sy harmonic 61.612 114.280 # SOURCE3 3 0.7341 + angle_coeff @angle:ca-c-ca harmonic 65.033 118.110 # SOURCE4_SOURCE5 506 1.8633 + angle_coeff @angle:ca-c-cc harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 + angle_coeff @angle:ca-c-cd harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 + angle_coeff @angle:ca-c-ce harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 + angle_coeff @angle:ca-c-cf harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 + angle_coeff @angle:ca-c-h4 harmonic 46.911 115.140 # SOURCE4_SOURCE5 122 0.7683 + angle_coeff @angle:ca-c-ha harmonic 47.184 114.120 # SOURCE3 1 + angle_coeff @angle:ca-c-n harmonic 85.392 115.250 # SOURCE4_SOURCE5 1494 1.4889 + angle_coeff @angle:ca-c-ne harmonic 85.290 114.710 # SOURCE4_SOURCE5 14 0.5855 + angle_coeff @angle:ca-c-o harmonic 86.207 122.600 # SOURCE3_SOURCE5 3960 1.5802 + angle_coeff @angle:ca-c-oh harmonic 86.748 113.450 # SOURCE4_SOURCE5 656 0.8414 + angle_coeff @angle:ca-c-os harmonic 86.963 112.440 # SOURCE3_SOURCE5 493 0.8365 + angle_coeff @angle:ca-c-s harmonic 64.593 122.680 # SOURCE4_SOURCE5 32 1.3788 + angle_coeff @angle:ca-c-sh harmonic 62.515 118.630 # SOURCE3 1 + angle_coeff @angle:ca-c-ss harmonic 63.406 115.050 # SOURCE4_SOURCE5 37 1.0695 + angle_coeff @angle:br-cc-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 32 1.1116 + angle_coeff @angle:br-cc-cc harmonic 63.389 124.050 # SOURCE4_SOURCE5 31 1.9388 + angle_coeff @angle:br-cc-cd harmonic 63.686 124.230 # SOURCE4_SOURCE5 116 2.3356 + angle_coeff @angle:br-cc-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 19 0.8500 + angle_coeff @angle:c2-cc-c3 harmonic 65.262 126.110 # SOURCE3 2 + angle_coeff @angle:c2-cc-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 + angle_coeff @angle:c2-cc-cc harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 + angle_coeff @angle:c2-cc-cd harmonic 71.286 117.020 # SOURCE3 2 0.0703 + angle_coeff @angle:c2-cc-ha harmonic 49.231 122.720 # SOURCE3 2 0.0092 + angle_coeff @angle:c2-cc-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 + angle_coeff @angle:c2-cc-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 + angle_coeff @angle:c-c-c3 harmonic 63.621 116.170 # SOURCE3_SOURCE5 58 1.1332 + angle_coeff @angle:c3-cc-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 + angle_coeff @angle:c3-cc-cc harmonic 66.709 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cc-cd harmonic 66.802 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cc-cf harmonic 67.395 117.840 # CORR 2 + angle_coeff @angle:c3-cc-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cc-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 + angle_coeff @angle:c3-cc-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 + angle_coeff @angle:c3-cc-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 + angle_coeff @angle:c3-cc-nc harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 + angle_coeff @angle:c3-cc-nd harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 + angle_coeff @angle:c3-cc-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 + angle_coeff @angle:c3-cc-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 + angle_coeff @angle:c-c-c harmonic 64.391 111.680 # SOURCE3 2 6.1226 + angle_coeff @angle:c-c-ca harmonic 63.623 118.600 # SOURCE4_SOURCE5 90 1.0263 + angle_coeff @angle:ca-cc-cc harmonic 69.336 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cc-cd harmonic 69.802 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cc-ce harmonic 64.258 127.010 # SOURCE4_SOURCE5 38 1.6763 + angle_coeff @angle:ca-cc-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 + angle_coeff @angle:ca-cc-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cc-n harmonic 85.642 117.670 # CORR 18 + angle_coeff @angle:ca-cc-nc harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 + angle_coeff @angle:ca-cc-nd harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 + angle_coeff @angle:ca-cc-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 20 1.7636 + angle_coeff @angle:ca-cc-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 + angle_coeff @angle:ca-cc-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 + angle_coeff @angle:ca-cc-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 + angle_coeff @angle:c-cc-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 + angle_coeff @angle:c-cc-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 + angle_coeff @angle:c-cc-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 + angle_coeff @angle:c-c-cc harmonic 66.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:c-cc-ca harmonic 65.005 122.950 # SOURCE3 1 + angle_coeff @angle:c-cc-cc harmonic 65.674 122.690 # SOURCE3 2 + angle_coeff @angle:cc-c-cc harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 + angle_coeff @angle:cc-cc-cc harmonic 70.129 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cc-cc-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cc-ce harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 + angle_coeff @angle:cc-cc-cf harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 + angle_coeff @angle:cc-cc-cg harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 + angle_coeff @angle:c-cc-cd harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 + angle_coeff @angle:cc-c-cd harmonic 67.592 112.790 # SOURCE3 1 + angle_coeff @angle:c-cc-ce harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 + angle_coeff @angle:cc-c-ce harmonic 66.433 115.570 # SOURCE4_SOURCE5 14 1.2088 + angle_coeff @angle:cc-cc-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 26 0.8983 + angle_coeff @angle:c-cc-cg harmonic 67.046 117.880 # SOURCE4_SOURCE5 26 0.6759 + angle_coeff @angle:cc-cc-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 + angle_coeff @angle:cc-cc-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 + angle_coeff @angle:c-cc-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 + angle_coeff @angle:cc-cc-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 + angle_coeff @angle:cc-cc-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cc-cc-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 865 1.5665 + angle_coeff @angle:cc-cc-nc harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 + angle_coeff @angle:cc-cc-nd harmonic 90.306 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cc-cc-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 + angle_coeff @angle:cc-cc-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 + angle_coeff @angle:cc-cc-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 + angle_coeff @angle:cc-cc-pd harmonic 84.517 115.360 # SOURCE3 84 + angle_coeff @angle:cc-cc-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 + angle_coeff @angle:cc-cc-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 20 0.9014 + angle_coeff @angle:c-c-cd harmonic 66.020 111.670 # SOURCE3 4 5.5146 + angle_coeff @angle:cd-cc-cd harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 + angle_coeff @angle:cd-cc-ce harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 + angle_coeff @angle:cd-cc-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 + angle_coeff @angle:cd-cc-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 82 0.7206 + angle_coeff @angle:cd-cc-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 + angle_coeff @angle:cd-cc-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 + angle_coeff @angle:cd-cc-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 + angle_coeff @angle:cd-cc-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 + angle_coeff @angle:cd-cc-nc harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 + angle_coeff @angle:cd-cc-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 + angle_coeff @angle:cd-cc-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 314 1.4409 + angle_coeff @angle:cd-cc-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 + angle_coeff @angle:cd-cc-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cd-cc-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 + angle_coeff @angle:cd-cc-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 + angle_coeff @angle:ce-cc-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 + angle_coeff @angle:ce-cc-nc harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 + angle_coeff @angle:ce-cc-nd harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 + angle_coeff @angle:ce-cc-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 + angle_coeff @angle:ce-cc-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 + angle_coeff @angle:c-cc-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 49 0.4690 + angle_coeff @angle:cg-cc-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 12 0.9695 + angle_coeff @angle:cg-cc-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 27 0.9221 + angle_coeff @angle:cc-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 25 0.5124 + angle_coeff @angle:c-cc-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 + angle_coeff @angle:cl-cc-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 37 0.7206 + angle_coeff @angle:cl-cc-nd harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 + angle_coeff @angle:cl-cc-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 27 0.9529 + angle_coeff @angle:c-cc-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 + angle_coeff @angle:c-cc-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 + angle_coeff @angle:cc-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 + angle_coeff @angle:c-cc-nc harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 + angle_coeff @angle:cc-c-nd harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 + angle_coeff @angle:c-cc-nd harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 + angle_coeff @angle:c-cc-ne harmonic 84.503 119.880 # SOURCE4 6 0.3139 + angle_coeff @angle:cc-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 + angle_coeff @angle:c-cc-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 + angle_coeff @angle:cc-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 + angle_coeff @angle:c-cc-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 + angle_coeff @angle:cc-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 + angle_coeff @angle:cc-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 69 1.9867 + angle_coeff @angle:cc-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 42 0.9902 + angle_coeff @angle:cx-cc-nd harmonic 83.147 127.820 # SOURCE4_SOURCE5 27 1.6288 + angle_coeff @angle:cx-cc-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 23 0.0923 + angle_coeff @angle:cd-c-cd harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 + angle_coeff @angle:cd-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 37 0.1506 + angle_coeff @angle:cd-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 + angle_coeff @angle:cd-c-nc harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 + angle_coeff @angle:cd-c-nd harmonic 86.534 113.750 # SOURCE4_SOURCE5 28 0.0860 + angle_coeff @angle:cd-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 + angle_coeff @angle:cd-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 + angle_coeff @angle:cd-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 + angle_coeff @angle:ce-c-ce harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 + angle_coeff @angle:ce-c-cf harmonic 65.875 116.370 # SOURCE4_SOURCE5 31 1.3157 + angle_coeff @angle:ce-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 19 0.7227 + angle_coeff @angle:ce-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 113 0.4718 + angle_coeff @angle:ce-c-ha harmonic 47.181 115.220 # SOURCE3 7 2.4188 + angle_coeff @angle:ce-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 + angle_coeff @angle:ce-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 + angle_coeff @angle:ce-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 + angle_coeff @angle:ce-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 + angle_coeff @angle:ce-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 + angle_coeff @angle:ce-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 13 0.5852 + angle_coeff @angle:cf-c-cf harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 + angle_coeff @angle:cf-c-ha harmonic 47.181 115.220 # SOURCE3 7 + angle_coeff @angle:cf-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 + angle_coeff @angle:cf-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 + angle_coeff @angle:cf-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 + angle_coeff @angle:cf-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 + angle_coeff @angle:cf-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 + angle_coeff @angle:cg-c-cg harmonic 67.584 115.380 # SOURCE3 1 + angle_coeff @angle:cg-c-ha harmonic 48.322 113.900 # SOURCE2 1 + angle_coeff @angle:cg-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 + angle_coeff @angle:c-c-h4 harmonic 45.243 115.800 # SOURCE4_SOURCE5 17 0.7492 + angle_coeff @angle:h4-cc-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 + angle_coeff @angle:h4-cc-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 + angle_coeff @angle:h4-cc-nc harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 + angle_coeff @angle:h4-cc-nd harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 + angle_coeff @angle:h4-cc-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 + angle_coeff @angle:h4-cc-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 + angle_coeff @angle:h5-cc-n harmonic 62.737 115.700 # CORR_SOURCE5 41 0.7665 + angle_coeff @angle:h5-cc-na harmonic 61.226 121.550 # SOURCE3_SOURCE5 1138 0.7136 + angle_coeff @angle:h5-cc-nc harmonic 61.265 122.920 # SOURCE3_SOURCE5 136 0.3532 + angle_coeff @angle:h5-cc-nd harmonic 62.461 125.520 # SOURCE3_SOURCE5 1309 0.7276 + angle_coeff @angle:h5-cc-os harmonic 63.110 116.830 # SOURCE3_SOURCE5 42 1.3051 + angle_coeff @angle:h5-cc-ss harmonic 42.272 121.020 # SOURCE3_SOURCE5 46 0.6462 + angle_coeff @angle:c-c-ha harmonic 45.358 115.430 # SOURCE2 3 0.6549 + angle_coeff @angle:ha-cc-na harmonic 61.218 121.500 # SOURCE2 1 + angle_coeff @angle:ha-cc-nc harmonic 62.898 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cc-nd harmonic 64.154 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cc-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cc-pd harmonic 54.856 121.760 # SOURCE3 84 + angle_coeff @angle:ha-cc-ss harmonic 42.168 121.640 # SOURCE2 5 1.3276 + angle_coeff @angle:ch-c-ch harmonic 67.584 115.380 # SOURCE3 1 + angle_coeff @angle:ch-c-ha harmonic 48.322 113.900 # SOURCE2 1 + angle_coeff @angle:ch-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 + angle_coeff @angle:cl-c-cl harmonic 80.720 111.300 # SOURCE2 1 + angle_coeff @angle:cl-c-f harmonic 93.155 112.000 # SOURCE2 1 + angle_coeff @angle:cl-c-ha harmonic 48.221 109.900 # SOURCE2 1 + angle_coeff @angle:cl-c-o harmonic 89.044 120.690 # SOURCE3_SOURCE5 14 1.1076 + angle_coeff @angle:cl-c-s harmonic 69.852 127.600 # SOURCE2 1 + angle_coeff @angle:c-c-n harmonic 84.329 112.740 # SOURCE4_SOURCE5 157 2.1770 + angle_coeff @angle:na-cc-nc harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 + angle_coeff @angle:na-cc-nd harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 + angle_coeff @angle:na-cc-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 162 0.8093 + angle_coeff @angle:na-cc-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 39 0.9806 + angle_coeff @angle:na-cc-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 32 0.3937 + angle_coeff @angle:na-cc-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 15 1.7292 + angle_coeff @angle:nc-cc-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 + angle_coeff @angle:nc-cc-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 + angle_coeff @angle:nc-cc-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 17 0.8729 + angle_coeff @angle:nc-cc-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 + angle_coeff @angle:nd-cc-nd harmonic 110.827 128.070 # SOURCE4_SOURCE5 17 0.2580 + angle_coeff @angle:nd-cc-ne harmonic 107.796 129.010 # SOURCE4_SOURCE5 20 1.2478 + angle_coeff @angle:nd-cc-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 + angle_coeff @angle:nd-cc-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 80 0.3006 + angle_coeff @angle:nd-cc-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 + angle_coeff @angle:nd-cc-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 + angle_coeff @angle:nd-cc-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 18 0.8493 + angle_coeff @angle:nd-cc-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cc-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 33 0.6804 + angle_coeff @angle:nd-cc-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 33 1.1587 + angle_coeff @angle:ne-cc-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 17 0.2106 + angle_coeff @angle:nh-cc-nh harmonic 111.696 115.960 # SOURCE3 1 + angle_coeff @angle:nh-cc-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 + angle_coeff @angle:nh-cc-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 + angle_coeff @angle:n-cc-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 28 1.2985 + angle_coeff @angle:n-cc-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 + angle_coeff @angle:n-cc-nc harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 + angle_coeff @angle:n-cc-nd harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 + angle_coeff @angle:n-cc-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 + angle_coeff @angle:no-cc-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 144 0.2521 + angle_coeff @angle:no-cc-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 33 0.2051 + angle_coeff @angle:n-cc-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 + angle_coeff @angle:c-c-o harmonic 84.325 120.850 # SOURCE4_SOURCE5 712 2.3365 + angle_coeff @angle:c-c-oh harmonic 85.170 112.070 # SOURCE3_SOURCE5 45 0.4339 + angle_coeff @angle:c-c-os harmonic 85.272 111.410 # SOURCE4_SOURCE5 34 0.4577 + angle_coeff @angle:os-cc-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 + angle_coeff @angle:ss-cc-ss harmonic 63.639 121.370 # CORR 22 + angle_coeff @angle:ss-cc-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 + angle_coeff @angle:cx-c-cx harmonic 87.506 64.600 # SOURCE2 1 + angle_coeff @angle:cx-c-n harmonic 85.409 114.530 # SOURCE4_SOURCE5 60 1.3306 + angle_coeff @angle:cx-c-o harmonic 85.839 122.750 # SOURCE4_SOURCE5 366 2.2300 + angle_coeff @angle:cx-c-oh harmonic 86.840 112.520 # SOURCE4_SOURCE5 43 1.3576 + angle_coeff @angle:cx-c-os harmonic 87.109 111.390 # SOURCE4_SOURCE5 64 2.0118 + angle_coeff @angle:cy-c-cy harmonic 70.855 91.910 # SOURCE2_SOURCE5 12 0.9858 + angle_coeff @angle:cy-c-n harmonic 93.471 91.560 # SOURCE4_SOURCE5 619 0.5374 + angle_coeff @angle:cy-c-o harmonic 79.625 135.160 # SOURCE4_SOURCE5 665 1.3860 + angle_coeff @angle:cy-c-oh harmonic 85.029 112.180 # SOURCE4_SOURCE5 17 0.7869 + angle_coeff @angle:cy-c-os harmonic 92.339 94.790 # SOURCE4_SOURCE5 25 0.5353 + angle_coeff @angle:c2-cd-c3 harmonic 65.262 126.110 # SOURCE3 2 + angle_coeff @angle:c2-cd-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 + angle_coeff @angle:c2-cd-cc harmonic 71.286 117.020 # SOURCE3 2 + angle_coeff @angle:c2-cd-cd harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 + angle_coeff @angle:c2-cd-ha harmonic 49.231 122.720 # SOURCE3 2 + angle_coeff @angle:c2-cd-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 + angle_coeff @angle:c2-cd-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 + angle_coeff @angle:c3-cd-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 + angle_coeff @angle:c3-cd-cc harmonic 66.802 119.450 # SOURCE3 35 8.2040 + angle_coeff @angle:c3-cd-cd harmonic 66.709 115.970 # SOURCE3 4 3.0507 + angle_coeff @angle:c3-cd-ce harmonic 67.395 117.840 # CORR 2 + angle_coeff @angle:c3-cd-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 + angle_coeff @angle:c3-cd-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 + angle_coeff @angle:c3-cd-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 + angle_coeff @angle:c3-cd-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 + angle_coeff @angle:c3-cd-nc harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 + angle_coeff @angle:c3-cd-nd harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 + angle_coeff @angle:c3-cd-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 + angle_coeff @angle:c3-cd-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 + angle_coeff @angle:ca-cd-cc harmonic 69.802 113.510 # SOURCE3 26 7.4229 + angle_coeff @angle:ca-cd-cd harmonic 69.336 111.040 # SOURCE3 9 7.9455 + angle_coeff @angle:ca-cd-ce harmonic 66.694 124.900 # SOURCE4_SOURCE5 41 1.7178 + angle_coeff @angle:ca-cd-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 + angle_coeff @angle:ca-cd-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 + angle_coeff @angle:ca-cd-n harmonic 85.642 117.670 # CORR 18 + angle_coeff @angle:ca-cd-na harmonic 83.626 123.450 # SOURCE4 39 1.9138 + angle_coeff @angle:ca-cd-nc harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 + angle_coeff @angle:ca-cd-nd harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 + angle_coeff @angle:ca-cd-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 + angle_coeff @angle:ca-cd-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 + angle_coeff @angle:ca-cd-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 + angle_coeff @angle:c-cd-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 + angle_coeff @angle:c-cd-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 + angle_coeff @angle:c-cd-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 + angle_coeff @angle:c-cd-ca harmonic 65.005 122.950 # SOURCE3 1 + angle_coeff @angle:c-cd-cc harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 + angle_coeff @angle:cc-cd-cc harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 + angle_coeff @angle:cc-cd-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 + angle_coeff @angle:cc-cd-cf harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 + angle_coeff @angle:cc-cd-ch harmonic 67.080 125.790 # SOURCE4_SOURCE5 84 1.6445 + angle_coeff @angle:cc-cd-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 + angle_coeff @angle:cc-cd-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 22 0.8483 + angle_coeff @angle:c-cd-cd harmonic 65.674 122.690 # SOURCE3 2 + angle_coeff @angle:c-cd-cf harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 + angle_coeff @angle:cc-cd-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 + angle_coeff @angle:cc-cd-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 + angle_coeff @angle:c-cd-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 + angle_coeff @angle:cc-cd-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 + angle_coeff @angle:cc-cd-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 + angle_coeff @angle:cc-cd-nc harmonic 88.069 123.820 # SOURCE4_SOURCE5 28 0.3678 + angle_coeff @angle:cc-cd-nd harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 + angle_coeff @angle:cc-cd-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 + angle_coeff @angle:cc-cd-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 + angle_coeff @angle:cc-cd-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 + angle_coeff @angle:cc-cd-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 + angle_coeff @angle:cc-cd-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 + angle_coeff @angle:cd-cd-cd harmonic 70.129 110.700 # SOURCE3 54 3.4091 + angle_coeff @angle:cd-cd-ce harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 + angle_coeff @angle:cd-cd-cf harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 + angle_coeff @angle:cd-cd-ch harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 + angle_coeff @angle:cd-cd-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 13 0.6868 + angle_coeff @angle:cd-cd-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 + angle_coeff @angle:cd-cd-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 + angle_coeff @angle:cd-cd-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 + angle_coeff @angle:cd-cd-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 + angle_coeff @angle:cd-cd-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 832 1.6037 + angle_coeff @angle:cd-cd-nc harmonic 90.306 112.560 # SOURCE3 141 4.2871 + angle_coeff @angle:cd-cd-nd harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 + angle_coeff @angle:cd-cd-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 + angle_coeff @angle:cd-cd-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 + angle_coeff @angle:cd-cd-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 + angle_coeff @angle:cd-cd-pc harmonic 84.517 115.360 # SOURCE3 84 3.2889 + angle_coeff @angle:cd-cd-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 + angle_coeff @angle:ce-cd-nd harmonic 86.641 123.980 # SOURCE4_SOURCE5 10 2.4097 + angle_coeff @angle:cf-cd-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 + angle_coeff @angle:cf-cd-nc harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 + angle_coeff @angle:cf-cd-nd harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 + angle_coeff @angle:cf-cd-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 + angle_coeff @angle:cf-cd-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 + angle_coeff @angle:c-cd-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 16 0.2226 + angle_coeff @angle:c-cd-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 + angle_coeff @angle:cl-cd-nc harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 + angle_coeff @angle:c-cd-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 + angle_coeff @angle:c-cd-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 + angle_coeff @angle:c-cd-nc harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 + angle_coeff @angle:c-cd-nd harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 + angle_coeff @angle:c-cd-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 + angle_coeff @angle:c-cd-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 + angle_coeff @angle:h4-cd-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 + angle_coeff @angle:h4-cd-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 + angle_coeff @angle:h4-cd-nc harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 + angle_coeff @angle:h4-cd-nd harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 + angle_coeff @angle:h4-cd-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 + angle_coeff @angle:h4-cd-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 + angle_coeff @angle:h5-cd-n harmonic 62.738 115.700 # CORR_SOURCE5 41 0.7665 + angle_coeff @angle:h5-cd-na harmonic 61.227 121.550 # SOURCE3_SOURCE5 1138 0.7136 + angle_coeff @angle:h5-cd-nc harmonic 62.462 125.520 # SOURCE3_SOURCE5 1309 0.7276 + angle_coeff @angle:h5-cd-nd harmonic 61.266 122.920 # SOURCE3_SOURCE5 136 0.3532 + angle_coeff @angle:h5-cd-os harmonic 63.111 116.830 # SOURCE3_SOURCE5 42 1.3051 + angle_coeff @angle:h5-cd-ss harmonic 42.271 121.020 # SOURCE3_SOURCE5 46 0.6462 + angle_coeff @angle:ha-cd-na harmonic 61.218 121.500 # SOURCE2 1 + angle_coeff @angle:ha-cd-nc harmonic 64.154 118.880 # SOURCE3 20 2.8923 + angle_coeff @angle:ha-cd-nd harmonic 62.898 116.540 # SOURCE3 5 1.4482 + angle_coeff @angle:ha-cd-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 + angle_coeff @angle:ha-cd-pc harmonic 54.856 121.760 # SOURCE3 84 2.2216 + angle_coeff @angle:ha-cd-ss harmonic 42.168 121.640 # SOURCE2 5 + angle_coeff @angle:na-cd-nc harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 + angle_coeff @angle:na-cd-nd harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 + angle_coeff @angle:na-cd-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 100 1.6359 + angle_coeff @angle:na-cd-ss harmonic 83.703 111.460 # SOURCE4 20 0.8600 + angle_coeff @angle:nc-cd-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 + angle_coeff @angle:nc-cd-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 + angle_coeff @angle:nc-cd-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 + angle_coeff @angle:nc-cd-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 + angle_coeff @angle:nc-cd-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 + angle_coeff @angle:nd-cd-nd harmonic 107.603 125.700 # SOURCE4_SOURCE5 31 0.5900 + angle_coeff @angle:nd-cd-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 + angle_coeff @angle:nd-cd-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 + angle_coeff @angle:nh-cd-nh harmonic 111.696 115.960 # SOURCE3 1 + angle_coeff @angle:nh-cd-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 + angle_coeff @angle:nh-cd-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 + angle_coeff @angle:n-cd-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 + angle_coeff @angle:n-cd-nc harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 + angle_coeff @angle:n-cd-nd harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 + angle_coeff @angle:n-cd-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 + angle_coeff @angle:n-cd-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 + angle_coeff @angle:oh-cd-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 12 1.1909 + angle_coeff @angle:os-cd-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 + angle_coeff @angle:ss-cd-ss harmonic 63.639 121.370 # CORR 22 + angle_coeff @angle:ss-cd-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 + angle_coeff @angle:c2-ce-c3 harmonic 66.042 122.530 # SOURCE3_SOURCE5 882 1.9288 + angle_coeff @angle:c2-ce-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 11 1.7099 + angle_coeff @angle:c2-ce-cc harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 + angle_coeff @angle:c2-ce-ce harmonic 67.482 123.260 # SOURCE3_SOURCE5 791 1.8772 + angle_coeff @angle:c2-ce-cg harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 + angle_coeff @angle:c2-ce-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 62 1.3986 + angle_coeff @angle:c2-ce-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 43 1.6498 + angle_coeff @angle:c2-ce-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1439 1.4338 + angle_coeff @angle:c2-ce-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 18 0.9047 + angle_coeff @angle:c2-ce-n2 harmonic 88.228 128.700 # SOURCE3 1 + angle_coeff @angle:c2-ce-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 10 0.8452 + angle_coeff @angle:c2-ce-ne harmonic 88.464 118.320 # SOURCE3 7 1.0468 + angle_coeff @angle:c2-ce-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 27 1.7525 + angle_coeff @angle:c2-ce-p2 harmonic 81.422 118.240 # SOURCE3 1 + angle_coeff @angle:c2-ce-pe harmonic 81.089 118.760 # SOURCE3 8 2.3984 + angle_coeff @angle:c2-ce-px harmonic 80.647 119.720 # SOURCE3 6 0.5213 + angle_coeff @angle:c2-ce-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 12 1.9482 + angle_coeff @angle:c2-ce-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 14 0.9863 + angle_coeff @angle:c2-ce-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 17 1.3599 + angle_coeff @angle:c3-ce-ca harmonic 64.464 119.240 # CORR_SOURCE5 312 1.7689 + angle_coeff @angle:c3-ce-cc harmonic 65.246 118.030 # CORR_SOURCE5 77 1.5840 + angle_coeff @angle:c3-ce-ce harmonic 65.430 117.120 # CORR_SOURCE5 524 1.4790 + angle_coeff @angle:c3-ce-cf harmonic 65.999 122.380 # CORR_SOURCE5 490 2.0752 + angle_coeff @angle:c3-ce-cg harmonic 66.008 117.220 # SOURCE4_SOURCE5 34 1.7153 + angle_coeff @angle:c3-ce-n2 harmonic 83.839 122.730 # CORR_SOURCE5 149 1.8752 + angle_coeff @angle:c3-ce-nf harmonic 84.370 120.680 # SOURCE4_SOURCE5 13 2.1196 + angle_coeff @angle:c3-ce-nh harmonic 82.726 119.560 # SOURCE4_SOURCE5 10 1.0079 + angle_coeff @angle:ca-ce-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 + angle_coeff @angle:ca-ce-cc harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 + angle_coeff @angle:ca-ce-ce harmonic 65.684 119.540 # SOURCE4_SOURCE5 32 1.9209 + angle_coeff @angle:ca-ce-cf harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 + angle_coeff @angle:ca-ce-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 14 1.1195 + angle_coeff @angle:ca-ce-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 255 1.0051 + angle_coeff @angle:ca-ce-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 + angle_coeff @angle:ca-ce-n2 harmonic 86.084 120.720 # SOURCE3 1 + angle_coeff @angle:ca-ce-nf harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 + angle_coeff @angle:ca-ce-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 240 1.0372 + angle_coeff @angle:ca-ce-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 + angle_coeff @angle:ca-ce-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 25 1.4247 + angle_coeff @angle:ca-ce-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 14 1.2435 + angle_coeff @angle:c-ce-c2 harmonic 67.566 120.420 # SOURCE3 13 1.8877 + angle_coeff @angle:c-ce-c3 harmonic 64.889 117.220 # CORR_SOURCE5 558 2.2754 + angle_coeff @angle:c-ce-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 + angle_coeff @angle:c-ce-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 25 1.6999 + angle_coeff @angle:cc-ce-cd harmonic 65.259 130.610 # SOURCE4_SOURCE5 24 1.1422 + angle_coeff @angle:cc-ce-cf harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 + angle_coeff @angle:c-ce-cd harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 + angle_coeff @angle:c-ce-ce harmonic 65.150 120.980 # SOURCE4_SOURCE5 53 2.2319 + angle_coeff @angle:c-ce-cf harmonic 65.856 126.410 # SOURCE3 2 5.7847 + angle_coeff @angle:c-ce-cg harmonic 66.500 118.420 # SOURCE4_SOURCE5 49 1.0600 + angle_coeff @angle:cc-ce-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 77 0.8454 + angle_coeff @angle:cc-ce-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 + angle_coeff @angle:c-ce-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 25 1.2041 + angle_coeff @angle:cc-ce-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 + angle_coeff @angle:cc-ce-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 21 1.8052 + angle_coeff @angle:c-ce-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 53 0.9126 + angle_coeff @angle:cd-ce-ce harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 + angle_coeff @angle:cd-ce-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 + angle_coeff @angle:ce-ce-ce harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 + angle_coeff @angle:ce-ce-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 + angle_coeff @angle:ce-ce-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 35 0.8344 + angle_coeff @angle:ce-ce-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 + angle_coeff @angle:ce-ce-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 + angle_coeff @angle:ce-ce-n1 harmonic 84.049 127.150 # CORR 4 + angle_coeff @angle:ce-ce-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 + angle_coeff @angle:ce-ce-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 30 1.7182 + angle_coeff @angle:cf-ce-cg harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 + angle_coeff @angle:cf-ce-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 31 0.9919 + angle_coeff @angle:cf-ce-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 23 1.1580 + angle_coeff @angle:cf-ce-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 + angle_coeff @angle:cf-ce-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 13 1.8896 + angle_coeff @angle:cf-ce-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 + angle_coeff @angle:cf-ce-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 39 1.7667 + angle_coeff @angle:cf-ce-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 + angle_coeff @angle:cg-ce-cg harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 + angle_coeff @angle:cg-ce-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 + angle_coeff @angle:cg-ce-n1 harmonic 87.835 119.500 # CORR 2 + angle_coeff @angle:cg-ce-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 14 0.8974 + angle_coeff @angle:c-ce-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 + angle_coeff @angle:c-ce-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 + angle_coeff @angle:c-ce-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 + angle_coeff @angle:c-ce-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 20 2.0254 + angle_coeff @angle:c-ce-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 47 2.1291 + angle_coeff @angle:h4-ce-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 19 0.4343 + angle_coeff @angle:h4-ce-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 + angle_coeff @angle:h4-ce-ne harmonic 62.153 115.650 # SOURCE4_SOURCE5 19 1.8165 + angle_coeff @angle:ha-ce-n1 harmonic 65.106 115.960 # CORR 4 + angle_coeff @angle:ha-ce-n2 harmonic 64.979 119.510 # SOURCE3 2 0.4623 + angle_coeff @angle:ha-ce-ne harmonic 61.414 118.590 # SOURCE3 5 1.1113 + angle_coeff @angle:ha-ce-nh harmonic 62.516 114.990 # CORR 2 + angle_coeff @angle:ha-ce-p2 harmonic 52.606 120.110 # SOURCE3 1 + angle_coeff @angle:ha-ce-pe harmonic 52.651 119.330 # SOURCE3 6 0.8966 + angle_coeff @angle:ha-ce-px harmonic 52.873 117.900 # SOURCE3 6 0.1809 + angle_coeff @angle:ha-ce-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 11 0.7169 + angle_coeff @angle:ha-ce-sx harmonic 41.698 115.450 # SOURCE3 3 0.6640 + angle_coeff @angle:ha-ce-sy harmonic 42.578 114.860 # SOURCE3 3 0.4717 + angle_coeff @angle:n2-ce-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 + angle_coeff @angle:n2-ce-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 19 0.3524 + angle_coeff @angle:n2-ce-ss harmonic 81.512 117.230 # SOURCE4 6 2.0518 + angle_coeff @angle:ne-ce-ne harmonic 106.467 123.870 # SOURCE3 1 + angle_coeff @angle:ne-ce-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 41 1.4024 + angle_coeff @angle:nf-ce-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 23 1.5487 + angle_coeff @angle:pe-ce-pe harmonic 97.908 129.790 # SOURCE3 1 + angle_coeff @angle:py-ce-py harmonic 108.039 108.060 # SOURCE3 1 + angle_coeff @angle:sx-ce-sx harmonic 61.727 120.320 # SOURCE3 1 + angle_coeff @angle:sy-ce-sy harmonic 62.867 119.970 # SOURCE3 1 + angle_coeff @angle:c2-cf-c3 harmonic 66.048 122.530 # SOURCE3_SOURCE5 875 1.9359 + angle_coeff @angle:c2-cf-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 5 1.1712 + angle_coeff @angle:c2-cf-cd harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 + angle_coeff @angle:c2-cf-cf harmonic 67.482 123.260 # SOURCE3_SOURCE5 779 1.8961 + angle_coeff @angle:c2-cf-ch harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 + angle_coeff @angle:c2-cf-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1393 1.4017 + angle_coeff @angle:c2-cf-n2 harmonic 88.228 128.700 # SOURCE3 1 + angle_coeff @angle:c2-cf-nf harmonic 88.464 118.320 # SOURCE3 7 + angle_coeff @angle:c2-cf-p2 harmonic 81.422 118.240 # SOURCE3 1 + angle_coeff @angle:c2-cf-pf harmonic 81.089 118.760 # SOURCE3 8 + angle_coeff @angle:c2-cf-px harmonic 80.647 119.720 # SOURCE3 6 + angle_coeff @angle:c2-cf-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 7 1.0992 + angle_coeff @angle:c2-cf-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 9 1.0588 + angle_coeff @angle:c2-cf-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 12 1.7015 + angle_coeff @angle:c3-cf-ca harmonic 64.468 119.240 # CORR_SOURCE5 312 1.7689 + angle_coeff @angle:c3-cf-cd harmonic 65.251 118.030 # CORR_SOURCE5 77 1.5840 + angle_coeff @angle:c3-cf-ce harmonic 66.005 122.380 # CORR_SOURCE5 490 2.0752 + angle_coeff @angle:c3-cf-cf harmonic 65.435 117.120 # CORR_SOURCE5 524 1.4790 + angle_coeff @angle:c3-cf-n2 harmonic 83.846 122.730 # CORR_SOURCE5 149 1.8752 + angle_coeff @angle:ca-cf-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 + angle_coeff @angle:ca-cf-cc harmonic 64.611 130.880 # SOURCE4_SOURCE5 41 1.2386 + angle_coeff @angle:ca-cf-cd harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 + angle_coeff @angle:ca-cf-ce harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 + angle_coeff @angle:ca-cf-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 + angle_coeff @angle:ca-cf-n2 harmonic 86.084 120.720 # SOURCE3 1 + angle_coeff @angle:ca-cf-ne harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 + angle_coeff @angle:ca-cf-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 + angle_coeff @angle:c-cf-c2 harmonic 67.566 120.420 # SOURCE3 13 + angle_coeff @angle:c-cf-c3 harmonic 64.893 117.220 # CORR_SOURCE5 558 2.2754 + angle_coeff @angle:c-cf-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 + angle_coeff @angle:c-cf-cc harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 + angle_coeff @angle:cc-cf-cf harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 + angle_coeff @angle:c-cf-cd harmonic 66.092 117.820 # SOURCE4_SOURCE5 29 1.0204 + angle_coeff @angle:c-cf-ce harmonic 65.856 126.410 # SOURCE3 2 + angle_coeff @angle:cc-cf-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 + angle_coeff @angle:cd-cf-ce harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 + angle_coeff @angle:cd-cf-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 + angle_coeff @angle:cd-cf-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 + angle_coeff @angle:ce-cf-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 + angle_coeff @angle:ce-cf-ch harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 + angle_coeff @angle:ce-cf-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 + angle_coeff @angle:ce-cf-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 + angle_coeff @angle:ce-cf-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 + angle_coeff @angle:cf-cf-cf harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 + angle_coeff @angle:cf-cf-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 + angle_coeff @angle:cf-cf-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 + angle_coeff @angle:cf-cf-n1 harmonic 84.049 127.150 # CORR 4 + angle_coeff @angle:cf-cf-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 + angle_coeff @angle:c-cf-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 + angle_coeff @angle:ch-cf-ch harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 + angle_coeff @angle:ch-cf-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 + angle_coeff @angle:ch-cf-n1 harmonic 87.835 119.500 # CORR 2 + angle_coeff @angle:c-cf-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 13 1.4243 + angle_coeff @angle:c-cf-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 + angle_coeff @angle:c-cf-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 + angle_coeff @angle:f-c-f harmonic 123.826 107.350 # SOURCE2 2 0.2500 + angle_coeff @angle:h4-cf-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 + angle_coeff @angle:h4-cf-ne harmonic 64.320 120.560 # SOURCE4_SOURCE5 39 0.8435 + angle_coeff @angle:ha-cf-n1 harmonic 65.106 115.960 # CORR 4 + angle_coeff @angle:ha-cf-n2 harmonic 64.979 119.510 # SOURCE3 2 + angle_coeff @angle:ha-cf-nf harmonic 61.414 118.590 # SOURCE3 5 + angle_coeff @angle:ha-cf-nh harmonic 62.516 114.990 # CORR 2 + angle_coeff @angle:ha-cf-p2 harmonic 52.606 120.110 # SOURCE3 1 + angle_coeff @angle:ha-cf-pf harmonic 52.651 119.330 # SOURCE3 6 + angle_coeff @angle:ha-cf-px harmonic 52.873 117.900 # SOURCE3 6 + angle_coeff @angle:ha-cf-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 8 0.8708 + angle_coeff @angle:ha-cf-sx harmonic 41.698 115.450 # SOURCE3 3 + angle_coeff @angle:ha-cf-sy harmonic 42.578 114.860 # SOURCE3 3 + angle_coeff @angle:n2-cf-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 + angle_coeff @angle:nf-cf-nf harmonic 106.467 123.870 # SOURCE3 1 + angle_coeff @angle:f-c-o harmonic 118.196 123.440 # SOURCE3 1 + angle_coeff @angle:pf-cf-pf harmonic 97.908 129.790 # SOURCE3 1 + angle_coeff @angle:py-cf-py harmonic 108.039 108.060 # SOURCE3 1 + angle_coeff @angle:f-c-s harmonic 84.396 124.000 # SOURCE2 1 + angle_coeff @angle:sx-cf-sx harmonic 61.727 120.320 # SOURCE3 1 + angle_coeff @angle:sy-cf-sy harmonic 62.867 119.970 # SOURCE3 1 + angle_coeff @angle:c1-cg-ca harmonic 58.572 179.570 # CORR_SOURCE5 38 0.4711 + angle_coeff @angle:c1-cg-cc harmonic 58.934 178.610 # SOURCE4_SOURCE5 13 0.3677 + angle_coeff @angle:c1-cg-ce harmonic 58.989 178.050 # CORR_SOURCE5 15 0.1905 + angle_coeff @angle:c1-cg-cg harmonic 60.378 179.670 # CORR_SOURCE5 90 0.1487 + angle_coeff @angle:c1-cg-ne harmonic 79.305 170.020 # SOURCE3 4 1.1724 + angle_coeff @angle:c1-cg-pe harmonic 75.149 173.290 # SOURCE3 11 4.9305 + angle_coeff @angle:ca-cg-ch harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 + angle_coeff @angle:ca-cg-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 + angle_coeff @angle:c-cg-c1 harmonic 58.113 179.140 # SOURCE3 2 + angle_coeff @angle:cc-cg-n1 harmonic 74.809 178.620 # CORR_SOURCE5 43 0.6454 + angle_coeff @angle:ce-cg-ch harmonic 59.157 177.940 # CORR 17 + angle_coeff @angle:ce-cg-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 + angle_coeff @angle:n1-cg-ne harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 + angle_coeff @angle:h4-c-o harmonic 66.570 120.700 # SOURCE4_SOURCE5 491 0.4811 + angle_coeff @angle:h5-c-n harmonic 63.496 112.160 # SOURCE4_SOURCE5 98 0.3632 + angle_coeff @angle:h5-c-o harmonic 65.930 123.650 # SOURCE4_SOURCE5 150 0.7654 + angle_coeff @angle:ha-c-ha harmonic 37.443 115.610 # SOURCE3 4 0.0458 + angle_coeff @angle:ha-c-i harmonic 38.168 110.580 # SOURCE3 1 + angle_coeff @angle:ha-c-n harmonic 63.490 112.370 # SOURCE3 4 0.6424 + angle_coeff @angle:ha-c-o harmonic 66.484 121.940 # SOURCE3 51 2.3235 + angle_coeff @angle:ha-c-oh harmonic 64.638 111.820 # SOURCE3 4 1.9375 + angle_coeff @angle:ha-c-os harmonic 64.813 110.340 # SOURCE3 8 1.9344 + angle_coeff @angle:ha-c-s harmonic 44.760 119.560 # SOURCE3 3 0.7586 + angle_coeff @angle:c1-ch-ca harmonic 58.522 179.570 # CORR_SOURCE5 38 0.4711 + angle_coeff @angle:c1-ch-cf harmonic 58.938 178.050 # CORR_SOURCE5 15 0.1905 + angle_coeff @angle:c1-ch-ch harmonic 60.316 179.670 # CORR_SOURCE5 90 0.1487 + angle_coeff @angle:c1-ch-nf harmonic 79.216 170.020 # SOURCE3 4 + angle_coeff @angle:c1-ch-pf harmonic 75.117 173.290 # SOURCE3 11 + angle_coeff @angle:ca-ch-cg harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 + angle_coeff @angle:ca-ch-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 + angle_coeff @angle:c-ch-c1 harmonic 58.066 179.140 # SOURCE3 2 + angle_coeff @angle:cd-ch-n1 harmonic 74.807 178.630 # CORR_SOURCE5 49 0.3708 + angle_coeff @angle:cf-ch-cg harmonic 59.157 177.940 # CORR 17 + angle_coeff @angle:cf-ch-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 + angle_coeff @angle:cg-ch-ch harmonic 60.571 179.580 # SOURCE4_SOURCE5 55 0.2973 + angle_coeff @angle:n1-ch-nf harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 + angle_coeff @angle:i-c-i harmonic 65.372 116.450 # SOURCE3 1 + angle_coeff @angle:i-c-o harmonic 71.718 122.020 # SOURCE3 4 1.2961 + angle_coeff @angle:f-cl-f harmonic 0.000 87.500 # SOURCE2 1 + angle_coeff @angle:n2-c-n2 harmonic 110.771 110.310 # SOURCE3 1 + angle_coeff @angle:n2-c-o harmonic 111.836 122.500 # SOURCE3 1 + angle_coeff @angle:n4-c-n4 harmonic 99.803 114.640 # SOURCE3 1 + angle_coeff @angle:n4-c-o harmonic 106.610 118.830 # SOURCE3 4 3.8516 + angle_coeff @angle:nc-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 + angle_coeff @angle:nd-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 + angle_coeff @angle:ne-c-ne harmonic 113.088 110.310 # CORR 2 + angle_coeff @angle:ne-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 + angle_coeff @angle:nf-c-nf harmonic 113.088 110.310 # CORR 2 + angle_coeff @angle:nf-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 + angle_coeff @angle:n-c-n harmonic 112.428 113.560 # SOURCE4_SOURCE5 1747 1.4619 + angle_coeff @angle:n-c-nc harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 + angle_coeff @angle:n-c-nd harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 + angle_coeff @angle:n-c-ne harmonic 113.600 110.260 # SOURCE4_SOURCE5 25 1.7043 + angle_coeff @angle:n-c-o harmonic 113.811 123.050 # SOURCE3_SOURCE5 8454 1.5552 + angle_coeff @angle:n-c-oh harmonic 113.913 112.820 # SOURCE4_SOURCE5 14 1.4518 + angle_coeff @angle:no-c-no harmonic 102.620 109.280 # SOURCE3 1 + angle_coeff @angle:no-c-o harmonic 104.115 125.360 # SOURCE3 1 + angle_coeff @angle:n-c-os harmonic 115.486 109.220 # SOURCE4_SOURCE5 821 0.9352 + angle_coeff @angle:n-c-s harmonic 82.398 124.050 # SOURCE3_SOURCE5 514 1.4099 + angle_coeff @angle:n-c-sh harmonic 81.620 112.970 # SOURCE4_SOURCE5 26 1.1725 + angle_coeff @angle:n-c-ss harmonic 82.496 110.290 # SOURCE4_SOURCE5 160 1.6051 + angle_coeff @angle:oh-c-oh harmonic 116.271 110.560 # SOURCE3 2 0.5498 + angle_coeff @angle:oh-c-s harmonic 83.019 123.440 # SOURCE3 1 + angle_coeff @angle:o-c-o harmonic 118.817 130.250 # SOURCE4_SOURCE5 1037 1.2396 + angle_coeff @angle:o-c-oh harmonic 115.745 122.100 # SOURCE3_SOURCE5 2859 0.8497 + angle_coeff @angle:o-c-os harmonic 114.822 123.250 # SOURCE4_SOURCE5 5492 1.1411 + angle_coeff @angle:o-c-p2 harmonic 96.161 123.100 # SOURCE3 1 + angle_coeff @angle:o-c-p3 harmonic 97.971 120.790 # SOURCE3 1 + angle_coeff @angle:o-c-p5 harmonic 97.881 121.170 # SOURCE4_SOURCE5 18 1.1433 + angle_coeff @angle:o-c-pe harmonic 95.623 123.020 # SOURCE3 3 0.1404 + angle_coeff @angle:o-c-pf harmonic 95.623 123.020 # SOURCE3 3 + angle_coeff @angle:o-c-px harmonic 97.552 119.100 # SOURCE3 1 + angle_coeff @angle:o-c-py harmonic 98.325 122.010 # SOURCE4_SOURCE5 14 1.0132 + angle_coeff @angle:o-c-s4 harmonic 76.764 121.150 # SOURCE3 1 + angle_coeff @angle:o-c-s6 harmonic 77.308 119.450 # SOURCE3 1 + angle_coeff @angle:o-c-s harmonic 85.589 120.440 # SOURCE3 2 + angle_coeff @angle:o-c-sh harmonic 79.543 122.050 # SOURCE3_SOURCE5 10 1.1120 + angle_coeff @angle:os-c-os harmonic 115.283 111.290 # SOURCE4_SOURCE5 32 0.8183 + angle_coeff @angle:o-c-ss harmonic 79.009 123.320 # SOURCE3_SOURCE5 190 1.2053 + angle_coeff @angle:os-c-s harmonic 82.392 125.010 # SOURCE4_SOURCE5 62 1.0980 + angle_coeff @angle:os-c-ss harmonic 82.286 111.400 # SOURCE4_SOURCE5 23 1.7283 + angle_coeff @angle:o-c-sx harmonic 76.145 121.150 # SOURCE3 5 3.6452 + angle_coeff @angle:o-c-sy harmonic 77.559 119.320 # SOURCE3 5 2.4495 + angle_coeff @angle:p2-c-p2 harmonic 100.070 113.750 # SOURCE3 1 + angle_coeff @angle:p3-c-p3 harmonic 99.122 118.040 # SOURCE3 1 + angle_coeff @angle:p3-c-py harmonic 113.947 90.080 # SOURCE3 1 + angle_coeff @angle:p5-c-p5 harmonic 96.866 123.760 # SOURCE3 1 + angle_coeff @angle:ca-cp-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 + angle_coeff @angle:ca-cp-cp harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 + angle_coeff @angle:ca-cp-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 59 0.7877 + angle_coeff @angle:ca-cp-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 174 0.6998 + angle_coeff @angle:cp-cp-cp harmonic 74.761 90.000 # SOURCE3 4 + angle_coeff @angle:cp-cp-cq harmonic 64.283 124.270 # CORR_SOURCE5 8 2.0477 + angle_coeff @angle:cp-cp-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 235 1.1595 + angle_coeff @angle:pe-c-pe harmonic 99.485 113.770 # SOURCE3 1 + angle_coeff @angle:pf-c-pf harmonic 99.485 113.770 # SOURCE3 1 + angle_coeff @angle:nb-cp-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 11 0.6658 + angle_coeff @angle:py-c-py harmonic 97.618 123.800 # SOURCE3 1 + angle_coeff @angle:ca-cq-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 + angle_coeff @angle:ca-cq-cq harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 + angle_coeff @angle:ca-cq-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 111 0.7244 + angle_coeff @angle:cp-cq-cq harmonic 64.278 124.290 # CORR_SOURCE5 8 1.4947 + angle_coeff @angle:cq-cq-cq harmonic 74.761 90.000 # SOURCE3 4 + angle_coeff @angle:cq-cq-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 147 1.1420 + angle_coeff @angle:s4-c-s4 harmonic 63.122 108.810 # SOURCE3 1 + angle_coeff @angle:s6-c-s6 harmonic 61.200 115.750 # SOURCE3 1 + angle_coeff @angle:sh-c-sh harmonic 63.799 115.330 # SOURCE3 1 + angle_coeff @angle:s-c-s harmonic 65.463 126.500 # SOURCE3_SOURCE5 14 1.3489 + angle_coeff @angle:s-c-sh harmonic 63.925 122.650 # SOURCE4_SOURCE5 37 1.5614 + angle_coeff @angle:s-c-ss harmonic 63.724 123.190 # SOURCE3_SOURCE5 85 1.7112 + angle_coeff @angle:ss-c-ss harmonic 64.515 112.420 # SOURCE3_SOURCE5 17 0.4533 + angle_coeff @angle:sx-c-sx harmonic 62.622 108.800 # SOURCE3 1 + angle_coeff @angle:sy-c-sy harmonic 61.356 115.780 # SOURCE3 1 + angle_coeff @angle:c2-cu-cx harmonic 61.131 148.500 # SOURCE4_SOURCE5 23 1.5654 + angle_coeff @angle:c-cu-cu harmonic 98.040 62.600 # SOURCE2 1 + angle_coeff @angle:cu-cu-cx harmonic 105.362 50.800 # SOURCE2 1 + angle_coeff @angle:cu-cu-ha harmonic 46.590 147.730 # SOURCE2 3 2.0950 + angle_coeff @angle:cv-cv-cy harmonic 75.476 94.410 # SOURCE3_SOURCE5 6 0.2122 + angle_coeff @angle:cv-cv-ha harmonic 47.789 133.700 # SOURCE3 2 + angle_coeff @angle:cx-cv-cx harmonic 87.395 63.900 # SOURCE2 1 + angle_coeff @angle:cy-cv-ha harmonic 43.281 132.140 # SOURCE3 2 + angle_coeff @angle:c1-cx-cx harmonic 65.298 119.570 # SOURCE4_SOURCE5 51 1.0503 + angle_coeff @angle:c2-cx-cx harmonic 64.271 120.300 # SOURCE4_SOURCE5 207 2.3490 + angle_coeff @angle:c2-cx-h1 harmonic 47.059 115.860 # SOURCE4_SOURCE5 34 0.6256 + angle_coeff @angle:c2-cx-hc harmonic 47.215 115.150 # SOURCE4_SOURCE5 45 0.9609 + angle_coeff @angle:c2-cx-os harmonic 83.614 116.550 # SOURCE4_SOURCE5 48 1.1122 + angle_coeff @angle:c3-cx-c3 harmonic 64.915 114.240 # SOURCE4_SOURCE5 207 2.2113 + angle_coeff @angle:c3-cx-cx harmonic 63.608 120.100 # SOURCE4_SOURCE5 1739 2.3197 + angle_coeff @angle:c3-cx-h1 harmonic 46.234 115.320 # SOURCE4_SOURCE5 326 1.1035 + angle_coeff @angle:c3-cx-hc harmonic 46.430 114.390 # SOURCE4_SOURCE5 291 1.4379 + angle_coeff @angle:c3-cx-n3 harmonic 81.063 118.500 # SOURCE4 17 2.4897 + angle_coeff @angle:c3-cx-os harmonic 82.886 115.680 # SOURCE4_SOURCE5 616 1.2862 + angle_coeff @angle:ca-cx-cx harmonic 63.720 121.950 # SOURCE4_SOURCE5 197 1.8192 + angle_coeff @angle:ca-cx-h1 harmonic 47.143 114.700 # SOURCE4_SOURCE5 19 0.6393 + angle_coeff @angle:ca-cx-hc harmonic 47.377 113.620 # SOURCE4_SOURCE5 57 0.9227 + angle_coeff @angle:ca-cx-oh harmonic 86.728 112.930 # SOURCE3 1 + angle_coeff @angle:ca-cx-os harmonic 82.823 118.310 # SOURCE4_SOURCE5 18 0.7292 + angle_coeff @angle:c-cx-c3 harmonic 64.445 117.470 # SOURCE4_SOURCE5 71 1.9181 + angle_coeff @angle:cc-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 + angle_coeff @angle:cc-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 44 0.6781 + angle_coeff @angle:c-cx-cx harmonic 64.620 117.970 # SOURCE4_SOURCE5 554 2.1023 + angle_coeff @angle:cd-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 + angle_coeff @angle:c-cx-h1 harmonic 46.552 116.550 # SOURCE4_SOURCE5 86 1.1535 + angle_coeff @angle:c-cx-hc harmonic 46.546 116.630 # SOURCE4_SOURCE5 122 1.5743 + angle_coeff @angle:cl-cx-cl harmonic 82.588 110.550 # SOURCE2_SOURCE5 14 0.4864 + angle_coeff @angle:cl-cx-cx harmonic 70.087 119.850 # SOURCE4_SOURCE5 84 0.7070 + angle_coeff @angle:cl-cx-h1 harmonic 48.861 111.430 # SOURCE3 1 + angle_coeff @angle:cl-cx-hc harmonic 47.924 115.800 # SOURCE2 1 + angle_coeff @angle:c-cx-os harmonic 83.552 115.590 # SOURCE4 36 0.8227 + angle_coeff @angle:cu-cx-cu harmonic 95.990 54.600 # SOURCE2 1 + angle_coeff @angle:cu-cx-cx harmonic 92.184 58.450 # SOURCE4_SOURCE5 35 0.3844 + angle_coeff @angle:cu-cx-hc harmonic 46.510 118.570 # SOURCE4_SOURCE5 36 0.6733 + angle_coeff @angle:cx-cx-cx harmonic 90.424 60.000 # SOURCE4_SOURCE5 2370 0.7579 + angle_coeff @angle:cx-cx-cy harmonic 69.603 100.530 # SOURCE3 4 + angle_coeff @angle:cx-cx-f harmonic 85.391 118.550 # SOURCE4_SOURCE5 24 1.1971 + angle_coeff @angle:cx-cx-h1 harmonic 45.959 118.700 # SOURCE3_SOURCE5 1351 1.3656 + angle_coeff @angle:cx-cx-hc harmonic 46.163 117.700 # SOURCE3_SOURCE5 3574 0.9510 + angle_coeff @angle:cx-cx-hx harmonic 45.802 119.610 # SOURCE4_SOURCE5 29 0.1468 + angle_coeff @angle:cx-cx-n3 harmonic 114.892 59.590 # SOURCE4_SOURCE5 400 0.3281 + angle_coeff @angle:cx-cx-na harmonic 79.232 126.020 # SOURCE4_SOURCE5 69 1.6659 + angle_coeff @angle:cx-cx-nh harmonic 115.868 59.170 # SOURCE4_SOURCE5 276 0.6810 + angle_coeff @angle:cx-cx-os harmonic 116.592 59.090 # SOURCE4_SOURCE5 1094 0.5727 + angle_coeff @angle:cy-cx-hc harmonic 44.429 125.430 # SOURCE3 2 + angle_coeff @angle:f-cx-f harmonic 120.884 106.900 # SOURCE2 2 1.4000 + angle_coeff @angle:f-cx-h1 harmonic 65.454 111.680 # SOURCE3 1 + angle_coeff @angle:f-cx-hc harmonic 65.300 112.300 # SOURCE2 1 + angle_coeff @angle:h1-cx-h1 harmonic 37.880 115.460 # SOURCE4_SOURCE5 585 0.3332 + angle_coeff @angle:h1-cx-n3 harmonic 59.281 116.470 # SOURCE4_SOURCE5 463 1.4379 + angle_coeff @angle:h1-cx-n harmonic 60.648 115.050 # SOURCE4_SOURCE5 36 1.2404 + angle_coeff @angle:h1-cx-na harmonic 61.785 108.360 # SOURCE4_SOURCE5 35 1.1443 + angle_coeff @angle:h1-cx-nh harmonic 59.869 116.290 # SOURCE4_SOURCE5 349 1.0287 + angle_coeff @angle:h1-cx-os harmonic 60.853 114.930 # SOURCE3_SOURCE5 531 0.5509 + angle_coeff @angle:h2-cx-h2 harmonic 37.352 119.430 # SOURCE3 1 + angle_coeff @angle:h2-cx-n2 harmonic 58.708 117.180 # SOURCE3 4 + angle_coeff @angle:hc-cx-hc harmonic 38.120 114.430 # SOURCE3_SOURCE5 595 0.4830 + angle_coeff @angle:hc-cx-os harmonic 61.092 114.100 # SOURCE2 1 + angle_coeff @angle:hx-cx-n4 harmonic 58.913 114.470 # SOURCE4_SOURCE5 28 0.1963 + angle_coeff @angle:n2-cx-n2 harmonic 157.396 50.160 # SOURCE3 1 + angle_coeff @angle:n-cx-oh harmonic 107.552 119.750 # SOURCE3 2 + angle_coeff @angle:n-cx-os harmonic 141.311 65.980 # SOURCE3 1 + angle_coeff @angle:oh-cx-oh harmonic 116.883 107.850 # SOURCE3 1 + angle_coeff @angle:oh-cx-os harmonic 108.501 118.120 # SOURCE3 4 1.3581 + angle_coeff @angle:os-cx-os harmonic 106.734 116.050 # SOURCE4_SOURCE5 15 2.1532 + angle_coeff @angle:c2-cy-cy harmonic 68.568 100.400 # SOURCE2 1 + angle_coeff @angle:c3-cy-c3 harmonic 65.146 111.440 # SOURCE4_SOURCE5 53 1.0307 + angle_coeff @angle:c3-cy-cy harmonic 62.618 118.700 # SOURCE4 293 1.8510 + angle_coeff @angle:c3-cy-h1 harmonic 46.561 111.780 # SOURCE4_SOURCE5 309 0.4521 + angle_coeff @angle:c3-cy-hc harmonic 46.907 110.140 # SOURCE3_SOURCE5 291 0.5598 + angle_coeff @angle:c3-cy-n3 harmonic 82.158 113.650 # SOURCE3_SOURCE5 15 2.3547 + angle_coeff @angle:c3-cy-n harmonic 86.069 104.130 # SOURCE4_SOURCE5 306 0.5952 + angle_coeff @angle:c3-cy-os harmonic 83.640 112.310 # SOURCE4_SOURCE5 40 1.1099 + angle_coeff @angle:c-cy-c3 harmonic 63.261 116.710 # SOURCE4_SOURCE5 332 0.5683 + angle_coeff @angle:cc-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 + angle_coeff @angle:c-cy-cy harmonic 73.514 85.090 # SOURCE4_SOURCE5 672 0.9017 + angle_coeff @angle:cd-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 + angle_coeff @angle:ce-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 38 0.5598 + angle_coeff @angle:ce-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 38 0.1933 + angle_coeff @angle:ce-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 34 1.4182 + angle_coeff @angle:c-cy-h1 harmonic 45.784 113.030 # SOURCE4_SOURCE5 167 0.8137 + angle_coeff @angle:c-cy-hc harmonic 46.135 111.320 # SOURCE3_SOURCE5 246 1.1605 + angle_coeff @angle:cl-cy-cy harmonic 69.535 117.010 # SOURCE3_SOURCE5 41 1.1740 + angle_coeff @angle:cl-cy-h1 harmonic 49.261 106.590 # SOURCE3 1 + angle_coeff @angle:cl-cy-hc harmonic 47.632 114.000 # SOURCE2 1 + angle_coeff @angle:c-cy-n harmonic 80.522 117.340 # SOURCE4_SOURCE5 164 1.1278 + angle_coeff @angle:c-cy-os harmonic 82.061 115.000 # SOURCE4_SOURCE5 17 1.7766 + angle_coeff @angle:cv-cy-cy harmonic 73.645 86.710 # SOURCE4_SOURCE5 30 1.1538 + angle_coeff @angle:cv-cy-hc harmonic 46.478 114.420 # SOURCE4_SOURCE5 25 1.1899 + angle_coeff @angle:cx-cy-cy harmonic 68.163 101.230 # SOURCE3 4 + angle_coeff @angle:cx-cy-hc harmonic 45.715 118.300 # SOURCE2 3 5.7799 + angle_coeff @angle:cy-cy-cy harmonic 72.002 88.400 # SOURCE3_SOURCE5 746 1.4921 + angle_coeff @angle:cy-cy-f harmonic 85.702 112.870 # SOURCE4 13 1.6772 + angle_coeff @angle:cy-cy-h1 harmonic 45.598 113.240 # SOURCE3_SOURCE5 501 1.2112 + angle_coeff @angle:cy-cy-h2 harmonic 44.908 116.780 # SOURCE4_SOURCE5 206 0.8496 + angle_coeff @angle:cy-cy-hc harmonic 45.290 114.790 # SOURCE3_SOURCE5 1632 2.3030 + angle_coeff @angle:cy-cy-n3 harmonic 92.778 87.580 # SOURCE3 4 0.6135 + angle_coeff @angle:cy-cy-n harmonic 91.445 90.630 # SOURCE3_SOURCE5 429 2.2980 + angle_coeff @angle:cy-cy-na harmonic 80.160 119.560 # SOURCE4_SOURCE5 26 0.4777 + angle_coeff @angle:cy-cy-oh harmonic 82.786 114.190 # SOURCE3 4 + angle_coeff @angle:cy-cy-os harmonic 83.069 111.770 # SOURCE4 18 2.1334 + angle_coeff @angle:cy-cy-s6 harmonic 60.829 117.220 # SOURCE4_SOURCE5 19 1.2938 + angle_coeff @angle:cy-cy-ss harmonic 60.567 118.400 # SOURCE4_SOURCE5 183 1.7650 + angle_coeff @angle:h1-cy-h1 harmonic 38.688 109.460 # SOURCE3_SOURCE5 73 0.6101 + angle_coeff @angle:h1-cy-n3 harmonic 59.591 113.930 # SOURCE3_SOURCE5 104 0.9602 + angle_coeff @angle:h1-cy-n harmonic 60.615 111.280 # SOURCE4_SOURCE5 377 0.6736 + angle_coeff @angle:h1-cy-oh harmonic 62.604 111.490 # SOURCE3 2 + angle_coeff @angle:h1-cy-os harmonic 62.029 110.130 # SOURCE3_SOURCE5 45 0.8913 + angle_coeff @angle:h1-cy-s6 harmonic 41.611 111.620 # SOURCE4_SOURCE5 16 1.2135 + angle_coeff @angle:h2-cy-n harmonic 59.772 114.500 # SOURCE4_SOURCE5 213 0.6904 + angle_coeff @angle:h2-cy-os harmonic 62.315 109.190 # SOURCE4_SOURCE5 19 0.6835 + angle_coeff @angle:h2-cy-s6 harmonic 41.906 110.010 # SOURCE4_SOURCE5 29 1.6175 + angle_coeff @angle:h2-cy-ss harmonic 41.997 109.770 # SOURCE4_SOURCE5 214 0.7540 + angle_coeff @angle:hc-cy-hc harmonic 38.780 108.980 # SOURCE3_SOURCE5 313 0.5379 + angle_coeff @angle:n-cy-os harmonic 109.575 107.420 # SOURCE4_SOURCE5 24 2.2897 + angle_coeff @angle:n-cy-s6 harmonic 82.361 103.180 # SOURCE4_SOURCE5 18 0.8204 + angle_coeff @angle:n-cy-ss harmonic 81.655 105.130 # SOURCE4_SOURCE5 165 0.4214 + angle_coeff @angle:nh-cz-nh harmonic 112.563 120.140 # SOURCE4_SOURCE5 67 0.3910 + angle_coeff @angle:br-n1-c1 harmonic 52.125 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c1 harmonic 65.921 179.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c2 harmonic 61.737 177.730 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-c3 harmonic 57.795 177.720 # HF/6-31G*_SOURCE5 6 0.4473 + angle_coeff @angle:c1-n1-ca harmonic 60.455 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-cl harmonic 62.197 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-f harmonic 73.857 179.960 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-hn harmonic 45.538 179.980 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-i harmonic 49.085 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n1 harmonic 83.205 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n2 harmonic 81.640 171.560 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n3 harmonic 76.060 175.590 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-n4 harmonic 74.800 179.690 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-na harmonic 75.122 180.000 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-nh harmonic 76.286 176.350 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-o harmonic 77.945 179.950 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-oh harmonic 78.300 174.310 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-os harmonic 77.399 176.610 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p2 harmonic 70.987 172.830 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p3 harmonic 71.573 173.510 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p4 harmonic 70.741 173.640 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-p5 harmonic 74.438 177.280 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s2 harmonic 61.878 178.110 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s4 harmonic 56.730 169.600 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s harmonic 54.789 179.990 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-s6 harmonic 63.372 175.920 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-sh harmonic 57.243 174.250 # HF/6-31G* 1 + angle_coeff @angle:c1-n1-ss harmonic 56.948 176.060 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-n1 harmonic 77.250 180.000 # HF/6-31G* 1 + angle_coeff @angle:c2-n1-o harmonic 91.430 116.940 # SOURCE3 2 0.0060 + angle_coeff @angle:c2-n1-s harmonic 66.557 118.000 # SOURCE3 2 0.0121 + angle_coeff @angle:c3-n1-n1 harmonic 72.180 180.000 # HF/6-31G* 1 + angle_coeff @angle:ca-n1-n1 harmonic 76.091 180.000 # HF/6-31G* 1 + angle_coeff @angle:ce-n1-o harmonic 89.183 122.400 # CORR 2 + angle_coeff @angle:ce-n1-s harmonic 66.690 117.340 # CORR 2 + angle_coeff @angle:cf-n1-o harmonic 89.183 122.400 # CORR 2 + angle_coeff @angle:cf-n1-s harmonic 66.690 117.340 # CORR 2 + angle_coeff @angle:cl-n1-n1 harmonic 77.983 179.940 # HF/6-31G* 1 + angle_coeff @angle:f-n1-n1 harmonic 92.867 179.930 # HF/6-31G* 1 + angle_coeff @angle:hn-n1-n1 harmonic 57.688 179.910 # HF/6-31G* 1 + angle_coeff @angle:i-n1-n1 harmonic 61.297 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n1 harmonic 105.090 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n2 harmonic 102.546 172.850 # HF/6-31G*_SOURCE5 38 0.7957 + angle_coeff @angle:n1-n1-n3 harmonic 95.850 175.090 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-n4 harmonic 94.056 179.910 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-na harmonic 94.541 179.970 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-nh harmonic 96.108 176.000 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-o harmonic 98.200 179.940 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-oh harmonic 98.761 173.770 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-os harmonic 97.594 176.120 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p2 harmonic 88.474 174.710 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-p3 harmonic 89.510 174.270 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-s harmonic 68.668 180.000 # SOURCE3 1 + angle_coeff @angle:n1-n1-sh harmonic 71.618 175.070 # HF/6-31G* 1 + angle_coeff @angle:n1-n1-ss harmonic 71.507 175.610 # HF/6-31G* 1 + angle_coeff @angle:o-n1-p2 harmonic 107.306 116.050 # SOURCE3 1 + angle_coeff @angle:p2-n1-s harmonic 83.718 119.930 # SOURCE3 1 + angle_coeff @angle:br-n2-br harmonic 64.457 106.600 # SOURCE3 1 + angle_coeff @angle:br-n2-c2 harmonic 60.247 112.400 # SOURCE3 1 + angle_coeff @angle:br-n2-n2 harmonic 76.071 110.420 # SOURCE3 1 + angle_coeff @angle:br-n2-o harmonic 74.480 114.470 # SOURCE3 1 + angle_coeff @angle:br-n2-p2 harmonic 82.651 111.030 # SOURCE3 1 + angle_coeff @angle:br-n2-s harmonic 63.537 115.780 # SOURCE3 1 + angle_coeff @angle:c1-n2-c1 harmonic 77.425 121.100 # SOURCE3 1 + angle_coeff @angle:c1-n2-c3 harmonic 60.897 151.880 # SOURCE3 4 15.8282 + angle_coeff @angle:c1-n2-cl harmonic 68.804 118.800 # SOURCE2 1 + angle_coeff @angle:c1-n2-hn harmonic 52.343 126.500 # SOURCE2 3 7.6267 + angle_coeff @angle:c1-n2-n2 harmonic 97.203 113.400 # SOURCE3 1 + angle_coeff @angle:c1-n2-o harmonic 99.262 113.590 # SOURCE3 1 + angle_coeff @angle:c1-n2-p2 harmonic 88.534 119.570 # SOURCE3 1 + angle_coeff @angle:c1-n2-s harmonic 71.943 117.670 # SOURCE3 1 + angle_coeff @angle:c2-n2-c2 harmonic 73.202 118.180 # SOURCE3 1 + angle_coeff @angle:c2-n2-c3 harmonic 68.517 115.300 # SOURCE3 8 4.2940 + angle_coeff @angle:c2-n2-ca harmonic 72.054 119.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-cl harmonic 70.470 112.640 # SOURCE3 1 + angle_coeff @angle:c2-n2-f harmonic 90.773 108.140 # SOURCE3 1 + angle_coeff @angle:c2-n2-hn harmonic 53.185 110.800 # SOURCE3_SOURCE5 419 0.5563 + angle_coeff @angle:c2-n2-i harmonic 54.902 114.740 # SOURCE3 2 0.0139 + angle_coeff @angle:c2-n2-n1 harmonic 94.708 115.090 # HF/6-31G* 1 + angle_coeff @angle:c2-n2-n2 harmonic 98.476 103.590 # SOURCE3 2 + angle_coeff @angle:c2-n2-n3 harmonic 89.963 118.140 # SOURCE3 1 + angle_coeff @angle:c2-n2-n4 harmonic 78.566 112.220 # SOURCE3 3 0.0406 + angle_coeff @angle:c2-n2-n harmonic 88.873 117.930 # SOURCE4_SOURCE5 32 1.2067 + angle_coeff @angle:c2-n2-na harmonic 88.734 117.580 # SOURCE3 8 1.6671 + angle_coeff @angle:c2-n2-nh harmonic 89.294 117.610 # SOURCE3 6 3.2642 + angle_coeff @angle:c2-n2-no harmonic 86.019 118.020 # SOURCE3_SOURCE5 8 0.7772 + angle_coeff @angle:c2-n2-o harmonic 94.405 116.940 # SOURCE3 1 + angle_coeff @angle:c2-n2-oh harmonic 90.358 111.120 # SOURCE4_SOURCE5 59 1.2303 + angle_coeff @angle:c2-n2-os harmonic 90.019 110.960 # SOURCE4_SOURCE5 46 1.0478 + angle_coeff @angle:c2-n2-p2 harmonic 88.774 116.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-p3 harmonic 80.914 119.300 # SOURCE3 3 2.8489 + angle_coeff @angle:c2-n2-p4 harmonic 82.737 118.770 # SOURCE3 1 + angle_coeff @angle:c2-n2-s4 harmonic 70.138 112.290 # SOURCE3 1 + angle_coeff @angle:c2-n2-s6 harmonic 70.821 116.240 # SOURCE3 1 + angle_coeff @angle:c2-n2-s harmonic 70.719 118.000 # SOURCE3 1 + angle_coeff @angle:c2-n2-sh harmonic 64.926 115.480 # SOURCE3 1 + angle_coeff @angle:c2-n2-ss harmonic 66.888 118.040 # SOURCE3 4 2.2804 + angle_coeff @angle:c3-n2-c3 harmonic 66.122 110.700 # SOURCE3 1 + angle_coeff @angle:c3-n2-ca harmonic 68.205 115.050 # SOURCE4_SOURCE5 12 1.0676 + angle_coeff @angle:c3-n2-ce harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 + angle_coeff @angle:c3-n2-cf harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 + angle_coeff @angle:c3-n2-hn harmonic 45.854 118.400 # SOURCE3 1 + angle_coeff @angle:c3-n2-n1 harmonic 86.587 116.100 # SOURCE4_SOURCE5 33 0.4557 + angle_coeff @angle:c3-n2-n2 harmonic 87.844 110.840 # SOURCE3_SOURCE5 20 1.2862 + angle_coeff @angle:c3-n2-nh harmonic 86.138 109.990 # SOURCE3 1 + angle_coeff @angle:c3-n2-o harmonic 88.263 112.400 # SOURCE2 1 + angle_coeff @angle:c3-n2-p2 harmonic 85.879 114.210 # SOURCE3 2 2.2772 + angle_coeff @angle:c3-n2-s6 harmonic 68.328 113.840 # SOURCE3 1 + angle_coeff @angle:c3-n2-s harmonic 67.797 116.720 # SOURCE3 1 + angle_coeff @angle:ca-n2-ca harmonic 73.899 112.200 # SOURCE3 1 + angle_coeff @angle:ca-n2-hn harmonic 50.447 120.000 # SOURCE3 1 + angle_coeff @angle:ca-n2-n2 harmonic 93.256 113.530 # SOURCE3 1 + angle_coeff @angle:ca-n2-o harmonic 93.893 116.000 # SOURCE2 1 + angle_coeff @angle:ca-n2-p2 harmonic 87.640 118.110 # SOURCE3 1 + angle_coeff @angle:ca-n2-s harmonic 69.770 120.110 # SOURCE3 1 + angle_coeff @angle:c-n2-c2 harmonic 68.290 120.970 # SOURCE3 1 + angle_coeff @angle:c-n2-c harmonic 64.555 123.800 # SOURCE3 1 + angle_coeff @angle:c-n2-ca harmonic 67.993 120.500 # SOURCE3 1 + angle_coeff @angle:cc-n2-cl harmonic 69.467 115.790 # CORR 2 + angle_coeff @angle:cc-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 + angle_coeff @angle:cc-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 23 1.5921 + angle_coeff @angle:cc-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 13 1.7276 + angle_coeff @angle:cd-n2-cl harmonic 69.467 115.790 # CORR 2 + angle_coeff @angle:cd-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 + angle_coeff @angle:ce-n2-hn harmonic 52.954 111.000 # CORR_SOURCE5 129 0.3980 + angle_coeff @angle:ce-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 + angle_coeff @angle:ce-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 + angle_coeff @angle:ce-n2-o harmonic 96.153 112.160 # SOURCE3 1 + angle_coeff @angle:ce-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 + angle_coeff @angle:ce-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 + angle_coeff @angle:ce-n2-s harmonic 71.153 116.280 # SOURCE3 1 + angle_coeff @angle:cf-n2-hn harmonic 52.942 111.050 # CORR_SOURCE5 5 0.7460 + angle_coeff @angle:cf-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 + angle_coeff @angle:cf-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 + angle_coeff @angle:cf-n2-o harmonic 96.153 112.160 # SOURCE3 1 + angle_coeff @angle:cf-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 + angle_coeff @angle:cf-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 + angle_coeff @angle:cf-n2-s harmonic 71.153 116.280 # SOURCE3 1 + angle_coeff @angle:cl-n2-n1 harmonic 90.032 108.700 # SOURCE2 1 + angle_coeff @angle:cl-n2-n2 harmonic 89.183 110.470 # SOURCE3 1 + angle_coeff @angle:cl-n2-o harmonic 87.927 114.030 # SOURCE3 1 + angle_coeff @angle:cl-n2-p2 harmonic 93.146 112.980 # SOURCE3 1 + angle_coeff @angle:cl-n2-s harmonic 72.639 115.770 # SOURCE3 1 + angle_coeff @angle:cx-n2-n2 harmonic 113.932 64.920 # SOURCE3 2 + angle_coeff @angle:f-n2-n2 harmonic 110.866 114.600 # SOURCE2 1 + angle_coeff @angle:f-n2-o harmonic 114.530 110.100 # SOURCE2 1 + angle_coeff @angle:f-n2-p2 harmonic 113.300 107.100 # SOURCE3 1 + angle_coeff @angle:f-n2-s harmonic 88.996 110.730 # SOURCE3 1 + angle_coeff @angle:hn-n2-hn harmonic 38.294 120.000 # SOURCE3 1 + angle_coeff @angle:hn-n2-n1 harmonic 67.682 114.100 # SOURCE2 1 + angle_coeff @angle:hn-n2-n2 harmonic 69.032 105.010 # SOURCE3 19 1.5183 + angle_coeff @angle:hn-n2-ne harmonic 67.706 108.560 # SOURCE3 29 5.5708 + angle_coeff @angle:hn-n2-nf harmonic 67.706 108.560 # SOURCE3 29 + angle_coeff @angle:hn-n2-o harmonic 70.317 107.370 # SOURCE3 1 + angle_coeff @angle:hn-n2-p2 harmonic 59.815 112.090 # SOURCE3 18 4.0663 + angle_coeff @angle:hn-n2-p4 harmonic 55.602 111.330 # SOURCE3 1 + angle_coeff @angle:hn-n2-p5 harmonic 57.476 122.340 # SOURCE3 1 + angle_coeff @angle:hn-n2-pe harmonic 62.556 111.410 # SOURCE3 20 4.9895 + angle_coeff @angle:hn-n2-pf harmonic 62.556 111.410 # SOURCE3 20 + angle_coeff @angle:hn-n2-s2 harmonic 47.686 115.800 # SOURCE2 1 + angle_coeff @angle:hn-n2-s4 harmonic 46.643 111.210 # SOURCE3 1 + angle_coeff @angle:hn-n2-s harmonic 49.437 108.170 # SOURCE3 1 + angle_coeff @angle:hn-n2-s6 harmonic 48.367 111.170 # SOURCE3_SOURCE5 7 0.7012 + angle_coeff @angle:i-n2-n2 harmonic 69.513 111.790 # SOURCE3 1 + angle_coeff @angle:i-n2-o harmonic 67.472 116.820 # SOURCE3 1 + angle_coeff @angle:i-n2-p2 harmonic 77.614 113.260 # SOURCE3 1 + angle_coeff @angle:i-n2-s harmonic 59.644 116.850 # SOURCE3 1 + angle_coeff @angle:n1-n2-n1 harmonic 122.832 112.000 # HF/6-31G* 1 + angle_coeff @angle:n2-n2-n1 harmonic 95.438 180.000 # dac_for_azides 0 + angle_coeff @angle:n2-n2-n2 harmonic 120.662 109.490 # SOURCE3 2 + angle_coeff @angle:n2-n2-n3 harmonic 117.964 108.880 # SOURCE3 1 + angle_coeff @angle:n2-n2-n4 harmonic 101.207 106.450 # SOURCE3 1 + angle_coeff @angle:n2-n2-na harmonic 114.285 112.230 # SOURCE3 1 + angle_coeff @angle:n2-n2-nh harmonic 115.311 111.700 # SOURCE3 5 0.3475 + angle_coeff @angle:n2-n2-no harmonic 114.147 105.970 # SOURCE3 1 + angle_coeff @angle:n2-n2-o harmonic 122.449 110.430 # SOURCE3 1 + angle_coeff @angle:n2-n2-oh harmonic 113.470 111.510 # SOURCE3 1 + angle_coeff @angle:n2-n2-os harmonic 114.570 108.380 # SOURCE3 1 + angle_coeff @angle:n2-n2-p2 harmonic 114.892 109.150 # SOURCE3 1 + angle_coeff @angle:n2-n2-p3 harmonic 104.216 113.050 # SOURCE3 1 + angle_coeff @angle:n2-n2-p4 harmonic 103.768 118.770 # SOURCE3 1 + angle_coeff @angle:n2-n2-p5 harmonic 114.546 110.460 # SOURCE3 1 + angle_coeff @angle:n2-n2-s4 harmonic 90.072 107.300 # SOURCE3 1 + angle_coeff @angle:n2-n2-s6 harmonic 90.924 111.250 # SOURCE3 1 + angle_coeff @angle:n2-n2-s harmonic 89.630 115.910 # SOURCE3 1 + angle_coeff @angle:n2-n2-sh harmonic 83.010 111.100 # SOURCE3 1 + angle_coeff @angle:n2-n2-ss harmonic 86.115 112.140 # SOURCE3 1 + angle_coeff @angle:n3-n2-n3 harmonic 112.191 115.070 # SOURCE3 1 + angle_coeff @angle:n3-n2-o harmonic 117.213 114.000 # SOURCE2 1 + angle_coeff @angle:n3-n2-p2 harmonic 110.501 115.340 # SOURCE3 1 + angle_coeff @angle:n3-n2-s harmonic 87.944 117.130 # SOURCE3 1 + angle_coeff @angle:n4-n2-n4 harmonic 92.222 106.700 # SOURCE3 1 + angle_coeff @angle:n4-n2-o harmonic 99.103 112.200 # SOURCE3 1 + angle_coeff @angle:n4-n2-p2 harmonic 101.387 113.070 # SOURCE3 1 + angle_coeff @angle:n4-n2-s harmonic 78.497 118.500 # SOURCE3 1 + angle_coeff @angle:na-n2-na harmonic 113.061 107.000 # SOURCE3 1 + angle_coeff @angle:na-n2-o harmonic 115.589 113.090 # SOURCE3 1 + angle_coeff @angle:na-n2-p2 harmonic 107.835 119.160 # SOURCE3 1 + angle_coeff @angle:na-n2-s harmonic 86.691 118.260 # SOURCE3 1 + angle_coeff @angle:ne-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 + angle_coeff @angle:ne-n2-o harmonic 122.270 110.310 # SOURCE3 1 + angle_coeff @angle:ne-n2-s harmonic 89.426 116.220 # SOURCE3 1 + angle_coeff @angle:nf-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 + angle_coeff @angle:nf-n2-o harmonic 122.270 110.310 # SOURCE3 1 + angle_coeff @angle:nf-n2-s harmonic 89.426 116.220 # SOURCE3 1 + angle_coeff @angle:nh-n2-nh harmonic 107.426 121.200 # SOURCE3 1 + angle_coeff @angle:nh-n2-o harmonic 116.027 113.850 # SOURCE4_SOURCE5 33 1.0590 + angle_coeff @angle:nh-n2-p2 harmonic 108.341 118.830 # SOURCE3 2 0.1024 + angle_coeff @angle:nh-n2-s harmonic 87.530 116.900 # SOURCE3 2 0.2276 + angle_coeff @angle:n-n2-n2 harmonic 116.779 108.160 # SOURCE4_SOURCE5 18 0.3340 + angle_coeff @angle:n-n2-o harmonic 114.959 115.110 # SOURCE4_SOURCE5 85 0.2779 + angle_coeff @angle:no-n2-no harmonic 109.483 103.700 # SOURCE3 1 + angle_coeff @angle:no-n2-o harmonic 118.569 100.760 # SOURCE3 1 + angle_coeff @angle:no-n2-p2 harmonic 109.507 111.950 # SOURCE3 1 + angle_coeff @angle:n-n2-p2 harmonic 108.858 117.300 # SOURCE3 1 + angle_coeff @angle:n-n2-s harmonic 87.790 115.740 # SOURCE3 1 + angle_coeff @angle:oh-n2-oh harmonic 114.003 101.700 # SOURCE3 1 + angle_coeff @angle:oh-n2-p2 harmonic 109.132 115.110 # SOURCE3 1 + angle_coeff @angle:oh-n2-s harmonic 86.961 116.080 # SOURCE3 1 + angle_coeff @angle:o-n2-o harmonic 122.337 115.370 # SOURCE3 1 + angle_coeff @angle:o-n2-oh harmonic 114.777 112.150 # SOURCE2 2 1.4500 + angle_coeff @angle:o-n2-os harmonic 115.139 110.350 # SOURCE3 2 0.0042 + angle_coeff @angle:o-n2-p2 harmonic 112.237 116.080 # SOURCE3 1 + angle_coeff @angle:o-n2-p3 harmonic 104.358 113.430 # SOURCE3 1 + angle_coeff @angle:o-n2-p4 harmonic 107.967 110.610 # SOURCE3 1 + angle_coeff @angle:o-n2-p5 harmonic 116.129 109.110 # SOURCE3 1 + angle_coeff @angle:o-n2-pe harmonic 107.813 134.560 # SOURCE3 1 + angle_coeff @angle:o-n2-pf harmonic 107.813 134.560 # SOURCE3 1 + angle_coeff @angle:o-n2-s4 harmonic 90.054 108.910 # SOURCE3 1 + angle_coeff @angle:o-n2-s6 harmonic 91.703 111.340 # SOURCE3 1 + angle_coeff @angle:o-n2-s harmonic 89.978 117.180 # SOURCE3 1 + angle_coeff @angle:o-n2-sh harmonic 81.901 114.980 # SOURCE3 1 + angle_coeff @angle:os-n2-os harmonic 108.669 110.290 # SOURCE3 1 + angle_coeff @angle:os-n2-p2 harmonic 111.268 110.200 # SOURCE3 1 + angle_coeff @angle:o-n2-ss harmonic 85.259 115.770 # SOURCE3_SOURCE5 7 0.2342 + angle_coeff @angle:os-n2-s harmonic 88.194 112.230 # SOURCE3 1 + angle_coeff @angle:p2-n2-p2 harmonic 113.183 116.800 # SOURCE3 1 + angle_coeff @angle:p2-n2-p3 harmonic 103.997 124.480 # SOURCE3 1 + angle_coeff @angle:p2-n2-p4 harmonic 103.837 128.370 # SOURCE3 1 + angle_coeff @angle:p2-n2-p5 harmonic 110.289 123.470 # SOURCE3 1 + angle_coeff @angle:p2-n2-s4 harmonic 89.884 112.100 # SOURCE3 1 + angle_coeff @angle:p2-n2-s6 harmonic 90.002 115.700 # SOURCE3 1 + angle_coeff @angle:p2-n2-s harmonic 89.517 117.840 # SOURCE3 1 + angle_coeff @angle:p2-n2-sh harmonic 83.828 118.450 # SOURCE3 1 + angle_coeff @angle:p2-n2-ss harmonic 85.455 120.430 # SOURCE3 1 + angle_coeff @angle:p3-n2-p3 harmonic 101.430 120.400 # SOURCE3 1 + angle_coeff @angle:p3-n2-s harmonic 83.445 120.860 # SOURCE3 1 + angle_coeff @angle:p4-n2-s harmonic 81.102 131.840 # SOURCE3 1 + angle_coeff @angle:p5-n2-p5 harmonic 111.803 120.600 # SOURCE3 1 + angle_coeff @angle:p5-n2-s harmonic 88.930 119.890 # SOURCE3 1 + angle_coeff @angle:pe-n2-s harmonic 92.311 115.730 # SOURCE3 1 + angle_coeff @angle:pf-n2-s harmonic 92.311 115.730 # SOURCE3 1 + angle_coeff @angle:s4-n2-s4 harmonic 67.822 119.180 # SOURCE3 1 + angle_coeff @angle:s4-n2-s6 harmonic 68.983 119.180 # SOURCE3 1 + angle_coeff @angle:s6-n2-s6 harmonic 70.275 119.180 # SOURCE3 1 + angle_coeff @angle:sh-n2-sh harmonic 61.611 123.930 # SOURCE3 1 + angle_coeff @angle:sh-n2-ss harmonic 63.026 123.930 # SOURCE3 1 + angle_coeff @angle:s-n2-s harmonic 70.359 120.880 # SOURCE3 1 + angle_coeff @angle:s-n2-s4 harmonic 71.109 113.000 # SOURCE3 1 + angle_coeff @angle:s-n2-s6 harmonic 70.436 119.610 # SOURCE3 1 + angle_coeff @angle:s-n2-sh harmonic 65.341 122.050 # SOURCE3 1 + angle_coeff @angle:s-n2-ss harmonic 68.418 118.190 # SOURCE3 1 + angle_coeff @angle:ss-n2-ss harmonic 64.662 123.930 # SOURCE3 1 + angle_coeff @angle:br-n3-br harmonic 67.124 107.150 # SOURCE3 1 + angle_coeff @angle:br-n3-c3 harmonic 63.925 106.930 # SOURCE3 2 + angle_coeff @angle:c1-n3-c1 harmonic 68.156 123.340 # SOURCE3 1 + angle_coeff @angle:c1-n3-f harmonic 91.888 104.700 # SOURCE2 1 + angle_coeff @angle:c1-n3-hn harmonic 50.216 114.780 # SOURCE3_SOURCE5 7 0.4776 + angle_coeff @angle:c1-n3-o harmonic 89.192 116.630 # SOURCE3 1 + angle_coeff @angle:c2-n3-c2 harmonic 68.168 124.680 # SOURCE3 1 + angle_coeff @angle:c2-n3-hn harmonic 49.470 119.380 # SOURCE3 1 + angle_coeff @angle:c3-n3-c3 harmonic 65.697 112.350 # SOURCE3_SOURCE5 10425 1.3688 + angle_coeff @angle:c3-n3-cl harmonic 72.005 107.230 # SOURCE3 3 0.3673 + angle_coeff @angle:c3-n3-cx harmonic 64.536 116.000 # SOURCE4_SOURCE5 93 0.9654 + angle_coeff @angle:c3-n3-cy harmonic 63.919 117.550 # SOURCE4_SOURCE5 52 1.6649 + angle_coeff @angle:c3-n3-f harmonic 88.810 103.130 # SOURCE3 2 + angle_coeff @angle:c3-n3-hn harmonic 47.782 109.290 # SOURCE3_SOURCE5 6742 0.6614 + angle_coeff @angle:c3-n3-i harmonic 60.375 108.480 # SOURCE3 2 + angle_coeff @angle:c3-n3-n2 harmonic 83.514 118.750 # SOURCE2 2 2.6500 + angle_coeff @angle:c3-n3-n3 harmonic 83.494 110.800 # SOURCE3_SOURCE5 91 1.4698 + angle_coeff @angle:c3-n3-n4 harmonic 84.250 109.650 # SOURCE3 3 0.1146 + angle_coeff @angle:c3-n3-n harmonic 84.170 111.710 # SOURCE4_SOURCE5 108 1.7154 + angle_coeff @angle:c3-n3-nh harmonic 83.840 111.770 # SOURCE4_SOURCE5 54 1.2232 + angle_coeff @angle:c3-n3-no harmonic 82.437 116.930 # SOURCE3_SOURCE5 25 0.8475 + angle_coeff @angle:c3-n3-o harmonic 86.116 113.310 # SOURCE3 5 8.9081 + angle_coeff @angle:c3-n3-oh harmonic 85.913 106.490 # SOURCE4_SOURCE5 51 1.1723 + angle_coeff @angle:c3-n3-os harmonic 85.469 105.800 # SOURCE4_SOURCE5 28 1.5996 + angle_coeff @angle:c3-n3-p3 harmonic 79.872 119.670 # SOURCE3_SOURCE5 17 1.9089 + angle_coeff @angle:c3-n3-p5 harmonic 81.775 119.860 # SOURCE4_SOURCE5 188 2.0452 + angle_coeff @angle:c3-n3-s4 harmonic 62.997 114.490 # SOURCE3_SOURCE5 8 1.8120 + angle_coeff @angle:c3-n3-s6 harmonic 64.550 116.550 # SOURCE4_SOURCE5 179 1.8765 + angle_coeff @angle:c3-n3-s harmonic 63.268 110.020 # SOURCE3 1 + angle_coeff @angle:c3-n3-sh harmonic 63.898 112.700 # SOURCE3 1 + angle_coeff @angle:c3-n3-ss harmonic 63.312 116.250 # SOURCE3_SOURCE5 14 1.9512 + angle_coeff @angle:c3-n3-sy harmonic 64.295 115.250 # SOURCE4_SOURCE5 250 1.7586 + angle_coeff @angle:cl-n3-cl harmonic 80.378 108.280 # SOURCE3 1 + angle_coeff @angle:cl-n3-hn harmonic 48.266 104.390 # SOURCE3 2 + angle_coeff @angle:cl-n3-n3 harmonic 90.354 107.650 # SOURCE3 1 + angle_coeff @angle:cx-n3-cx harmonic 89.029 60.730 # SOURCE4_SOURCE5 147 0.2518 + angle_coeff @angle:cx-n3-hn harmonic 47.500 109.830 # SOURCE4_SOURCE5 76 0.6684 + angle_coeff @angle:cx-n3-p5 harmonic 81.827 119.410 # SOURCE4_SOURCE5 173 1.2386 + angle_coeff @angle:cx-n3-py harmonic 80.259 121.750 # SOURCE4_SOURCE5 20 1.0295 + angle_coeff @angle:cy-n3-cy harmonic 72.263 91.110 # SOURCE4_SOURCE5 36 0.9119 + angle_coeff @angle:cy-n3-hn harmonic 47.059 110.670 # SOURCE4_SOURCE5 48 0.9592 + angle_coeff @angle:f-n3-f harmonic 115.777 102.220 # SOURCE2 4 0.7562 + angle_coeff @angle:f-n3-hn harmonic 65.935 99.800 # SOURCE2 1 + angle_coeff @angle:hn-n3-hn harmonic 40.828 106.400 # SOURCE3_SOURCE5 2019 0.9777 + angle_coeff @angle:hn-n3-i harmonic 36.749 109.980 # SOURCE3 2 + angle_coeff @angle:hn-n3-n1 harmonic 64.085 110.170 # HF/6-31G* 1 + angle_coeff @angle:hn-n3-n2 harmonic 63.293 115.940 # SOURCE3 1 + angle_coeff @angle:hn-n3-n3 harmonic 61.180 107.680 # SOURCE3_SOURCE5 107 1.7630 + angle_coeff @angle:hn-n3-n4 harmonic 61.852 106.910 # SOURCE3_SOURCE5 18 0.7068 + angle_coeff @angle:hn-n3-n harmonic 62.520 108.120 # SOURCE3_SOURCE5 90 1.1435 + angle_coeff @angle:hn-n3-na harmonic 61.963 107.890 # SOURCE3 1 + angle_coeff @angle:hn-n3-nh harmonic 62.016 108.310 # SOURCE3_SOURCE5 85 1.2609 + angle_coeff @angle:hn-n3-no harmonic 63.767 104.780 # SOURCE3 3 1.1126 + angle_coeff @angle:hn-n3-o harmonic 65.058 113.320 # SOURCE3 3 4.3945 + angle_coeff @angle:hn-n3-oh harmonic 63.840 102.300 # SOURCE3_SOURCE5 14 0.6850 + angle_coeff @angle:hn-n3-os harmonic 62.667 102.750 # SOURCE3_SOURCE5 43 0.6086 + angle_coeff @angle:hn-n3-p2 harmonic 55.368 120.260 # SOURCE3 1 + angle_coeff @angle:hn-n3-p3 harmonic 54.032 116.890 # SOURCE3 9 3.8816 + angle_coeff @angle:hn-n3-p4 harmonic 56.121 113.050 # SOURCE3 2 + angle_coeff @angle:hn-n3-p5 harmonic 56.803 114.320 # SOURCE3_SOURCE5 63 1.6600 + angle_coeff @angle:hn-n3-s4 harmonic 42.895 109.140 # SOURCE3_SOURCE5 13 1.2903 + angle_coeff @angle:hn-n3-s harmonic 41.811 109.470 # SOURCE3 1 + angle_coeff @angle:hn-n3-s6 harmonic 45.126 109.600 # SOURCE4_SOURCE5 234 1.2605 + angle_coeff @angle:hn-n3-sh harmonic 43.414 108.670 # SOURCE3 3 2.5025 + angle_coeff @angle:hn-n3-ss harmonic 43.417 110.830 # SOURCE3_SOURCE5 14 1.1613 + angle_coeff @angle:hn-n3-sy harmonic 44.457 109.500 # SOURCE4_SOURCE5 617 0.8005 + angle_coeff @angle:i-n3-i harmonic 65.458 111.270 # SOURCE3 1 + angle_coeff @angle:n1-n3-n1 harmonic 111.350 113.210 # HF/6-31G* 1 + angle_coeff @angle:n2-n3-n2 harmonic 110.449 118.730 # SOURCE3 1 + angle_coeff @angle:n2-n3-o harmonic 113.356 114.910 # SOURCE3 1 + angle_coeff @angle:n3-n3-n3 harmonic 107.918 105.710 # SOURCE3 3 0.3561 + angle_coeff @angle:n4-n3-n4 harmonic 104.995 113.480 # SOURCE3 1 + angle_coeff @angle:n4-n3-nh harmonic 108.598 107.140 # SOURCE3 1 + angle_coeff @angle:na-n3-na harmonic 106.431 112.000 # SOURCE3 1 + angle_coeff @angle:nh-n3-nh harmonic 109.151 107.150 # SOURCE3 1 + angle_coeff @angle:n-n3-n harmonic 108.332 110.550 # SOURCE3 1 + angle_coeff @angle:no-n3-no harmonic 106.581 115.260 # SOURCE3 1 + angle_coeff @angle:oh-n3-oh harmonic 109.190 107.180 # SOURCE3 1 + angle_coeff @angle:o-n3-o harmonic 109.294 126.140 # SOURCE3 1 + angle_coeff @angle:o-n3-p2 harmonic 106.891 117.020 # SOURCE3 1 + angle_coeff @angle:o-n3-p4 harmonic 105.671 116.650 # SOURCE3 1 + angle_coeff @angle:o-n3-s4 harmonic 80.957 114.090 # SOURCE3 1 + angle_coeff @angle:o-n3-s6 harmonic 84.368 113.800 # SOURCE3 1 + angle_coeff @angle:o-n3-s harmonic 77.548 119.810 # SOURCE3 1 + angle_coeff @angle:os-n3-os harmonic 107.574 106.520 # SOURCE3 1 + angle_coeff @angle:p2-n3-p2 harmonic 103.056 130.130 # SOURCE3 1 + angle_coeff @angle:p3-n3-p3 harmonic 104.144 118.740 # SOURCE3 3 3.3755 + angle_coeff @angle:p4-n3-p4 harmonic 107.254 116.350 # SOURCE3 1 + angle_coeff @angle:p5-n3-p5 harmonic 107.603 119.420 # SOURCE3 1 + angle_coeff @angle:s4-n3-s4 harmonic 62.022 120.020 # SOURCE3 1 + angle_coeff @angle:s4-n3-s6 harmonic 63.190 120.950 # SOURCE3 1 + angle_coeff @angle:s6-n3-s6 harmonic 65.471 118.540 # SOURCE3_SOURCE5 18 1.1456 + angle_coeff @angle:sh-n3-sh harmonic 62.936 118.630 # SOURCE3 1 + angle_coeff @angle:sh-n3-ss harmonic 62.938 119.670 # SOURCE3 1 + angle_coeff @angle:s-n3-s harmonic 58.040 131.360 # SOURCE3 1 + angle_coeff @angle:ss-n3-ss harmonic 63.249 119.570 # SOURCE3 1 + angle_coeff @angle:br-n4-br harmonic 65.719 114.820 # SOURCE3 1 + angle_coeff @angle:br-n4-hn harmonic 41.251 108.440 # SOURCE3 7 0.5630 + angle_coeff @angle:c1-n4-c1 harmonic 67.454 113.870 # SOURCE3 1 + angle_coeff @angle:c1-n4-hn harmonic 48.997 110.190 # SOURCE3 7 1.0847 + angle_coeff @angle:c2-n4-c2 harmonic 63.556 112.580 # SOURCE3 1 + angle_coeff @angle:c2-n4-c3 harmonic 64.050 110.960 # SOURCE4 13 2.4632 + angle_coeff @angle:c2-n4-hn harmonic 46.094 110.370 # SOURCE3_SOURCE5 39 1.1227 + angle_coeff @angle:c3-n4-c3 harmonic 64.460 109.660 # SOURCE3_SOURCE5 2931 1.1695 + angle_coeff @angle:c3-n4-ca harmonic 64.770 110.530 # SOURCE4_SOURCE5 127 1.4968 + angle_coeff @angle:c3-n4-cc harmonic 64.438 111.040 # SOURCE4_SOURCE5 18 1.4876 + angle_coeff @angle:c3-n4-cl harmonic 71.792 108.040 # SOURCE3 3 + angle_coeff @angle:c3-n4-hn harmonic 46.193 110.110 # SOURCE3 100 1.3136 + angle_coeff @angle:c3-n4-n3 harmonic 83.568 107.700 # SOURCE3_SOURCE5 11 1.5498 + angle_coeff @angle:c3-n4-n4 harmonic 79.845 114.070 # SOURCE3 4 + angle_coeff @angle:c3-n4-n harmonic 82.738 109.740 # SOURCE4_SOURCE5 17 2.0520 + angle_coeff @angle:c3-n4-nh harmonic 81.141 111.730 # SOURCE3 1 + angle_coeff @angle:c3-n4-no harmonic 81.756 109.080 # SOURCE3 1 + angle_coeff @angle:c3-n4-o harmonic 84.145 110.520 # SOURCE3_SOURCE5 7 0.8910 + angle_coeff @angle:c3-n4-oh harmonic 82.047 113.730 # SOURCE3 1 + angle_coeff @angle:c3-n4-os harmonic 83.903 107.420 # SOURCE3 3 3.5920 + angle_coeff @angle:c3-n4-p2 harmonic 74.897 112.520 # SOURCE3 1 + angle_coeff @angle:c3-n4-p3 harmonic 77.458 110.730 # SOURCE3 3 2.1084 + angle_coeff @angle:c3-n4-p5 harmonic 78.172 113.220 # SOURCE3 3 0.4021 + angle_coeff @angle:c3-n4-s4 harmonic 58.766 108.230 # SOURCE3 3 0.4195 + angle_coeff @angle:c3-n4-s6 harmonic 59.297 111.560 # SOURCE3 3 1.8851 + angle_coeff @angle:c3-n4-s harmonic 60.776 113.550 # SOURCE3 1 + angle_coeff @angle:c3-n4-sh harmonic 60.690 115.810 # SOURCE3 1 + angle_coeff @angle:c3-n4-ss harmonic 61.231 113.680 # SOURCE3 3 1.1405 + angle_coeff @angle:ca-n4-ca harmonic 64.228 114.480 # SOURCE3 1 + angle_coeff @angle:ca-n4-hn harmonic 46.901 110.500 # SOURCE3_SOURCE5 23 1.4863 + angle_coeff @angle:c-n4-c harmonic 63.305 108.610 # SOURCE3 1 + angle_coeff @angle:c-n4-hn harmonic 44.970 111.120 # SOURCE3_SOURCE5 17 0.9627 + angle_coeff @angle:cl-n4-cl harmonic 79.101 114.910 # SOURCE3 1 + angle_coeff @angle:cl-n4-hn harmonic 48.065 108.870 # SOURCE3 7 0.7719 + angle_coeff @angle:f-n4-f harmonic 120.491 109.050 # SOURCE3 1 + angle_coeff @angle:f-n4-hn harmonic 67.122 108.390 # SOURCE3 4 + angle_coeff @angle:hn-n4-hn harmonic 40.020 108.300 # SOURCE3_SOURCE5 588 1.8224 + angle_coeff @angle:hn-n4-i harmonic 37.762 108.720 # SOURCE3 7 1.2717 + angle_coeff @angle:hn-n4-n1 harmonic 63.803 109.390 # HF/6-31G* 1 + angle_coeff @angle:hn-n4-n2 harmonic 52.071 109.680 # SOURCE3 19 0.6266 + angle_coeff @angle:hn-n4-n3 harmonic 60.801 110.400 # SOURCE3 11 0.7307 + angle_coeff @angle:hn-n4-n4 harmonic 59.235 108.660 # SOURCE3 18 1.2967 + angle_coeff @angle:hn-n4-n harmonic 61.091 109.080 # SOURCE3 13 1.6047 + angle_coeff @angle:hn-n4-na harmonic 60.973 109.090 # SOURCE3_SOURCE5 31 1.0459 + angle_coeff @angle:hn-n4-nh harmonic 59.568 109.920 # SOURCE3 12 0.7304 + angle_coeff @angle:hn-n4-no harmonic 60.590 104.380 # SOURCE3 2 + angle_coeff @angle:hn-n4-o harmonic 63.200 111.350 # SOURCE3_SOURCE5 11 1.4866 + angle_coeff @angle:hn-n4-oh harmonic 62.612 108.090 # SOURCE3 6 1.6728 + angle_coeff @angle:hn-n4-os harmonic 61.427 109.390 # SOURCE3 10 1.4403 + angle_coeff @angle:hn-n4-p2 harmonic 48.678 110.500 # SOURCE3 25 1.0664 + angle_coeff @angle:hn-n4-p3 harmonic 50.742 109.890 # SOURCE3 10 2.3870 + angle_coeff @angle:hn-n4-p4 harmonic 48.617 111.330 # SOURCE3 3 + angle_coeff @angle:hn-n4-p5 harmonic 52.339 110.000 # SOURCE3 10 1.0282 + angle_coeff @angle:hn-n4-py harmonic 48.319 117.890 # SOURCE3 8 + angle_coeff @angle:hn-n4-s4 harmonic 37.298 110.100 # SOURCE3 6 0.8471 + angle_coeff @angle:hn-n4-s harmonic 41.320 106.890 # SOURCE3 6 1.0775 + angle_coeff @angle:hn-n4-s6 harmonic 38.875 108.940 # SOURCE3 10 0.5715 + angle_coeff @angle:hn-n4-sh harmonic 41.549 108.560 # SOURCE3 6 0.8535 + angle_coeff @angle:hn-n4-ss harmonic 41.406 109.170 # SOURCE3 10 0.8455 + angle_coeff @angle:i-n4-i harmonic 64.315 118.490 # SOURCE3 1 + angle_coeff @angle:n1-n4-n1 harmonic 111.792 110.670 # HF/6-31G* 1 + angle_coeff @angle:n2-n4-n2 harmonic 91.394 108.640 # SOURCE3 1 + angle_coeff @angle:n3-n4-n3 harmonic 106.128 111.070 # SOURCE3 1 + angle_coeff @angle:n4-n4-n4 harmonic 100.290 115.490 # SOURCE3 1 + angle_coeff @angle:na-n4-na harmonic 101.917 119.600 # SOURCE3 1 + angle_coeff @angle:nh-n4-nh harmonic 104.319 109.380 # SOURCE3 1 + angle_coeff @angle:n-n4-n harmonic 102.552 118.620 # SOURCE3 1 + angle_coeff @angle:oh-n4-oh harmonic 109.836 108.190 # SOURCE3 1 + angle_coeff @angle:o-n4-o harmonic 106.848 120.970 # SOURCE3 1 + angle_coeff @angle:os-n4-os harmonic 110.159 104.400 # SOURCE3 1 + angle_coeff @angle:p2-n4-p2 harmonic 94.721 113.910 # SOURCE3 2 + angle_coeff @angle:p3-n4-p3 harmonic 94.786 121.380 # SOURCE3 1 + angle_coeff @angle:p5-n4-p5 harmonic 103.704 107.020 # SOURCE3 1 + angle_coeff @angle:py-n4-py harmonic 123.558 69.790 # SOURCE3 2 + angle_coeff @angle:s4-n4-s4 harmonic 56.264 115.430 # SOURCE3 1 + angle_coeff @angle:s6-n4-s6 harmonic 59.515 109.510 # SOURCE3 1 + angle_coeff @angle:sh-n4-sh harmonic 62.034 112.590 # SOURCE3 1 + angle_coeff @angle:s-n4-s harmonic 58.304 124.550 # SOURCE3 1 + angle_coeff @angle:ss-n4-ss harmonic 62.955 109.200 # SOURCE3 1 + angle_coeff @angle:br-na-br harmonic 61.086 123.000 # SOURCE3 1 + angle_coeff @angle:br-na-c2 harmonic 64.788 100.480 # SOURCE3 2 1.0536 + angle_coeff @angle:br-na-ca harmonic 58.177 124.810 # SOURCE3 1 + angle_coeff @angle:br-na-cc harmonic 58.230 124.620 # SOURCE3 3 0.5348 + angle_coeff @angle:br-na-cd harmonic 58.230 124.620 # SOURCE3 3 + angle_coeff @angle:br-na-nc harmonic 74.547 119.420 # SOURCE3 4 1.6703 + angle_coeff @angle:br-na-nd harmonic 74.550 119.420 # SOURCE3 4 + angle_coeff @angle:br-na-os harmonic 79.164 104.990 # SOURCE3 1 + angle_coeff @angle:br-na-p2 harmonic 78.377 121.010 # SOURCE3 1 + angle_coeff @angle:br-na-pc harmonic 78.871 120.260 # SOURCE3 3 2.1456 + angle_coeff @angle:br-na-pd harmonic 78.871 120.260 # SOURCE3 3 + angle_coeff @angle:br-na-ss harmonic 63.599 112.280 # SOURCE3 1 + angle_coeff @angle:c1-na-c1 harmonic 69.174 117.200 # SOURCE3 1 + angle_coeff @angle:c1-na-c2 harmonic 65.944 125.200 # SOURCE3 1 + angle_coeff @angle:c1-na-ca harmonic 67.645 120.570 # SOURCE3 1 + angle_coeff @angle:c1-na-cc harmonic 67.523 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-cd harmonic 67.523 121.350 # SOURCE3 6 0.6517 + angle_coeff @angle:c1-na-nc harmonic 85.715 120.240 # SOURCE3 4 1.6849 + angle_coeff @angle:c1-na-nd harmonic 85.768 120.240 # SOURCE3 4 + angle_coeff @angle:c1-na-os harmonic 87.875 106.960 # SOURCE3 2 + angle_coeff @angle:c1-na-p2 harmonic 79.771 122.250 # SOURCE3 1 + angle_coeff @angle:c1-na-pc harmonic 80.652 121.480 # SOURCE3 3 2.1681 + angle_coeff @angle:c1-na-pd harmonic 80.652 121.480 # SOURCE3 3 + angle_coeff @angle:c1-na-ss harmonic 63.670 118.300 # SOURCE3 1 + angle_coeff @angle:c2-na-c2 harmonic 69.273 110.370 # SOURCE3 6 0.5121 + angle_coeff @angle:c2-na-c3 harmonic 65.723 117.200 # SOURCE3 2 + angle_coeff @angle:c2-na-ca harmonic 65.505 124.970 # SOURCE4_SOURCE5 19 0.9360 + angle_coeff @angle:c2-na-cc harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 + angle_coeff @angle:c2-na-cd harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 + angle_coeff @angle:c2-na-cl harmonic 73.039 101.010 # SOURCE3 2 1.5799 + angle_coeff @angle:c2-na-f harmonic 90.731 103.110 # SOURCE3 1 + angle_coeff @angle:c2-na-hn harmonic 47.660 119.280 # SOURCE3 14 6.6027 + angle_coeff @angle:c2-na-i harmonic 62.480 106.740 # SOURCE3 1 + angle_coeff @angle:c2-na-n1 harmonic 83.043 124.810 # HF/6-31G* 1 + angle_coeff @angle:c2-na-n2 harmonic 82.486 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-n3 harmonic 81.036 124.800 # SOURCE3 1 + angle_coeff @angle:c2-na-n4 harmonic 81.740 121.320 # SOURCE3 1 + angle_coeff @angle:c2-na-n harmonic 81.447 124.700 # SOURCE3 1 + angle_coeff @angle:c2-na-na harmonic 81.658 124.600 # SOURCE3 1 + angle_coeff @angle:c2-na-nc harmonic 84.246 120.800 # CORR_SOURCE5 5 1.0225 + angle_coeff @angle:c2-na-nd harmonic 84.294 120.800 # CORR_SOURCE5 5 1.0225 + angle_coeff @angle:c2-na-nh harmonic 81.563 124.980 # SOURCE3 1 + angle_coeff @angle:c2-na-no harmonic 80.798 124.200 # SOURCE3 1 + angle_coeff @angle:c2-na-o harmonic 85.559 125.900 # SOURCE3 1 + angle_coeff @angle:c2-na-oh harmonic 82.136 123.900 # SOURCE3 1 + angle_coeff @angle:c2-na-os harmonic 85.429 110.330 # SOURCE3 4 3.2172 + angle_coeff @angle:c2-na-p2 harmonic 79.329 122.140 # SOURCE3 1 + angle_coeff @angle:c2-na-p3 harmonic 77.626 126.100 # SOURCE3 1 + angle_coeff @angle:c2-na-p4 harmonic 84.849 125.000 # SOURCE3 1 + angle_coeff @angle:c2-na-p5 harmonic 79.565 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-pc harmonic 80.116 121.560 # SOURCE3 3 1.6252 + angle_coeff @angle:c2-na-pd harmonic 80.116 121.560 # SOURCE3 3 + angle_coeff @angle:c2-na-s4 harmonic 59.943 124.900 # SOURCE3 1 + angle_coeff @angle:c2-na-s6 harmonic 61.964 124.400 # SOURCE3 1 + angle_coeff @angle:c2-na-s harmonic 60.479 125.800 # SOURCE3 1 + angle_coeff @angle:c2-na-sh harmonic 61.837 125.100 # SOURCE3 1 + angle_coeff @angle:c2-na-ss harmonic 64.023 115.530 # SOURCE3 5 1.4036 + angle_coeff @angle:c3-na-c3 harmonic 62.214 125.590 # SOURCE3 1 + angle_coeff @angle:c3-na-ca harmonic 64.155 124.360 # SOURCE3 5 4.2557 + angle_coeff @angle:c3-na-cc harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 + angle_coeff @angle:c3-na-cd harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 + angle_coeff @angle:c3-na-cp harmonic 65.414 119.620 # SOURCE4_SOURCE5 17 0.4924 + angle_coeff @angle:c3-na-n2 harmonic 82.460 119.240 # SOURCE4_SOURCE5 15 0.8410 + angle_coeff @angle:c3-na-n harmonic 83.711 112.880 # SOURCE4_SOURCE5 34 0.6363 + angle_coeff @angle:c3-na-nc harmonic 82.430 120.180 # SOURCE3_SOURCE5 266 0.9487 + angle_coeff @angle:c3-na-nd harmonic 82.472 120.180 # SOURCE3_SOURCE5 266 0.9487 + angle_coeff @angle:c3-na-os harmonic 86.002 104.390 # SOURCE3 3 1.2017 + angle_coeff @angle:c3-na-p2 harmonic 78.161 123.120 # SOURCE3 1 + angle_coeff @angle:c3-na-pc harmonic 79.034 122.110 # SOURCE3 3 2.8504 + angle_coeff @angle:c3-na-pd harmonic 79.034 122.110 # SOURCE3 3 + angle_coeff @angle:c3-na-sh harmonic 65.096 110.280 # SOURCE3 1 + angle_coeff @angle:c3-na-ss harmonic 64.618 110.870 # SOURCE3 3 0.8260 + angle_coeff @angle:ca-na-ca harmonic 67.261 120.050 # SOURCE4_SOURCE5 899 1.7177 + angle_coeff @angle:ca-na-cc harmonic 69.377 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cd harmonic 69.377 113.150 # SOURCE3 18 9.8644 + angle_coeff @angle:ca-na-cl harmonic 65.846 124.790 # SOURCE3 1 + angle_coeff @angle:ca-na-cp harmonic 67.035 120.860 # SOURCE4_SOURCE5 58 1.3836 + angle_coeff @angle:ca-na-cx harmonic 64.141 124.590 # SOURCE4_SOURCE5 51 1.7589 + angle_coeff @angle:ca-na-f harmonic 85.915 116.400 # SOURCE3 1 + angle_coeff @angle:ca-na-hn harmonic 46.979 125.540 # SOURCE4_SOURCE5 1396 1.1217 + angle_coeff @angle:ca-na-i harmonic 58.530 121.620 # SOURCE3 1 + angle_coeff @angle:ca-na-n2 harmonic 85.072 119.070 # SOURCE4_SOURCE5 19 2.0667 + angle_coeff @angle:ca-na-n4 harmonic 82.602 120.190 # SOURCE3 1 + angle_coeff @angle:ca-na-n harmonic 82.849 122.000 # SOURCE3 1 + angle_coeff @angle:ca-na-na harmonic 82.443 123.760 # SOURCE3 1 + angle_coeff @angle:ca-na-nb harmonic 84.426 122.640 # SOURCE4_SOURCE5 30 1.1363 + angle_coeff @angle:ca-na-nc harmonic 85.867 117.850 # SOURCE3 6 3.6536 + angle_coeff @angle:ca-na-nd harmonic 85.918 117.850 # SOURCE3 6 + angle_coeff @angle:ca-na-nh harmonic 82.258 124.410 # SOURCE4_SOURCE5 15 1.3695 + angle_coeff @angle:ca-na-o harmonic 88.288 120.170 # SOURCE4_SOURCE5 161 1.3927 + angle_coeff @angle:ca-na-oh harmonic 83.969 120.050 # SOURCE3_SOURCE5 6 2.2969 + angle_coeff @angle:ca-na-os harmonic 86.259 109.460 # SOURCE3 1 + angle_coeff @angle:ca-na-p2 harmonic 78.367 125.850 # SOURCE3 1 + angle_coeff @angle:ca-na-p3 harmonic 78.367 124.380 # SOURCE3 1 + angle_coeff @angle:ca-na-p4 harmonic 85.239 124.970 # SOURCE3 1 + angle_coeff @angle:ca-na-p5 harmonic 80.389 123.300 # SOURCE3 1 + angle_coeff @angle:ca-na-pc harmonic 80.162 122.130 # SOURCE3 3 2.2393 + angle_coeff @angle:ca-na-pd harmonic 80.162 122.130 # SOURCE3 3 + angle_coeff @angle:ca-na-py harmonic 75.307 140.880 # SOURCE3 2 + angle_coeff @angle:ca-na-s4 harmonic 62.021 117.230 # SOURCE3 1 + angle_coeff @angle:ca-na-s6 harmonic 63.097 120.690 # SOURCE3 1 + angle_coeff @angle:ca-na-s harmonic 60.676 125.640 # SOURCE3 1 + angle_coeff @angle:ca-na-sh harmonic 61.938 125.440 # SOURCE3 1 + angle_coeff @angle:ca-na-ss harmonic 60.549 129.920 # SOURCE4_SOURCE5 17 0.1432 + angle_coeff @angle:cc-na-cc harmonic 70.492 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cc-na-cd harmonic 65.316 128.010 # SOURCE3 1 + angle_coeff @angle:cc-na-ce harmonic 64.694 126.610 # SOURCE4_SOURCE5 16 0.5158 + angle_coeff @angle:cc-na-cl harmonic 65.922 124.610 # SOURCE3 3 0.5208 + angle_coeff @angle:cc-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cc-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 + angle_coeff @angle:cc-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cc-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 + angle_coeff @angle:cc-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 + angle_coeff @angle:cc-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 + angle_coeff @angle:cc-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 + angle_coeff @angle:cc-na-nc harmonic 88.067 112.360 # SOURCE3_SOURCE5 209 2.0210 + angle_coeff @angle:cc-na-nd harmonic 83.137 126.230 # CORR_SOURCE5 157 1.3576 + angle_coeff @angle:cc-na-nh harmonic 82.640 123.590 # SOURCE3_SOURCE5 33 0.7437 + angle_coeff @angle:cc-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 + angle_coeff @angle:cc-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cc-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cc-na-os harmonic 83.586 116.860 # CORR 48 + angle_coeff @angle:cc-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cc-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cc-na-p4 harmonic 84.394 127.730 # SOURCE3 7 3.6077 + angle_coeff @angle:cc-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cc-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cc-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 + angle_coeff @angle:cc-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cc-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cc-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 + angle_coeff @angle:cd-na-cd harmonic 70.492 109.900 # SOURCE3 109 1.5547 + angle_coeff @angle:cd-na-cl harmonic 65.922 124.610 # SOURCE3 3 + angle_coeff @angle:cd-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 + angle_coeff @angle:cd-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 + angle_coeff @angle:cd-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 + angle_coeff @angle:cd-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 + angle_coeff @angle:cd-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 + angle_coeff @angle:cd-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 + angle_coeff @angle:cd-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 + angle_coeff @angle:cd-na-nc harmonic 83.088 126.230 # CORR_SOURCE5 157 1.3576 + angle_coeff @angle:cd-na-nd harmonic 88.120 112.360 # SOURCE3_SOURCE5 209 2.0210 + angle_coeff @angle:cd-na-nh harmonic 82.624 123.640 # SOURCE3_SOURCE5 34 0.8283 + angle_coeff @angle:cd-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 + angle_coeff @angle:cd-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 + angle_coeff @angle:cd-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 + angle_coeff @angle:cd-na-os harmonic 83.586 116.860 # CORR 48 + angle_coeff @angle:cd-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 + angle_coeff @angle:cd-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 + angle_coeff @angle:cd-na-p4 harmonic 84.394 127.730 # SOURCE3 7 + angle_coeff @angle:cd-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 + angle_coeff @angle:cd-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 + angle_coeff @angle:cd-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 + angle_coeff @angle:cd-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 + angle_coeff @angle:cd-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 + angle_coeff @angle:cd-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 + angle_coeff @angle:cl-na-cl harmonic 73.099 122.800 # SOURCE3 1 + angle_coeff @angle:cl-na-nc harmonic 84.560 119.360 # SOURCE3 4 1.7128 + angle_coeff @angle:cl-na-nd harmonic 84.574 119.360 # SOURCE3 4 + angle_coeff @angle:cl-na-os harmonic 88.543 106.580 # SOURCE3 1 + angle_coeff @angle:cl-na-p2 harmonic 86.459 121.290 # SOURCE3 1 + angle_coeff @angle:cl-na-pc harmonic 87.107 120.510 # SOURCE3 3 2.1985 + angle_coeff @angle:cl-na-pd harmonic 87.107 120.510 # SOURCE3 3 + angle_coeff @angle:cl-na-ss harmonic 70.427 111.910 # SOURCE3 1 + angle_coeff @angle:f-na-f harmonic 106.388 120.200 # SOURCE3 1 + angle_coeff @angle:f-na-nc harmonic 107.856 118.050 # SOURCE3 4 1.7931 + angle_coeff @angle:f-na-nd harmonic 107.917 118.050 # SOURCE3 4 + angle_coeff @angle:f-na-os harmonic 111.494 103.860 # SOURCE3 1 + angle_coeff @angle:f-na-p2 harmonic 101.527 119.950 # SOURCE3 1 + angle_coeff @angle:f-na-pc harmonic 102.647 119.100 # SOURCE3 3 2.3967 + angle_coeff @angle:f-na-pd harmonic 102.647 119.100 # SOURCE3 3 + angle_coeff @angle:f-na-ss harmonic 83.972 108.010 # SOURCE3 1 + angle_coeff @angle:hn-na-hn harmonic 39.315 116.800 # SOURCE3 1 + angle_coeff @angle:hn-na-n harmonic 61.525 111.440 # SOURCE4_SOURCE5 14 1.2883 + angle_coeff @angle:hn-na-nc harmonic 61.377 119.550 # SOURCE3_SOURCE5 196 1.0024 + angle_coeff @angle:hn-na-nd harmonic 61.443 119.550 # SOURCE3_SOURCE5 196 1.0024 + angle_coeff @angle:hn-na-os harmonic 62.765 102.120 # SOURCE3_SOURCE5 20 2.5614 + angle_coeff @angle:hn-na-p2 harmonic 52.077 122.520 # SOURCE3 1 + angle_coeff @angle:hn-na-pc harmonic 52.878 121.480 # SOURCE3 3 2.9355 + angle_coeff @angle:hn-na-pd harmonic 52.878 121.480 # SOURCE3 3 + angle_coeff @angle:hn-na-ss harmonic 42.530 113.950 # SOURCE3 1 + angle_coeff @angle:i-na-i harmonic 63.587 124.200 # SOURCE3 1 + angle_coeff @angle:i-na-nc harmonic 73.745 120.030 # SOURCE3 4 2.0032 + angle_coeff @angle:i-na-nd harmonic 73.742 120.030 # SOURCE3 4 + angle_coeff @angle:i-na-os harmonic 77.062 109.910 # SOURCE3 1 + angle_coeff @angle:i-na-p2 harmonic 78.740 122.280 # SOURCE3 1 + angle_coeff @angle:i-na-pc harmonic 79.219 121.400 # SOURCE3 3 2.4763 + angle_coeff @angle:i-na-pd harmonic 79.219 121.400 # SOURCE3 3 + angle_coeff @angle:i-na-ss harmonic 62.502 118.400 # SOURCE3 1 + angle_coeff @angle:n2-na-n2 harmonic 108.256 116.710 # SOURCE3 1 + angle_coeff @angle:n2-na-nc harmonic 107.238 119.960 # SOURCE3 4 4.5041 + angle_coeff @angle:n2-na-nd harmonic 107.304 119.960 # SOURCE3 4 + angle_coeff @angle:n2-na-os harmonic 107.573 111.530 # SOURCE3 1 + angle_coeff @angle:n2-na-p2 harmonic 98.756 124.880 # SOURCE3 1 + angle_coeff @angle:n2-na-pc harmonic 100.212 123.180 # SOURCE3 3 4.7947 + angle_coeff @angle:n2-na-pd harmonic 100.212 123.180 # SOURCE3 3 + angle_coeff @angle:n2-na-ss harmonic 77.611 124.640 # SOURCE3 1 + angle_coeff @angle:n3-na-n3 harmonic 101.150 124.000 # SOURCE3 1 + angle_coeff @angle:n4-na-n4 harmonic 105.460 111.700 # SOURCE3 1 + angle_coeff @angle:n4-na-nc harmonic 106.051 116.440 # SOURCE3 4 3.6604 + angle_coeff @angle:n4-na-nd harmonic 106.108 116.440 # SOURCE3 4 + angle_coeff @angle:n4-na-os harmonic 109.494 102.970 # SOURCE3 1 + angle_coeff @angle:n4-na-p2 harmonic 98.207 123.560 # SOURCE3 1 + angle_coeff @angle:n4-na-pc harmonic 99.557 121.980 # SOURCE3 3 4.4884 + angle_coeff @angle:n4-na-pd harmonic 99.557 121.980 # SOURCE3 3 + angle_coeff @angle:na-na-na harmonic 102.688 123.600 # SOURCE3 1 + angle_coeff @angle:na-na-nc harmonic 106.027 119.640 # SOURCE3 4 1.6920 + angle_coeff @angle:na-na-nd harmonic 106.088 119.640 # SOURCE3 4 + angle_coeff @angle:na-na-os harmonic 107.416 109.470 # SOURCE3 1 + angle_coeff @angle:na-na-p2 harmonic 99.520 121.720 # SOURCE3 1 + angle_coeff @angle:na-na-pc harmonic 100.604 120.910 # SOURCE3 3 2.3033 + angle_coeff @angle:na-na-pd harmonic 100.604 120.910 # SOURCE3 3 + angle_coeff @angle:na-na-ss harmonic 79.845 116.500 # SOURCE3 1 + angle_coeff @angle:nc-na-nc harmonic 109.391 116.300 # SOURCE3_SOURCE5 57 1.3191 + angle_coeff @angle:nc-na-nd harmonic 106.540 122.760 # SOURCE4_SOURCE5 12 0.1496 + angle_coeff @angle:nc-na-nh harmonic 105.667 120.550 # SOURCE3 8 1.1436 + angle_coeff @angle:nc-na-no harmonic 104.829 119.210 # SOURCE3_SOURCE5 9 1.2751 + angle_coeff @angle:nc-na-o harmonic 110.789 122.790 # SOURCE3 6 1.3154 + angle_coeff @angle:nc-na-oh harmonic 106.562 119.220 # SOURCE3 4 1.7201 + angle_coeff @angle:nc-na-os harmonic 104.244 119.650 # SOURCE3 4 1.5019 + angle_coeff @angle:nc-na-p2 harmonic 100.917 119.990 # SOURCE3 4 3.6009 + angle_coeff @angle:nc-na-p3 harmonic 100.275 120.070 # SOURCE3 4 3.7188 + angle_coeff @angle:nc-na-p4 harmonic 109.789 119.770 # SOURCE3 3 0.3747 + angle_coeff @angle:nc-na-p5 harmonic 102.963 118.950 # SOURCE3 4 3.1194 + angle_coeff @angle:nc-na-pc harmonic 102.284 118.660 # SOURCE3 27 1.5082 + angle_coeff @angle:nc-na-s4 harmonic 77.292 119.200 # SOURCE3 4 2.3841 + angle_coeff @angle:nc-na-s6 harmonic 79.850 119.240 # SOURCE3 4 2.2262 + angle_coeff @angle:nc-na-s harmonic 77.325 122.260 # SOURCE3 4 0.9173 + angle_coeff @angle:nc-na-sh harmonic 79.494 120.500 # SOURCE3 4 1.5016 + angle_coeff @angle:nc-na-ss harmonic 79.073 120.500 # SOURCE3 4 1.5615 + angle_coeff @angle:nd-na-nd harmonic 109.528 116.300 # SOURCE3_SOURCE5 57 1.3191 + angle_coeff @angle:nd-na-nh harmonic 105.728 120.550 # SOURCE3 8 + angle_coeff @angle:nd-na-no harmonic 104.885 119.210 # SOURCE3_SOURCE5 5 1.0113 + angle_coeff @angle:nd-na-o harmonic 110.874 122.790 # SOURCE3 6 + angle_coeff @angle:nd-na-oh harmonic 106.624 119.220 # SOURCE3 4 + angle_coeff @angle:nd-na-os harmonic 104.299 119.650 # SOURCE3 4 + angle_coeff @angle:nd-na-p2 harmonic 100.941 119.990 # SOURCE3 4 + angle_coeff @angle:nd-na-p3 harmonic 100.297 120.070 # SOURCE3 4 + angle_coeff @angle:nd-na-p4 harmonic 109.833 119.770 # SOURCE3 3 + angle_coeff @angle:nd-na-p5 harmonic 102.991 118.950 # SOURCE3 4 + angle_coeff @angle:nd-na-pd harmonic 102.309 118.660 # SOURCE3 27 + angle_coeff @angle:nd-na-s4 harmonic 77.307 119.200 # SOURCE3 4 + angle_coeff @angle:nd-na-s6 harmonic 79.870 119.240 # SOURCE3 4 + angle_coeff @angle:nd-na-s harmonic 77.342 122.260 # SOURCE3 4 + angle_coeff @angle:nd-na-sh harmonic 79.514 120.500 # SOURCE3 4 + angle_coeff @angle:nd-na-ss harmonic 79.092 120.500 # SOURCE3 4 + angle_coeff @angle:nh-na-nh harmonic 102.761 123.600 # SOURCE3 1 + angle_coeff @angle:nh-na-os harmonic 106.530 111.370 # SOURCE3 1 + angle_coeff @angle:nh-na-p2 harmonic 99.889 120.860 # SOURCE3 1 + angle_coeff @angle:nh-na-pc harmonic 100.842 120.380 # SOURCE3 6 1.3513 + angle_coeff @angle:nh-na-pd harmonic 100.842 120.380 # SOURCE3 6 + angle_coeff @angle:nh-na-ss harmonic 81.320 112.350 # SOURCE3 2 5.2951 + angle_coeff @angle:n-na-n harmonic 102.160 123.800 # SOURCE3 1 + angle_coeff @angle:n-na-nc harmonic 105.685 119.850 # SOURCE3 4 1.6156 + angle_coeff @angle:n-na-nd harmonic 105.745 119.850 # SOURCE3 4 + angle_coeff @angle:no-na-no harmonic 100.609 122.800 # SOURCE3 1 + angle_coeff @angle:no-na-os harmonic 107.653 106.550 # SOURCE3 1 + angle_coeff @angle:no-na-pc harmonic 100.336 120.110 # SOURCE3 3 2.0821 + angle_coeff @angle:no-na-pd harmonic 100.336 120.110 # SOURCE3 3 + angle_coeff @angle:n-na-os harmonic 109.608 104.710 # SOURCE3 1 + angle_coeff @angle:no-na-ss harmonic 79.903 114.950 # SOURCE3 1 + angle_coeff @angle:n-na-p2 harmonic 99.572 121.350 # SOURCE3 1 + angle_coeff @angle:n-na-pc harmonic 100.611 120.640 # SOURCE3 3 2.0168 + angle_coeff @angle:n-na-pd harmonic 100.611 120.640 # SOURCE3 3 + angle_coeff @angle:n-na-ss harmonic 79.899 116.100 # SOURCE3 1 + angle_coeff @angle:oh-na-oh harmonic 103.905 122.200 # SOURCE3 1 + angle_coeff @angle:oh-na-p2 harmonic 100.050 120.760 # SOURCE3 1 + angle_coeff @angle:oh-na-pc harmonic 101.133 119.990 # SOURCE3 3 2.1734 + angle_coeff @angle:oh-na-pd harmonic 101.133 119.990 # SOURCE3 3 + angle_coeff @angle:oh-na-ss harmonic 81.173 113.040 # SOURCE3 1 + angle_coeff @angle:o-na-o harmonic 114.875 126.200 # SOURCE3 1 + angle_coeff @angle:o-na-os harmonic 108.116 118.780 # SOURCE3_SOURCE5 6 0.4047 + angle_coeff @angle:o-na-p2 harmonic 100.973 122.800 # SOURCE3 1 + angle_coeff @angle:o-na-pc harmonic 102.067 122.340 # SOURCE3 3 1.2908 + angle_coeff @angle:o-na-pd harmonic 102.067 122.340 # SOURCE3 3 + angle_coeff @angle:os-na-os harmonic 108.379 104.450 # SOURCE3 2 0.0983 + angle_coeff @angle:os-na-p2 harmonic 100.391 117.860 # SOURCE3 1 + angle_coeff @angle:os-na-p3 harmonic 105.930 104.700 # SOURCE3 1 + angle_coeff @angle:os-na-p5 harmonic 104.736 111.410 # SOURCE3 1 + angle_coeff @angle:os-na-pc harmonic 100.242 119.910 # SOURCE3 3 1.9002 + angle_coeff @angle:os-na-pd harmonic 100.242 119.910 # SOURCE3 3 + angle_coeff @angle:os-na-s4 harmonic 81.006 105.880 # SOURCE3 2 + angle_coeff @angle:os-na-s6 harmonic 81.137 112.000 # SOURCE3 2 + angle_coeff @angle:os-na-ss harmonic 81.670 109.640 # SOURCE3 3 4.1395 + angle_coeff @angle:p2-na-p2 harmonic 102.084 120.910 # SOURCE3 1 + angle_coeff @angle:p2-na-p3 harmonic 100.105 124.800 # SOURCE3 1 + angle_coeff @angle:p2-na-p5 harmonic 101.778 123.990 # SOURCE3 1 + angle_coeff @angle:p2-na-pc harmonic 102.658 120.720 # SOURCE3 3 0.2407 + angle_coeff @angle:p2-na-pd harmonic 102.658 120.720 # SOURCE3 3 + angle_coeff @angle:p2-na-s4 harmonic 78.032 122.470 # SOURCE3 1 + angle_coeff @angle:p2-na-s6 harmonic 79.617 122.500 # SOURCE3 1 + angle_coeff @angle:p2-na-s harmonic 78.874 121.850 # SOURCE3 1 + angle_coeff @angle:p2-na-sh harmonic 79.900 121.750 # SOURCE3 1 + angle_coeff @angle:p2-na-ss harmonic 79.600 121.880 # SOURCE3 1 + angle_coeff @angle:p3-na-p3 harmonic 99.027 126.600 # SOURCE3 1 + angle_coeff @angle:p3-na-pc harmonic 101.182 123.320 # SOURCE3 3 4.1781 + angle_coeff @angle:p3-na-pd harmonic 101.182 123.320 # SOURCE3 3 + angle_coeff @angle:p5-na-p5 harmonic 102.554 124.600 # SOURCE3 1 + angle_coeff @angle:p5-na-pc harmonic 102.835 122.690 # SOURCE3 3 3.6738 + angle_coeff @angle:p5-na-pd harmonic 102.835 122.690 # SOURCE3 3 + angle_coeff @angle:p5-na-ss harmonic 81.516 118.520 # SOURCE3 1 + angle_coeff @angle:pc-na-pc harmonic 103.141 120.780 # SOURCE3 27 1.6457 + angle_coeff @angle:pc-na-s4 harmonic 78.694 121.510 # SOURCE3 3 2.7242 + angle_coeff @angle:pc-na-s6 harmonic 80.329 121.550 # SOURCE3 3 2.7065 + angle_coeff @angle:pc-na-s harmonic 79.371 121.470 # SOURCE3 3 1.0668 + angle_coeff @angle:pc-na-sh harmonic 80.524 121.080 # SOURCE3 3 1.8942 + angle_coeff @angle:pc-na-ss harmonic 80.219 121.200 # SOURCE3 3 1.9295 + angle_coeff @angle:pd-na-pd harmonic 103.141 120.780 # SOURCE3 27 + angle_coeff @angle:pd-na-s4 harmonic 78.694 121.510 # SOURCE3 3 + angle_coeff @angle:pd-na-s6 harmonic 80.329 121.550 # SOURCE3 3 + angle_coeff @angle:pd-na-s harmonic 79.371 121.470 # SOURCE3 3 + angle_coeff @angle:pd-na-sh harmonic 80.524 121.080 # SOURCE3 3 + angle_coeff @angle:pd-na-ss harmonic 80.219 121.200 # SOURCE3 3 + angle_coeff @angle:py-na-py harmonic 129.638 78.250 # SOURCE3 1 + angle_coeff @angle:s4-na-s4 harmonic 59.656 124.200 # SOURCE3 1 + angle_coeff @angle:s4-na-s6 harmonic 63.782 112.860 # SOURCE3 1 + angle_coeff @angle:s4-na-ss harmonic 63.885 111.920 # SOURCE3 1 + angle_coeff @angle:s6-na-s6 harmonic 62.342 123.200 # SOURCE3 1 + angle_coeff @angle:s6-na-ss harmonic 63.225 119.100 # SOURCE3 1 + angle_coeff @angle:sh-na-sh harmonic 62.052 124.600 # SOURCE3 1 + angle_coeff @angle:sh-na-ss harmonic 63.339 118.790 # SOURCE3 1 + angle_coeff @angle:s-na-s harmonic 60.168 126.000 # SOURCE3 1 + angle_coeff @angle:s-na-ss harmonic 64.260 112.490 # SOURCE3 1 + angle_coeff @angle:ss-na-ss harmonic 64.658 113.240 # SOURCE3 2 6.6084 + angle_coeff @angle:sy-na-sy harmonic 62.187 123.200 # SOURCE3 1 + angle_coeff @angle:ca-nb-ca harmonic 70.356 117.220 # SOURCE3_SOURCE5 3343 1.0306 + angle_coeff @angle:ca-nb-cp harmonic 70.116 118.050 # SOURCE4_SOURCE5 160 0.7542 + angle_coeff @angle:ca-nb-cq harmonic 70.116 118.050 # SOURCE4_SOURCE5 102 0.7384 + angle_coeff @angle:ca-nb-nb harmonic 87.237 120.050 # SOURCE3_SOURCE5 159 0.6095 + angle_coeff @angle:cp-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 32 0.5601 + angle_coeff @angle:nb-nb-nb harmonic 109.020 121.040 # SOURCE3 1 + angle_coeff @angle:br-n-br harmonic 67.176 116.200 # SOURCE3 1 + angle_coeff @angle:br-n-c harmonic 62.729 121.250 # SOURCE3_SOURCE5 10 1.6266 + angle_coeff @angle:br-n-ca harmonic 63.323 118.190 # SOURCE3 1 + angle_coeff @angle:br-n-cc harmonic 63.525 118.190 # SOURCE3 1 + angle_coeff @angle:br-n-cd harmonic 63.525 118.190 # SOURCE3 1 + angle_coeff @angle:c1-n-c1 harmonic 75.677 102.690 # SOURCE3 1 + angle_coeff @angle:c1-n-ca harmonic 68.108 118.880 # SOURCE3 1 + angle_coeff @angle:c1-n-cc harmonic 68.972 118.880 # SOURCE3 1 + angle_coeff @angle:c1-n-cd harmonic 68.972 118.880 # SOURCE3 1 + angle_coeff @angle:c2-n-c2 harmonic 67.455 116.750 # SOURCE3 1 + angle_coeff @angle:c2-n-c3 harmonic 64.992 120.100 # SOURCE4_SOURCE5 62 2.3796 + angle_coeff @angle:c2-n-ca harmonic 67.208 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-cc harmonic 67.963 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-cd harmonic 67.963 116.540 # SOURCE3 1 + angle_coeff @angle:c2-n-hn harmonic 47.988 117.900 # SOURCE4_SOURCE5 115 1.4688 + angle_coeff @angle:c3-n-c3 harmonic 64.880 115.640 # SOURCE4_SOURCE5 1017 2.0256 + angle_coeff @angle:c3-n-ca harmonic 64.801 119.830 # SOURCE4_SOURCE5 448 1.9961 + angle_coeff @angle:c3-n-cc harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 + angle_coeff @angle:c3-n-cd harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 + angle_coeff @angle:c3-n-cy harmonic 64.307 117.080 # SOURCE4_SOURCE5 120 1.3701 + angle_coeff @angle:c3-n-hn harmonic 46.147 117.680 # SOURCE3_SOURCE5 1934 1.5065 + angle_coeff @angle:c3-n-n2 harmonic 81.830 121.710 # SOURCE4_SOURCE5 131 1.2251 + angle_coeff @angle:c3-n-n harmonic 82.901 115.390 # SOURCE4_SOURCE5 28 1.0963 + angle_coeff @angle:c3-n-nc harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 + angle_coeff @angle:c3-n-nd harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 + angle_coeff @angle:c3-n-oh harmonic 83.734 112.970 # SOURCE4_SOURCE5 82 0.8203 + angle_coeff @angle:c3-n-os harmonic 83.821 112.540 # SOURCE4_SOURCE5 42 1.7642 + angle_coeff @angle:c3-n-sy harmonic 62.308 120.880 # SOURCE4_SOURCE5 13 1.1569 + angle_coeff @angle:ca-n-ca harmonic 66.671 117.370 # SOURCE4_SOURCE5 99 1.5139 + angle_coeff @angle:ca-n-cc harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 + angle_coeff @angle:ca-n-cd harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 + angle_coeff @angle:ca-n-cl harmonic 71.199 117.720 # SOURCE3 1 + angle_coeff @angle:ca-n-f harmonic 86.043 114.920 # SOURCE3 1 + angle_coeff @angle:ca-n-hn harmonic 47.989 116.000 # SOURCE4_SOURCE5 1451 1.8612 + angle_coeff @angle:ca-n-i harmonic 59.954 119.300 # SOURCE3 1 + angle_coeff @angle:ca-n-n2 harmonic 83.352 122.020 # SOURCE4_SOURCE5 12 0.9977 + angle_coeff @angle:ca-n-n4 harmonic 80.984 122.980 # SOURCE3 1 + angle_coeff @angle:ca-n-n harmonic 83.301 118.550 # SOURCE4_SOURCE5 46 0.3283 + angle_coeff @angle:ca-n-na harmonic 82.957 119.300 # SOURCE4_SOURCE5 47 0.3131 + angle_coeff @angle:ca-n-nc harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 + angle_coeff @angle:ca-n-nd harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 + angle_coeff @angle:ca-n-nh harmonic 84.129 116.450 # SOURCE3 1 + angle_coeff @angle:ca-n-p2 harmonic 83.158 112.320 # SOURCE3 1 + angle_coeff @angle:ca-n-p3 harmonic 77.529 125.110 # SOURCE3 1 + angle_coeff @angle:ca-n-s4 harmonic 62.152 118.400 # SOURCE3 1 + angle_coeff @angle:ca-n-s6 harmonic 63.800 117.320 # SOURCE3 1 + angle_coeff @angle:ca-n-ss harmonic 63.794 116.600 # SOURCE3 1 + angle_coeff @angle:c-n-c1 harmonic 69.561 117.040 # SOURCE3 1 + angle_coeff @angle:c-n-c2 harmonic 66.426 122.150 # SOURCE3 9 5.1016 + angle_coeff @angle:c-n-c3 harmonic 65.252 120.690 # SOURCE3_SOURCE5 4556 2.1510 + angle_coeff @angle:c3-nc-cd harmonic 69.940 109.510 # SOURCE3 9 5.4142 + angle_coeff @angle:c-n-c harmonic 65.616 127.080 # SOURCE4_SOURCE5 1415 2.1363 + angle_coeff @angle:c-n-ca harmonic 65.694 123.710 # SOURCE3 10 3.8159 + angle_coeff @angle:ca-nc-ca harmonic 71.962 109.950 # SOURCE3 1 + angle_coeff @angle:ca-nc-cd harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 + angle_coeff @angle:ca-nc-n harmonic 92.070 104.690 # CORR 2 + angle_coeff @angle:ca-nc-na harmonic 93.072 102.760 # CORR_SOURCE5 25 0.7558 + angle_coeff @angle:ca-nc-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 + angle_coeff @angle:ca-nc-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 + angle_coeff @angle:c-n-cc harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 + angle_coeff @angle:c-nc-ca harmonic 67.794 120.660 # CORR 2 + angle_coeff @angle:cc-n-cc harmonic 70.783 108.920 # SOURCE3 11 0.3167 + angle_coeff @angle:cc-nc-cc harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 + angle_coeff @angle:cc-nc-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 + angle_coeff @angle:c-nc-cd harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 + angle_coeff @angle:cc-n-cl harmonic 71.592 117.720 # SOURCE3 1 + angle_coeff @angle:cc-nc-na harmonic 92.369 102.970 # SOURCE3 1 + angle_coeff @angle:cc-nc-nd harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 + angle_coeff @angle:c-n-cd harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 + angle_coeff @angle:cd-nc-cd harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 + angle_coeff @angle:cd-nc-n harmonic 88.099 117.190 # CORR 64 + angle_coeff @angle:cd-nc-na harmonic 93.753 103.820 # SOURCE3_SOURCE5 919 1.7445 + angle_coeff @angle:cd-nc-nc harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 + angle_coeff @angle:cd-nc-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 + angle_coeff @angle:cd-nc-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 + angle_coeff @angle:c-n-ce harmonic 63.457 131.380 # SOURCE4_SOURCE5 371 1.5975 + angle_coeff @angle:cc-n-f harmonic 87.015 114.920 # SOURCE3 1 + angle_coeff @angle:cc-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 + angle_coeff @angle:cc-n-i harmonic 59.973 119.300 # SOURCE3 1 + angle_coeff @angle:c-n-cl harmonic 72.034 116.350 # SOURCE4 11 0.6829 + angle_coeff @angle:cc-n-n2 harmonic 88.496 110.870 # SOURCE3 1 + angle_coeff @angle:cc-n-n harmonic 83.245 121.370 # SOURCE3 1 + angle_coeff @angle:cc-n-na harmonic 84.492 117.570 # SOURCE3 1 + angle_coeff @angle:cc-n-nc harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 + angle_coeff @angle:cc-n-nh harmonic 84.683 117.520 # SOURCE3 1 + angle_coeff @angle:cc-n-no harmonic 83.522 115.920 # SOURCE3 1 + angle_coeff @angle:cc-n-o harmonic 88.192 120.540 # SOURCE3 1 + angle_coeff @angle:cc-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 + angle_coeff @angle:cc-n-os harmonic 85.167 115.560 # SOURCE3 1 + angle_coeff @angle:cc-n-p2 harmonic 83.596 112.320 # SOURCE3 1 + angle_coeff @angle:cc-n-p3 harmonic 77.892 125.110 # SOURCE3 1 + angle_coeff @angle:cc-n-p5 harmonic 81.119 121.000 # SOURCE3 1 + angle_coeff @angle:cc-n-s4 harmonic 62.446 118.400 # SOURCE3 1 + angle_coeff @angle:cc-n-s6 harmonic 64.150 117.320 # SOURCE3 1 + angle_coeff @angle:cc-n-s harmonic 62.506 118.290 # SOURCE3 1 + angle_coeff @angle:cc-n-sh harmonic 63.393 119.130 # SOURCE3 1 + angle_coeff @angle:cc-n-ss harmonic 64.137 116.600 # SOURCE3 2 + angle_coeff @angle:c-n-cx harmonic 65.394 122.070 # SOURCE4 11 1.9478 + angle_coeff @angle:c-n-cy harmonic 73.625 94.220 # SOURCE4_SOURCE5 674 1.8186 + angle_coeff @angle:cd-n-cd harmonic 70.783 108.920 # SOURCE3 11 + angle_coeff @angle:cd-n-cl harmonic 71.592 117.720 # SOURCE3 1 + angle_coeff @angle:cd-n-f harmonic 87.015 114.920 # SOURCE3 1 + angle_coeff @angle:cd-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 + angle_coeff @angle:cd-n-i harmonic 59.973 119.300 # SOURCE3 1 + angle_coeff @angle:cd-n-n2 harmonic 88.496 110.870 # SOURCE3 1 + angle_coeff @angle:cd-n-n harmonic 83.245 121.370 # SOURCE3 1 + angle_coeff @angle:cd-n-na harmonic 84.492 117.570 # SOURCE3 1 + angle_coeff @angle:cd-n-nd harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 + angle_coeff @angle:cd-n-nh harmonic 84.683 117.520 # SOURCE3 1 + angle_coeff @angle:cd-n-no harmonic 83.522 115.920 # SOURCE3 1 + angle_coeff @angle:cd-n-o harmonic 88.192 120.540 # SOURCE3 1 + angle_coeff @angle:cd-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 + angle_coeff @angle:cd-n-os harmonic 85.167 115.560 # SOURCE3 1 + angle_coeff @angle:cd-n-p2 harmonic 83.596 112.320 # SOURCE3 1 + angle_coeff @angle:cd-n-p3 harmonic 77.892 125.110 # SOURCE3 1 + angle_coeff @angle:cd-n-p5 harmonic 81.119 121.000 # SOURCE3 1 + angle_coeff @angle:cd-n-s4 harmonic 62.446 118.400 # SOURCE3 1 + angle_coeff @angle:cd-n-s6 harmonic 64.150 117.320 # SOURCE3 1 + angle_coeff @angle:cd-n-s harmonic 62.506 118.290 # SOURCE3 1 + angle_coeff @angle:cd-n-sh harmonic 63.393 119.130 # SOURCE3 1 + angle_coeff @angle:cd-n-ss harmonic 64.137 116.600 # SOURCE3 2 1.8318 + angle_coeff @angle:ce-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 + angle_coeff @angle:c-n-f harmonic 89.555 108.630 # SOURCE3 3 4.6785 + angle_coeff @angle:cf-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 + angle_coeff @angle:c-n-hn harmonic 48.691 117.550 # SOURCE3_SOURCE5 5866 1.6058 + angle_coeff @angle:c-n-i harmonic 59.703 120.380 # SOURCE3 5 2.1600 + angle_coeff @angle:cl-n-cl harmonic 81.959 111.690 # SOURCE3 1 + angle_coeff @angle:c-n-n2 harmonic 85.152 119.910 # SOURCE3_SOURCE5 237 1.7782 + angle_coeff @angle:c-n-n3 harmonic 83.740 120.100 # SOURCE3_SOURCE5 90 1.4705 + angle_coeff @angle:c-n-n4 harmonic 85.688 112.320 # SOURCE3 5 1.2622 + angle_coeff @angle:c-n-n harmonic 84.328 118.420 # SOURCE3 10 2.8922 + angle_coeff @angle:c-n-na harmonic 86.815 111.500 # SOURCE3_SOURCE5 60 1.0005 + angle_coeff @angle:na-nc-nd harmonic 116.802 106.240 # SOURCE3_SOURCE5 145 0.6824 + angle_coeff @angle:c-n-nc harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 + angle_coeff @angle:nc-nc-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 + angle_coeff @angle:c-n-nd harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 + angle_coeff @angle:nd-nc-os harmonic 114.084 107.220 # SOURCE3 3 0.4707 + angle_coeff @angle:c-n-nh harmonic 84.310 118.710 # SOURCE4_SOURCE5 52 1.7764 + angle_coeff @angle:c-n-no harmonic 82.773 118.160 # SOURCE3 4 5.4870 + angle_coeff @angle:c-n-o harmonic 89.074 118.360 # SOURCE3_SOURCE5 14 3.9188 + angle_coeff @angle:c-n-oh harmonic 85.324 115.510 # SOURCE3_SOURCE5 128 0.8808 + angle_coeff @angle:c-n-os harmonic 86.126 113.140 # SOURCE3 7 3.0839 + angle_coeff @angle:c-n-p2 harmonic 79.405 124.560 # SOURCE3 8 3.6907 + angle_coeff @angle:c-n-p3 harmonic 78.725 122.540 # SOURCE3 9 4.4802 + angle_coeff @angle:c-n-p4 harmonic 79.728 123.440 # SOURCE3 1 + angle_coeff @angle:c-n-p5 harmonic 78.739 128.500 # SOURCE4 6 0.5353 + angle_coeff @angle:c-n-pc harmonic 79.905 122.230 # SOURCE3 3 2.8787 + angle_coeff @angle:c-n-pd harmonic 79.905 122.230 # SOURCE3 3 + angle_coeff @angle:c-n-s4 harmonic 61.938 120.410 # SOURCE3 4 3.1760 + angle_coeff @angle:c-n-s6 harmonic 62.226 124.760 # SOURCE4_SOURCE5 44 1.7490 + angle_coeff @angle:c-n-s harmonic 60.447 126.550 # SOURCE3 3 4.3365 + angle_coeff @angle:c-n-sh harmonic 63.302 119.540 # SOURCE3 4 1.7681 + angle_coeff @angle:c-n-ss harmonic 62.795 121.710 # SOURCE3_SOURCE5 23 1.8428 + angle_coeff @angle:c-n-sy harmonic 62.308 124.690 # SOURCE4_SOURCE5 124 1.1647 + angle_coeff @angle:cx-n-hn harmonic 46.588 118.500 # SOURCE4_SOURCE5 12 0.6959 + angle_coeff @angle:cx-n-os harmonic 121.869 54.040 # SOURCE3 1 + angle_coeff @angle:cy-n-hn harmonic 45.639 119.110 # SOURCE4_SOURCE5 156 1.4586 + angle_coeff @angle:c3-nd-cc harmonic 69.940 109.510 # SOURCE3 9 + angle_coeff @angle:ca-nd-ca harmonic 71.962 109.950 # SOURCE3 1 + angle_coeff @angle:ca-nd-cc harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 + angle_coeff @angle:ca-nd-n harmonic 92.070 104.690 # CORR 2 + angle_coeff @angle:ca-nd-na harmonic 93.131 102.760 # CORR_SOURCE5 25 0.7558 + angle_coeff @angle:ca-nd-nc harmonic 92.520 108.340 # SOURCE4_SOURCE5 23 0.2293 + angle_coeff @angle:ca-nd-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 + angle_coeff @angle:ca-nd-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 + angle_coeff @angle:c-nd-ca harmonic 67.794 120.660 # CORR 2 + angle_coeff @angle:c-nd-cc harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 + angle_coeff @angle:cc-nd-cc harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 + angle_coeff @angle:cc-nd-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 + angle_coeff @angle:cc-nd-n harmonic 88.099 117.190 # CORR 64 + angle_coeff @angle:cc-nd-na harmonic 93.815 103.820 # SOURCE3_SOURCE5 919 1.7445 + angle_coeff @angle:cc-nd-nd harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 + angle_coeff @angle:cc-nd-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 + angle_coeff @angle:cc-nd-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 + angle_coeff @angle:cd-nd-cd harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 + angle_coeff @angle:cd-nd-na harmonic 92.426 102.970 # SOURCE3 1 + angle_coeff @angle:cd-nd-nc harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 + angle_coeff @angle:na-nd-nc harmonic 116.883 106.240 # SOURCE3_SOURCE5 145 0.6824 + angle_coeff @angle:nc-nd-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 + angle_coeff @angle:nc-nd-os harmonic 114.084 107.220 # SOURCE3 3 + angle_coeff @angle:c1-ne-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 + angle_coeff @angle:c1-ne-cg harmonic 67.861 140.000 # SOURCE2 1 + angle_coeff @angle:c2-ne-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 + angle_coeff @angle:c2-ne-ce harmonic 70.313 116.010 # SOURCE3_SOURCE5 34 2.0813 + angle_coeff @angle:c2-ne-cg harmonic 70.178 123.230 # SOURCE4_SOURCE5 39 1.0918 + angle_coeff @angle:c2-ne-n2 harmonic 93.623 113.310 # SOURCE3 1 + angle_coeff @angle:c2-ne-ne harmonic 88.990 110.860 # SOURCE3 7 4.5874 + angle_coeff @angle:c2-ne-p2 harmonic 84.105 134.030 # SOURCE3 1 + angle_coeff @angle:c2-ne-pe harmonic 82.533 120.520 # SOURCE3 8 8.1381 + angle_coeff @angle:c2-ne-px harmonic 83.910 117.750 # SOURCE3 5 0.8581 + angle_coeff @angle:c2-ne-py harmonic 88.230 117.040 # SOURCE3 3 1.4398 + angle_coeff @angle:c2-ne-sx harmonic 62.652 111.980 # SOURCE3 3 0.4090 + angle_coeff @angle:c2-ne-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 + angle_coeff @angle:ca-ne-cf harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 + angle_coeff @angle:ca-ne-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 + angle_coeff @angle:ca-ne-nf harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 + angle_coeff @angle:ca-ne-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 18 1.7090 + angle_coeff @angle:ca-ne-p2 harmonic 87.186 118.090 # SOURCE3 1 + angle_coeff @angle:ca-ne-s harmonic 68.068 120.110 # SOURCE3 1 + angle_coeff @angle:c-ne-c2 harmonic 69.660 118.530 # CORR 6 + angle_coeff @angle:ce-ne-n2 harmonic 90.497 111.190 # SOURCE3 1 + angle_coeff @angle:ce-ne-o harmonic 91.180 112.160 # SOURCE3 1 + angle_coeff @angle:ce-ne-p2 harmonic 87.896 117.020 # SOURCE3 1 + angle_coeff @angle:ce-ne-s harmonic 69.440 116.280 # SOURCE3 1 + angle_coeff @angle:cg-ne-n1 harmonic 90.226 120.200 # SOURCE2 1 + angle_coeff @angle:cg-ne-n2 harmonic 92.273 113.390 # SOURCE3 1 + angle_coeff @angle:cg-ne-o harmonic 93.028 114.700 # SOURCE2 1 + angle_coeff @angle:cg-ne-p2 harmonic 88.388 119.570 # SOURCE3 1 + angle_coeff @angle:cg-ne-s harmonic 70.232 117.700 # SOURCE3 1 + angle_coeff @angle:c-ne-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 16 1.7300 + angle_coeff @angle:n2-ne-n2 harmonic 121.491 107.220 # SOURCE3 1 + angle_coeff @angle:n2-ne-ne harmonic 112.157 110.720 # SOURCE3 9 6.1488 + angle_coeff @angle:n2-ne-o harmonic 119.624 114.100 # SOURCE3 1 + angle_coeff @angle:n2-ne-p2 harmonic 116.902 109.660 # SOURCE3 1 + angle_coeff @angle:n2-ne-pe harmonic 107.386 112.150 # SOURCE3 7 6.5273 + angle_coeff @angle:n2-ne-px harmonic 106.135 115.970 # SOURCE3 3 1.9854 + angle_coeff @angle:n2-ne-py harmonic 112.046 114.600 # SOURCE3 3 2.9261 + angle_coeff @angle:n2-ne-s harmonic 89.721 115.900 # SOURCE3 1 + angle_coeff @angle:n2-ne-sx harmonic 80.235 107.290 # SOURCE3 1 + angle_coeff @angle:n2-ne-sy harmonic 85.721 111.210 # SOURCE3 1 + angle_coeff @angle:ne-ne-o harmonic 113.544 110.450 # SOURCE3 10 1.8535 + angle_coeff @angle:ne-ne-p2 harmonic 110.510 114.390 # SOURCE3 6 4.0528 + angle_coeff @angle:ne-ne-s harmonic 86.406 115.950 # SOURCE3 6 3.4604 + angle_coeff @angle:o-ne-o harmonic 116.666 124.090 # SOURCE3 2 8.7534 + angle_coeff @angle:o-ne-pe harmonic 99.245 132.320 # SOURCE3 11 23.9559 + angle_coeff @angle:o-ne-px harmonic 109.115 110.620 # SOURCE3 1 + angle_coeff @angle:o-ne-py harmonic 114.678 110.790 # SOURCE3 4 1.6818 + angle_coeff @angle:o-ne-s harmonic 89.941 117.190 # SOURCE3 2 0.0225 + angle_coeff @angle:o-ne-sx harmonic 79.732 108.920 # SOURCE3 1 + angle_coeff @angle:o-ne-sy harmonic 86.078 111.340 # SOURCE3 1 + angle_coeff @angle:p2-ne-pe harmonic 110.473 116.810 # SOURCE3 1 + angle_coeff @angle:p2-ne-px harmonic 105.767 128.350 # SOURCE3 1 + angle_coeff @angle:p2-ne-py harmonic 111.507 123.470 # SOURCE3 1 + angle_coeff @angle:p2-ne-sx harmonic 83.857 112.120 # SOURCE3 1 + angle_coeff @angle:p2-ne-sy harmonic 87.708 115.730 # SOURCE3 1 + angle_coeff @angle:pe-ne-s harmonic 87.031 115.730 # SOURCE3 1 + angle_coeff @angle:px-ne-s harmonic 81.843 131.840 # SOURCE3 1 + angle_coeff @angle:py-ne-s harmonic 90.262 116.180 # SOURCE3 4 3.7135 + angle_coeff @angle:s-ne-s harmonic 70.545 120.870 # SOURCE3 1 + angle_coeff @angle:s-ne-sx harmonic 65.416 112.960 # SOURCE3 1 + angle_coeff @angle:s-ne-sy harmonic 67.679 119.630 # SOURCE3 1 + angle_coeff @angle:c1-nf-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 + angle_coeff @angle:c1-nf-ch harmonic 67.861 140.000 # SOURCE2 1 + angle_coeff @angle:c2-nf-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 + angle_coeff @angle:c2-nf-cf harmonic 70.313 116.010 # SOURCE3_SOURCE5 31 2.1630 + angle_coeff @angle:c2-nf-n2 harmonic 93.623 113.310 # SOURCE3 1 + angle_coeff @angle:c2-nf-nf harmonic 88.990 110.860 # SOURCE3 7 + angle_coeff @angle:c2-nf-p2 harmonic 84.105 134.030 # SOURCE3 1 + angle_coeff @angle:c2-nf-pf harmonic 82.533 120.520 # SOURCE3 8 + angle_coeff @angle:c2-nf-px harmonic 83.910 117.750 # SOURCE3 5 + angle_coeff @angle:c2-nf-py harmonic 88.230 117.040 # SOURCE3 3 + angle_coeff @angle:c2-nf-sx harmonic 62.652 111.980 # SOURCE3 3 + angle_coeff @angle:c2-nf-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 + angle_coeff @angle:ca-nf-ce harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 + angle_coeff @angle:ca-nf-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 + angle_coeff @angle:ca-nf-ne harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 + angle_coeff @angle:ca-nf-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 15 1.8257 + angle_coeff @angle:ca-nf-p2 harmonic 87.186 118.090 # SOURCE3 1 + angle_coeff @angle:ca-nf-s harmonic 68.068 120.110 # SOURCE3 1 + angle_coeff @angle:c-nf-c2 harmonic 69.660 118.530 # CORR 6 + angle_coeff @angle:cf-nf-n2 harmonic 90.497 111.190 # SOURCE3 1 + angle_coeff @angle:cf-nf-o harmonic 91.180 112.160 # SOURCE3 1 + angle_coeff @angle:cf-nf-p2 harmonic 87.896 117.020 # SOURCE3 1 + angle_coeff @angle:cf-nf-s harmonic 69.440 116.280 # SOURCE3 1 + angle_coeff @angle:ch-nf-n1 harmonic 90.226 120.200 # SOURCE2 1 + angle_coeff @angle:ch-nf-n2 harmonic 92.273 113.390 # SOURCE3 1 + angle_coeff @angle:ch-nf-o harmonic 93.028 114.700 # SOURCE2 1 + angle_coeff @angle:ch-nf-p2 harmonic 88.388 119.570 # SOURCE3 1 + angle_coeff @angle:ch-nf-s harmonic 70.232 117.700 # SOURCE3 1 + angle_coeff @angle:f-n-f harmonic 116.092 102.980 # SOURCE3 1 + angle_coeff @angle:n2-nf-n2 harmonic 121.491 107.220 # SOURCE3 1 + angle_coeff @angle:n2-nf-nf harmonic 112.157 110.720 # SOURCE3 9 + angle_coeff @angle:n2-nf-o harmonic 119.624 114.100 # SOURCE3 1 + angle_coeff @angle:n2-nf-p2 harmonic 116.902 109.660 # SOURCE3 1 + angle_coeff @angle:n2-nf-pf harmonic 107.386 112.150 # SOURCE3 7 + angle_coeff @angle:n2-nf-px harmonic 106.135 115.970 # SOURCE3 3 + angle_coeff @angle:n2-nf-py harmonic 112.046 114.600 # SOURCE3 3 + angle_coeff @angle:n2-nf-s harmonic 89.721 115.900 # SOURCE3 1 + angle_coeff @angle:n2-nf-sx harmonic 80.235 107.290 # SOURCE3 1 + angle_coeff @angle:n2-nf-sy harmonic 85.721 111.210 # SOURCE3 1 + angle_coeff @angle:nf-nf-o harmonic 113.544 110.450 # SOURCE3 10 + angle_coeff @angle:nf-nf-p2 harmonic 110.510 114.390 # SOURCE3 6 + angle_coeff @angle:nf-nf-s harmonic 86.406 115.950 # SOURCE3 6 + angle_coeff @angle:o-nf-o harmonic 116.666 124.090 # SOURCE3 2 + angle_coeff @angle:o-nf-pf harmonic 99.245 132.320 # SOURCE3 11 + angle_coeff @angle:o-nf-px harmonic 109.115 110.620 # SOURCE3 1 + angle_coeff @angle:o-nf-py harmonic 114.678 110.790 # SOURCE3 4 + angle_coeff @angle:o-nf-s harmonic 89.941 117.190 # SOURCE3 2 + angle_coeff @angle:o-nf-sx harmonic 79.732 108.920 # SOURCE3 1 + angle_coeff @angle:o-nf-sy harmonic 86.078 111.340 # SOURCE3 1 + angle_coeff @angle:p2-nf-pf harmonic 110.473 116.810 # SOURCE3 1 + angle_coeff @angle:p2-nf-px harmonic 105.767 128.350 # SOURCE3 1 + angle_coeff @angle:p2-nf-py harmonic 111.507 123.470 # SOURCE3 1 + angle_coeff @angle:p2-nf-sx harmonic 83.857 112.120 # SOURCE3 1 + angle_coeff @angle:p2-nf-sy harmonic 87.708 115.730 # SOURCE3 1 + angle_coeff @angle:pf-nf-s harmonic 87.031 115.730 # SOURCE3 1 + angle_coeff @angle:px-nf-s harmonic 81.843 131.840 # SOURCE3 1 + angle_coeff @angle:py-nf-s harmonic 90.262 116.180 # SOURCE3 4 + angle_coeff @angle:s-nf-s harmonic 70.545 120.870 # SOURCE3 1 + angle_coeff @angle:s-nf-sx harmonic 65.416 112.960 # SOURCE3 1 + angle_coeff @angle:s-nf-sy harmonic 67.679 119.630 # SOURCE3 1 + angle_coeff @angle:br-nh-br harmonic 67.679 106.270 # SOURCE3 1 + angle_coeff @angle:br-nh-ca harmonic 63.138 111.880 # SOURCE3 1 + angle_coeff @angle:br-nh-hn harmonic 41.986 101.560 # SOURCE3 1 + angle_coeff @angle:c1-nh-c1 harmonic 70.255 116.980 # SOURCE3 1 + angle_coeff @angle:c1-nh-c2 harmonic 67.255 123.350 # SOURCE4_SOURCE5 17 1.3108 + angle_coeff @angle:c1-nh-ca harmonic 67.561 122.360 # SOURCE3 3 1.2016 + angle_coeff @angle:c1-nh-hn harmonic 49.868 117.400 # SOURCE4_SOURCE5 22 0.6517 + angle_coeff @angle:c2-nh-c2 harmonic 65.835 124.730 # SOURCE4_SOURCE5 107 1.4158 + angle_coeff @angle:c2-nh-c3 harmonic 64.232 123.710 # SOURCE3 8 3.5348 + angle_coeff @angle:c2-nh-ca harmonic 65.131 127.560 # SOURCE4_SOURCE5 258 2.3985 + angle_coeff @angle:c2-nh-cc harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 + angle_coeff @angle:c2-nh-cd harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 + angle_coeff @angle:c2-nh-cx harmonic 64.299 124.350 # SOURCE4_SOURCE5 21 1.6877 + angle_coeff @angle:c2-nh-hn harmonic 48.954 115.090 # SOURCE4_SOURCE5 2743 1.5424 + angle_coeff @angle:c2-nh-n2 harmonic 85.013 120.220 # SOURCE4_SOURCE5 101 1.0922 + angle_coeff @angle:c2-nh-n3 harmonic 84.289 116.870 # SOURCE4_SOURCE5 35 1.4173 + angle_coeff @angle:c2-nh-no harmonic 82.173 125.620 # SOURCE4_SOURCE5 19 0.8850 + angle_coeff @angle:c2-nh-oh harmonic 86.014 112.180 # SOURCE4_SOURCE5 38 1.3409 + angle_coeff @angle:c2-nh-os harmonic 85.749 112.950 # SOURCE4_SOURCE5 14 0.4455 + angle_coeff @angle:c2-nh-sy harmonic 63.190 121.130 # SOURCE4_SOURCE5 20 0.5133 + angle_coeff @angle:c3-nh-c3 harmonic 65.106 114.510 # SOURCE4_SOURCE5 1386 2.1206 + angle_coeff @angle:c3-nh-ca harmonic 65.249 119.980 # SOURCE3_SOURCE5 1640 2.1716 + angle_coeff @angle:c3-nh-cc harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 + angle_coeff @angle:c3-nh-cd harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 + angle_coeff @angle:c3-nh-cf harmonic 65.126 120.120 # SOURCE4_SOURCE5 52 2.0459 + angle_coeff @angle:c3-nh-cz harmonic 64.716 125.460 # SOURCE4_SOURCE5 25 0.5651 + angle_coeff @angle:c3-nh-hn harmonic 46.421 115.990 # SOURCE3_SOURCE5 1206 1.7716 + angle_coeff @angle:c3-nh-n2 harmonic 85.302 112.350 # SOURCE3 9 4.0058 + angle_coeff @angle:c3-nh-n harmonic 84.428 111.270 # SOURCE4_SOURCE5 20 2.2657 + angle_coeff @angle:c3-nh-na harmonic 84.049 112.390 # SOURCE4_SOURCE5 18 1.3421 + angle_coeff @angle:c3-nh-p2 harmonic 80.321 123.350 # SOURCE3 1 + angle_coeff @angle:c3-nh-sy harmonic 63.547 116.320 # SOURCE4_SOURCE5 31 1.3018 + angle_coeff @angle:ca-nh-ca harmonic 65.187 127.460 # SOURCE3 2 0.0002 + angle_coeff @angle:ca-nh-cc harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 + angle_coeff @angle:ca-nh-cd harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 + angle_coeff @angle:ca-nh-cl harmonic 71.441 113.150 # SOURCE3 1 + angle_coeff @angle:ca-nh-cx harmonic 64.495 123.700 # SOURCE4_SOURCE5 80 0.6122 + angle_coeff @angle:ca-nh-f harmonic 89.432 106.090 # SOURCE3 3 1.0660 + angle_coeff @angle:ca-nh-hn harmonic 48.787 116.070 # SOURCE4_SOURCE5 5026 1.3182 + angle_coeff @angle:ca-nh-i harmonic 58.875 117.830 # SOURCE3 1 + angle_coeff @angle:ca-nh-n1 harmonic 86.539 117.130 # HF/6-31G* 1 + angle_coeff @angle:ca-nh-n2 harmonic 84.736 121.130 # SOURCE4_SOURCE5 61 1.2262 + angle_coeff @angle:ca-nh-n3 harmonic 83.982 117.830 # SOURCE3_SOURCE5 31 1.9504 + angle_coeff @angle:ca-nh-n4 harmonic 85.682 108.940 # SOURCE3 5 0.6562 + angle_coeff @angle:ca-nh-n harmonic 85.070 116.030 # SOURCE4_SOURCE5 31 1.0216 + angle_coeff @angle:ca-nh-na harmonic 85.145 115.960 # SOURCE3_SOURCE5 14 0.6985 + angle_coeff @angle:ca-nh-nh harmonic 85.491 114.840 # SOURCE3_SOURCE5 14 1.2270 + angle_coeff @angle:ca-nh-no harmonic 86.330 113.920 # SOURCE3 4 2.9561 + angle_coeff @angle:ca-nh-o harmonic 86.968 121.920 # SOURCE3 2 3.9630 + angle_coeff @angle:ca-nh-oh harmonic 85.751 112.970 # SOURCE3_SOURCE5 7 0.3980 + angle_coeff @angle:ca-nh-os harmonic 86.208 111.850 # SOURCE3_SOURCE5 8 0.6032 + angle_coeff @angle:ca-nh-p2 harmonic 81.008 125.270 # SOURCE3 8 5.1798 + angle_coeff @angle:ca-nh-p3 harmonic 79.062 125.700 # SOURCE3 3 5.7796 + angle_coeff @angle:ca-nh-p4 harmonic 80.454 124.010 # SOURCE3 3 2.5810 + angle_coeff @angle:ca-nh-p5 harmonic 80.367 128.170 # SOURCE3_SOURCE5 9 0.9847 + angle_coeff @angle:ca-nh-s4 harmonic 63.691 115.620 # SOURCE3 3 0.3434 + angle_coeff @angle:ca-nh-s6 harmonic 63.224 122.850 # SOURCE4_SOURCE5 92 2.1278 + angle_coeff @angle:ca-nh-s harmonic 60.896 122.540 # SOURCE3 3 2.7001 + angle_coeff @angle:ca-nh-sh harmonic 63.303 121.410 # SOURCE3 1 + angle_coeff @angle:ca-nh-ss harmonic 63.248 121.500 # SOURCE3 3 2.6255 + angle_coeff @angle:ca-nh-sy harmonic 62.161 125.230 # SOURCE4_SOURCE5 116 1.6241 + angle_coeff @angle:cc-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 + angle_coeff @angle:cc-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 + angle_coeff @angle:cc-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 21 1.0306 + angle_coeff @angle:cc-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 60 1.2839 + angle_coeff @angle:cd-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 + angle_coeff @angle:cd-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 + angle_coeff @angle:ce-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 + angle_coeff @angle:ce-nh-o harmonic 84.249 129.430 # CORR 2 + angle_coeff @angle:ce-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 15 1.0862 + angle_coeff @angle:cf-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 + angle_coeff @angle:cf-nh-o harmonic 84.249 129.430 # CORR 2 + angle_coeff @angle:cl-nh-cl harmonic 81.661 106.600 # SOURCE3 1 + angle_coeff @angle:cl-nh-hn harmonic 48.722 104.140 # SOURCE3 1 + angle_coeff @angle:cx-nh-cx harmonic 89.045 62.010 # SOURCE4_SOURCE5 98 0.5911 + angle_coeff @angle:cx-nh-hn harmonic 46.132 118.880 # SOURCE4_SOURCE5 23 0.1930 + angle_coeff @angle:cz-nh-hn harmonic 49.192 121.150 # SOURCE4_SOURCE5 116 0.7805 + angle_coeff @angle:f-nh-f harmonic 114.444 101.700 # SOURCE3 1 + angle_coeff @angle:f-nh-hn harmonic 64.681 101.230 # SOURCE3 1 + angle_coeff @angle:hn-nh-hn harmonic 39.519 115.120 # SOURCE4_SOURCE5 3024 2.1393 + angle_coeff @angle:hn-nh-i harmonic 37.873 107.570 # SOURCE3 1 + angle_coeff @angle:hn-nh-n1 harmonic 64.440 110.570 # HF/6-31G* 1 + angle_coeff @angle:hn-nh-n2 harmonic 61.856 118.140 # SOURCE4_SOURCE5 220 2.1956 + angle_coeff @angle:hn-nh-n3 harmonic 60.496 113.970 # SOURCE3_SOURCE5 53 1.8422 + angle_coeff @angle:hn-nh-n4 harmonic 61.193 104.400 # SOURCE3 3 0.5056 + angle_coeff @angle:hn-nh-n harmonic 62.655 108.170 # SOURCE4_SOURCE5 39 1.1076 + angle_coeff @angle:hn-nh-na harmonic 62.699 108.240 # SOURCE3_SOURCE5 48 1.3913 + angle_coeff @angle:hn-nh-nh harmonic 61.867 110.860 # SOURCE4_SOURCE5 20 1.2814 + angle_coeff @angle:hn-nh-no harmonic 62.754 109.940 # SOURCE4_SOURCE5 17 0.1843 + angle_coeff @angle:hn-nh-o harmonic 65.877 116.450 # SOURCE3 2 0.6063 + angle_coeff @angle:hn-nh-oh harmonic 62.561 106.490 # SOURCE4_SOURCE5 45 1.2492 + angle_coeff @angle:hn-nh-os harmonic 62.721 106.070 # SOURCE3_SOURCE5 11 1.1257 + angle_coeff @angle:hn-nh-p2 harmonic 55.498 118.180 # SOURCE3 21 3.6927 + angle_coeff @angle:hn-nh-p3 harmonic 54.152 116.190 # SOURCE3 3 3.0539 + angle_coeff @angle:hn-nh-p4 harmonic 55.870 112.600 # SOURCE3 3 0.8237 + angle_coeff @angle:hn-nh-p5 harmonic 56.530 115.090 # SOURCE3_SOURCE5 12 1.4234 + angle_coeff @angle:hn-nh-s4 harmonic 43.338 107.480 # SOURCE3 3 1.3960 + angle_coeff @angle:hn-nh-s harmonic 41.075 114.370 # SOURCE3 1 + angle_coeff @angle:hn-nh-s6 harmonic 44.306 109.920 # SOURCE4_SOURCE5 70 0.7219 + angle_coeff @angle:hn-nh-sh harmonic 43.546 112.250 # SOURCE3 1 + angle_coeff @angle:hn-nh-ss harmonic 43.161 114.100 # SOURCE3_SOURCE5 9 0.8638 + angle_coeff @angle:hn-nh-sy harmonic 43.636 110.910 # SOURCE4_SOURCE5 174 1.2855 + angle_coeff @angle:i-nh-i harmonic 65.204 115.820 # SOURCE3 1 + angle_coeff @angle:n1-nh-n1 harmonic 115.547 106.710 # HF/6-31G* 1 + angle_coeff @angle:n2-nh-n2 harmonic 109.104 117.500 # SOURCE3 2 1.1907 + angle_coeff @angle:n2-nh-n3 harmonic 105.802 119.060 # SOURCE3_SOURCE5 5 1.1057 + angle_coeff @angle:n2-nh-o harmonic 108.688 126.060 # SOURCE3 1 + angle_coeff @angle:n3-nh-n3 harmonic 107.251 110.980 # SOURCE3 1 + angle_coeff @angle:n4-nh-n4 harmonic 104.809 108.360 # SOURCE3 1 + angle_coeff @angle:na-nh-na harmonic 107.947 112.010 # SOURCE3 1 + angle_coeff @angle:hn-n-hn harmonic 39.011 117.950 # SOURCE3_SOURCE5 619 1.1004 + angle_coeff @angle:nh-nh-nh harmonic 107.672 112.230 # SOURCE3 1 + angle_coeff @angle:hn-n-i harmonic 37.457 117.240 # SOURCE3 2 0.4435 + angle_coeff @angle:hn-n-n2 harmonic 61.294 119.080 # SOURCE3_SOURCE5 133 1.1985 + angle_coeff @angle:hn-n-n3 harmonic 60.078 117.240 # SOURCE4_SOURCE5 85 1.3614 + angle_coeff @angle:hn-n-n4 harmonic 60.201 112.680 # SOURCE3 3 1.9746 + angle_coeff @angle:hn-n-n harmonic 61.137 113.200 # SOURCE3_SOURCE5 44 1.5099 + angle_coeff @angle:hn-n-na harmonic 60.720 114.350 # SOURCE3_SOURCE5 14 1.6595 + angle_coeff @angle:hn-n-nc harmonic 62.278 115.420 # SOURCE4_SOURCE5 34 0.6814 + angle_coeff @angle:hn-n-nh harmonic 61.240 113.210 # SOURCE4_SOURCE5 34 1.4195 + angle_coeff @angle:hn-n-no harmonic 59.968 110.110 # SOURCE3 1 + angle_coeff @angle:hn-n-o harmonic 66.701 116.320 # SOURCE3 2 0.0175 + angle_coeff @angle:n-nh-o harmonic 111.046 115.630 # SOURCE3 1 + angle_coeff @angle:hn-n-oh harmonic 61.737 110.740 # SOURCE4_SOURCE5 106 1.1526 + angle_coeff @angle:no-nh-no harmonic 110.729 108.550 # SOURCE3 1 + angle_coeff @angle:hn-n-os harmonic 61.835 110.010 # SOURCE4_SOURCE5 28 0.8603 + angle_coeff @angle:hn-n-p2 harmonic 53.625 118.050 # SOURCE3 7 3.0564 + angle_coeff @angle:hn-n-p3 harmonic 52.013 119.630 # SOURCE3 2 + angle_coeff @angle:hn-n-p4 harmonic 54.129 115.710 # SOURCE3 1 + angle_coeff @angle:hn-n-p5 harmonic 55.227 113.610 # SOURCE4_SOURCE5 12 0.8598 + angle_coeff @angle:hn-n-s4 harmonic 41.853 112.460 # SOURCE3 1 + angle_coeff @angle:hn-n-s harmonic 41.432 114.920 # SOURCE3 2 0.0260 + angle_coeff @angle:hn-n-s6 harmonic 43.193 112.560 # SOURCE4_SOURCE5 18 0.6934 + angle_coeff @angle:hn-n-sh harmonic 42.490 114.910 # SOURCE3 1 + angle_coeff @angle:hn-n-ss harmonic 42.420 115.600 # SOURCE3 3 0.6414 + angle_coeff @angle:hn-n-sy harmonic 43.301 112.330 # SOURCE4_SOURCE5 87 0.6324 + angle_coeff @angle:oh-nh-oh harmonic 109.556 106.270 # SOURCE3 1 + angle_coeff @angle:o-nh-o harmonic 111.924 128.060 # SOURCE3 1 + angle_coeff @angle:os-nh-os harmonic 110.145 105.270 # SOURCE3 1 + angle_coeff @angle:p2-nh-p2 harmonic 103.624 127.330 # SOURCE3 2 2.7857 + angle_coeff @angle:p3-nh-p3 harmonic 101.470 125.080 # SOURCE3 1 + angle_coeff @angle:p5-nh-p5 harmonic 110.643 112.760 # SOURCE3 1 + angle_coeff @angle:s4-nh-s4 harmonic 64.290 112.390 # SOURCE3 1 + angle_coeff @angle:s6-nh-s6 harmonic 64.034 120.270 # SOURCE3 1 + angle_coeff @angle:sh-nh-sh harmonic 63.979 119.000 # SOURCE3 1 + angle_coeff @angle:s-nh-s harmonic 61.323 118.730 # SOURCE3 1 + angle_coeff @angle:ss-nh-ss harmonic 63.871 119.250 # SOURCE3 1 + angle_coeff @angle:i-n-i harmonic 66.144 118.200 # SOURCE3 1 + angle_coeff @angle:n2-n-n2 harmonic 108.745 116.890 # SOURCE3 1 + angle_coeff @angle:n3-n-n3 harmonic 104.883 117.940 # SOURCE3 1 + angle_coeff @angle:n4-n-n4 harmonic 105.215 112.690 # SOURCE3 1 + angle_coeff @angle:na-n-na harmonic 104.916 117.380 # SOURCE3 1 + angle_coeff @angle:nc-n-nc harmonic 109.009 116.410 # CORR 2 + angle_coeff @angle:nc-n-p2 harmonic 102.805 117.210 # CORR 2 + angle_coeff @angle:nc-n-pc harmonic 102.474 117.210 # CORR 2 + angle_coeff @angle:nd-n-nd harmonic 109.009 116.410 # CORR 2 + angle_coeff @angle:nd-n-p2 harmonic 102.805 117.210 # CORR 2 + angle_coeff @angle:nd-n-pd harmonic 102.474 117.210 # CORR 2 + angle_coeff @angle:nh-n-nh harmonic 106.329 115.180 # SOURCE3 1 + angle_coeff @angle:n-n-n harmonic 106.384 114.620 # SOURCE3 1 + angle_coeff @angle:no-n-no harmonic 105.383 108.660 # SOURCE3 1 + angle_coeff @angle:br-no-o harmonic 72.469 113.190 # SOURCE3 2 + angle_coeff @angle:c1-no-o harmonic 89.075 116.630 # SOURCE3 6 + angle_coeff @angle:c2-no-o harmonic 86.856 117.670 # SOURCE3_SOURCE5 49 0.7530 + angle_coeff @angle:c3-no-o harmonic 83.512 116.930 # SOURCE3_SOURCE5 182 0.7108 + angle_coeff @angle:ca-no-o harmonic 85.942 117.760 # SOURCE3_SOURCE5 886 0.2929 + angle_coeff @angle:cc-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 624 0.5662 + angle_coeff @angle:cl-no-o harmonic 86.532 115.080 # SOURCE3 2 + angle_coeff @angle:c-no-o harmonic 83.834 115.260 # SOURCE3 1 + angle_coeff @angle:hn-no-o harmonic 67.449 115.490 # SOURCE3 2 + angle_coeff @angle:oh-n-oh harmonic 109.825 107.260 # SOURCE3 1 + angle_coeff @angle:i-no-o harmonic 70.372 116.310 # SOURCE3 2 + angle_coeff @angle:n1-no-o harmonic 112.600 115.000 # HF/6-31G* 1 + angle_coeff @angle:n2-no-o harmonic 110.021 116.520 # SOURCE2_SOURCE5 17 2.4833 + angle_coeff @angle:n3-no-o harmonic 111.860 116.770 # SOURCE3_SOURCE5 35 0.4158 + angle_coeff @angle:n4-no-o harmonic 111.250 109.000 # SOURCE3 2 + angle_coeff @angle:na-no-o harmonic 110.472 115.570 # SOURCE3_SOURCE5 29 0.5293 + angle_coeff @angle:nh-no-o harmonic 112.798 116.080 # SOURCE3_SOURCE5 32 0.8573 + angle_coeff @angle:n-no-o harmonic 109.317 115.590 # SOURCE3_SOURCE5 14 0.7108 + angle_coeff @angle:no-no-o harmonic 91.614 112.380 # SOURCE3 4 + angle_coeff @angle:o-n-o harmonic 113.464 128.610 # SOURCE3 3 1.0626 + angle_coeff @angle:o-no-o harmonic 116.649 125.080 # SOURCE4_SOURCE5 1464 0.8585 + angle_coeff @angle:o-no-oh harmonic 112.426 114.700 # SOURCE3 2 + angle_coeff @angle:o-no-os harmonic 111.586 114.760 # SOURCE3_SOURCE5 147 2.2227 + angle_coeff @angle:o-no-p2 harmonic 103.970 117.380 # SOURCE3 20 0.8083 + angle_coeff @angle:o-no-p3 harmonic 98.510 116.780 # SOURCE3 6 0.4929 + angle_coeff @angle:o-no-p4 harmonic 97.206 116.640 # SOURCE3 6 0.0089 + angle_coeff @angle:o-no-p5 harmonic 99.077 116.690 # SOURCE3 8 0.4507 + angle_coeff @angle:o-no-s4 harmonic 71.457 114.490 # SOURCE3 6 0.5674 + angle_coeff @angle:o-no-s6 harmonic 72.259 114.390 # SOURCE3 6 0.8311 + angle_coeff @angle:o-no-s harmonic 80.020 119.810 # SOURCE3 4 0.0042 + angle_coeff @angle:o-no-sh harmonic 78.649 116.100 # SOURCE3 2 + angle_coeff @angle:o-no-ss harmonic 77.822 115.580 # SOURCE3 6 0.5860 + angle_coeff @angle:os-n-os harmonic 109.989 106.530 # SOURCE3 1 + angle_coeff @angle:p2-n-p2 harmonic 103.580 119.620 # SOURCE3 1 + angle_coeff @angle:p3-n-p3 harmonic 106.372 108.730 # SOURCE3 3 0.2591 + angle_coeff @angle:p4-n-p4 harmonic 108.671 108.550 # SOURCE3 1 + angle_coeff @angle:p5-n-p5 harmonic 114.341 99.990 # SOURCE3 1 + angle_coeff @angle:pc-n-pc harmonic 103.163 119.620 # SOURCE3 1 + angle_coeff @angle:pd-n-pd harmonic 103.163 119.620 # SOURCE3 1 + angle_coeff @angle:s4-n-s4 harmonic 63.214 113.750 # SOURCE3 1 + angle_coeff @angle:s6-n-s6 harmonic 63.403 119.680 # SOURCE3 1 + angle_coeff @angle:sh-n-sh harmonic 63.230 119.030 # SOURCE3 1 + angle_coeff @angle:s-n-s harmonic 60.100 126.000 # SOURCE3 1 + angle_coeff @angle:ss-n-ss harmonic 63.451 118.490 # SOURCE3 1 + angle_coeff @angle:br-oh-ho harmonic 43.172 101.600 # SOURCE3 1 + angle_coeff @angle:c1-oh-ho harmonic 51.954 108.760 # SOURCE3 1 + angle_coeff @angle:c2-oh-ho harmonic 51.795 107.630 # SOURCE3_SOURCE5 86 1.5038 + angle_coeff @angle:c3-oh-ho harmonic 49.027 107.260 # SOURCE3_SOURCE5 7781 0.7665 + angle_coeff @angle:ca-oh-ho harmonic 50.712 108.580 # SOURCE3_SOURCE5 3580 0.7052 + angle_coeff @angle:cc-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 + angle_coeff @angle:cd-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 + angle_coeff @angle:ce-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 + angle_coeff @angle:cf-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 + angle_coeff @angle:c-oh-ho harmonic 51.617 106.550 # SOURCE3_SOURCE5 2765 1.0627 + angle_coeff @angle:cl-oh-ho harmonic 50.601 102.400 # SOURCE2 1 + angle_coeff @angle:cx-oh-ho harmonic 51.376 106.170 # SOURCE3 3 0.0644 + angle_coeff @angle:cy-oh-ho harmonic 49.289 107.690 # SOURCE4_SOURCE5 21 0.5952 + angle_coeff @angle:f-oh-ho harmonic 64.650 96.800 # SOURCE2 1 + angle_coeff @angle:ho-oh-ho harmonic 42.178 106.490 # SOURCE2_SOURCE5 23 1.3050 + angle_coeff @angle:ho-oh-i harmonic 37.979 107.980 # SOURCE3 2 + angle_coeff @angle:ho-oh-n1 harmonic 66.474 107.810 # HF/6-31G* 1 + angle_coeff @angle:ho-oh-n2 harmonic 63.987 103.090 # SOURCE3_SOURCE5 185 1.2900 + angle_coeff @angle:ho-oh-n3 harmonic 63.233 102.260 # SOURCE3_SOURCE5 28 0.5790 + angle_coeff @angle:ho-oh-n4 harmonic 62.546 106.630 # SOURCE3 3 0.2770 + angle_coeff @angle:ho-oh-n harmonic 63.907 101.290 # SOURCE3_SOURCE5 114 1.0315 + angle_coeff @angle:ho-oh-na harmonic 63.538 104.370 # SOURCE3_SOURCE5 16 0.9188 + angle_coeff @angle:ho-oh-nh harmonic 63.021 102.770 # SOURCE4_SOURCE5 57 0.7554 + angle_coeff @angle:ho-oh-no harmonic 63.640 102.170 # SOURCE3 1 + angle_coeff @angle:ho-oh-o harmonic 59.432 100.870 # SOURCE3 1 + angle_coeff @angle:ho-oh-oh harmonic 62.055 98.720 # SOURCE3 2 + angle_coeff @angle:ho-oh-os harmonic 62.321 99.680 # SOURCE4_SOURCE5 45 0.3142 + angle_coeff @angle:ho-oh-p2 harmonic 58.567 109.450 # SOURCE3 8 3.3491 + angle_coeff @angle:ho-oh-p3 harmonic 56.437 110.640 # SOURCE3 3 0.5191 + angle_coeff @angle:ho-oh-p4 harmonic 57.939 110.190 # SOURCE3 4 0.2372 + angle_coeff @angle:ho-oh-p5 harmonic 58.997 110.080 # SOURCE3_SOURCE5 1074 1.1258 + angle_coeff @angle:ho-oh-py harmonic 58.835 110.490 # SOURCE3_SOURCE5 115 1.4927 + angle_coeff @angle:ho-oh-s4 harmonic 44.189 106.850 # SOURCE4_SOURCE5 28 0.5669 + angle_coeff @angle:ho-oh-s harmonic 42.242 100.150 # SOURCE3 2 + angle_coeff @angle:ho-oh-s6 harmonic 45.957 107.260 # SOURCE3_SOURCE5 180 0.7965 + angle_coeff @angle:ho-oh-sh harmonic 44.429 106.240 # SOURCE3 2 0.0661 + angle_coeff @angle:ho-oh-ss harmonic 44.367 107.110 # SOURCE3_SOURCE5 12 1.0472 + angle_coeff @angle:ho-oh-sy harmonic 45.671 106.420 # SOURCE4_SOURCE5 121 0.3216 + angle_coeff @angle:br-os-br harmonic 67.436 110.630 # SOURCE3 1 + angle_coeff @angle:c1-os-c1 harmonic 71.202 115.020 # SOURCE3 1 + angle_coeff @angle:c1-os-c3 harmonic 68.518 113.390 # SOURCE3 1 + angle_coeff @angle:c2-os-c2 harmonic 69.600 113.140 # SOURCE3 6 2.1932 + angle_coeff @angle:c2-os-c3 harmonic 66.993 115.590 # SOURCE3_SOURCE5 149 2.3501 + angle_coeff @angle:c2-os-ca harmonic 67.843 118.200 # SOURCE3_SOURCE5 13 0.6779 + angle_coeff @angle:c2-os-n2 harmonic 83.963 118.130 # SOURCE3 1 + angle_coeff @angle:c2-os-na harmonic 88.073 103.850 # SOURCE3 4 0.6297 + angle_coeff @angle:c2-os-os harmonic 87.781 102.770 # SOURCE3 1 + angle_coeff @angle:c2-os-p5 harmonic 82.312 126.370 # SOURCE4 7 1.7939 + angle_coeff @angle:c2-os-ss harmonic 66.609 108.130 # SOURCE3 1 + angle_coeff @angle:c3-os-c3 harmonic 66.293 112.480 # SOURCE4_SOURCE5 4012 1.7399 + angle_coeff @angle:c3-os-ca harmonic 66.103 117.960 # SOURCE4_SOURCE5 7354 1.4497 + angle_coeff @angle:c3-os-cc harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 + angle_coeff @angle:c3-os-cd harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 + angle_coeff @angle:c3-os-ce harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 + angle_coeff @angle:c3-os-cf harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 + angle_coeff @angle:c3-os-cl harmonic 71.832 110.500 # SOURCE2 1 + angle_coeff @angle:c3-os-cy harmonic 66.337 111.750 # SOURCE4_SOURCE5 19 0.7990 + angle_coeff @angle:c3-os-i harmonic 59.723 113.700 # SOURCE3 1 + angle_coeff @angle:c3-os-n1 harmonic 85.969 113.500 # HF/6-31G* 1 + angle_coeff @angle:c3-os-n2 harmonic 85.118 109.230 # SOURCE3_SOURCE5 93 0.8090 + angle_coeff @angle:c3-os-n3 harmonic 83.747 109.830 # SOURCE4_SOURCE5 46 1.7350 + angle_coeff @angle:c3-os-n4 harmonic 84.065 110.500 # SOURCE3 3 0.5426 + angle_coeff @angle:c3-os-n harmonic 84.730 109.680 # SOURCE4_SOURCE5 42 0.9897 + angle_coeff @angle:c3-os-na harmonic 83.212 110.980 # SOURCE3_SOURCE5 17 1.2781 + angle_coeff @angle:c3-os-nc harmonic 83.792 112.730 # SOURCE3 2 1.0358 + angle_coeff @angle:c3-os-nd harmonic 83.792 112.730 # SOURCE3 2 + angle_coeff @angle:c3-os-nh harmonic 84.502 109.790 # SOURCE4_SOURCE5 22 0.2157 + angle_coeff @angle:c3-os-no harmonic 82.802 113.890 # SOURCE4_SOURCE5 112 0.3140 + angle_coeff @angle:c3-os-o harmonic 84.510 103.000 # SOURCE3 1 + angle_coeff @angle:c3-os-oh harmonic 83.965 108.110 # SOURCE4_SOURCE5 34 0.5701 + angle_coeff @angle:c3-os-os harmonic 83.957 107.370 # SOURCE3_SOURCE5 55 0.9835 + angle_coeff @angle:c3-os-p2 harmonic 86.122 115.470 # SOURCE3 8 2.6374 + angle_coeff @angle:c3-os-p3 harmonic 81.943 117.510 # SOURCE3_SOURCE5 11 0.9552 + angle_coeff @angle:c3-os-p4 harmonic 83.257 117.480 # SOURCE3 4 0.3850 + angle_coeff @angle:c3-os-p5 harmonic 83.251 119.540 # SOURCE3_SOURCE5 665 1.1338 + angle_coeff @angle:c3-os-py harmonic 83.113 119.570 # SOURCE3_SOURCE5 59 1.1952 + angle_coeff @angle:c3-os-s4 harmonic 64.572 113.210 # SOURCE3_SOURCE5 18 1.1865 + angle_coeff @angle:c3-os-s6 harmonic 65.683 115.870 # SOURCE4_SOURCE5 144 1.2750 + angle_coeff @angle:c3-os-s harmonic 62.691 109.550 # SOURCE3 1 + angle_coeff @angle:c3-os-sh harmonic 65.257 112.820 # SOURCE3 1 + angle_coeff @angle:c3-os-ss harmonic 64.028 114.010 # SOURCE3_SOURCE5 8 0.2853 + angle_coeff @angle:ca-os-ca harmonic 67.119 119.890 # SOURCE4_SOURCE5 312 1.5712 + angle_coeff @angle:ca-os-cc harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 + angle_coeff @angle:ca-os-cd harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 + angle_coeff @angle:ca-os-n3 harmonic 84.583 112.190 # SOURCE3 1 + angle_coeff @angle:ca-os-na harmonic 85.998 108.240 # SOURCE3 1 + angle_coeff @angle:ca-os-nc harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 + angle_coeff @angle:ca-os-nd harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 + angle_coeff @angle:ca-os-p5 harmonic 83.193 123.180 # SOURCE4_SOURCE5 136 1.2191 + angle_coeff @angle:ca-os-s6 harmonic 66.238 117.180 # SOURCE4_SOURCE5 46 1.0420 + angle_coeff @angle:c-os-c2 harmonic 68.118 118.220 # SOURCE4_SOURCE5 22 0.6933 + angle_coeff @angle:c-os-c3 harmonic 66.906 115.980 # SOURCE3_SOURCE5 2731 1.0103 + angle_coeff @angle:c-os-c harmonic 67.462 120.640 # SOURCE4 7 1.5114 + angle_coeff @angle:c-os-ca harmonic 67.041 121.150 # SOURCE4_SOURCE5 731 1.7389 + angle_coeff @angle:c-os-cc harmonic 67.659 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-cc harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 + angle_coeff @angle:cc-os-cd harmonic 67.837 118.680 # SOURCE4_SOURCE5 49 2.2289 + angle_coeff @angle:c-os-cd harmonic 67.659 119.620 # SOURCE3 5 6.0675 + angle_coeff @angle:cc-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cc-os-nc harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 + angle_coeff @angle:cc-os-os harmonic 85.382 108.470 # SOURCE3 2 + angle_coeff @angle:cc-os-ss harmonic 63.313 119.590 # SOURCE3 1 + angle_coeff @angle:c-os-cy harmonic 75.270 91.100 # SOURCE3 2 0.0155 + angle_coeff @angle:cd-os-cd harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 + angle_coeff @angle:cd-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 + angle_coeff @angle:cd-os-nd harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 + angle_coeff @angle:cd-os-os harmonic 85.382 108.470 # SOURCE3 2 + angle_coeff @angle:cd-os-ss harmonic 63.313 119.590 # SOURCE3 1 + angle_coeff @angle:cl-os-cl harmonic 80.567 110.760 # SOURCE3 2 + angle_coeff @angle:c-os-n2 harmonic 86.219 112.120 # SOURCE4_SOURCE5 16 0.1285 + angle_coeff @angle:c-os-n harmonic 85.927 112.240 # SOURCE4_SOURCE5 17 0.6206 + angle_coeff @angle:c-os-oh harmonic 85.021 110.500 # SOURCE3 1 + angle_coeff @angle:c-os-os harmonic 84.800 110.200 # SOURCE4_SOURCE5 22 1.3187 + angle_coeff @angle:c-os-p5 harmonic 83.749 122.130 # SOURCE4_SOURCE5 11 0.5685 + angle_coeff @angle:c-os-sy harmonic 65.179 113.490 # SOURCE3 1 + angle_coeff @angle:cx-os-cx harmonic 89.127 61.780 # SOURCE4_SOURCE5 379 0.2104 + angle_coeff @angle:cx-os-n harmonic 114.351 59.990 # SOURCE3 1 + angle_coeff @angle:cx-os-os harmonic 115.519 56.520 # SOURCE3 2 + angle_coeff @angle:cy-os-cy harmonic 72.980 91.860 # SOURCE2_SOURCE5 16 1.0042 + angle_coeff @angle:f-os-f harmonic 112.297 103.300 # SOURCE2 1 + angle_coeff @angle:f-os-os harmonic 105.904 109.500 # SOURCE2 1 + angle_coeff @angle:i-os-i harmonic 65.023 115.670 # SOURCE3 1 + angle_coeff @angle:n1-os-n1 harmonic 111.016 117.790 # HF/6-31G* 1 + angle_coeff @angle:n2-os-n2 harmonic 108.962 106.830 # SOURCE3 1 + angle_coeff @angle:n2-os-s6 harmonic 84.516 111.300 # SOURCE4_SOURCE5 14 0.5651 + angle_coeff @angle:n3-os-n3 harmonic 106.985 104.880 # SOURCE3 1 + angle_coeff @angle:n4-os-n4 harmonic 103.723 114.680 # SOURCE3 1 + angle_coeff @angle:na-os-na harmonic 104.414 109.590 # SOURCE3 1 + angle_coeff @angle:na-os-ss harmonic 83.603 104.340 # SOURCE3 1 + angle_coeff @angle:nc-os-nc harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 + angle_coeff @angle:nc-os-ss harmonic 81.743 110.970 # SOURCE3 1 + angle_coeff @angle:nd-os-nd harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 + angle_coeff @angle:nd-os-ss harmonic 81.743 110.970 # SOURCE3 1 + angle_coeff @angle:nh-os-nh harmonic 107.169 108.290 # SOURCE3 1 + angle_coeff @angle:n-os-n harmonic 107.646 108.310 # SOURCE3 1 + angle_coeff @angle:no-os-no harmonic 105.015 111.860 # SOURCE3 1 + angle_coeff @angle:n-os-s6 harmonic 83.504 113.630 # SOURCE4_SOURCE5 13 0.1799 + angle_coeff @angle:o-os-o harmonic 97.999 114.680 # SOURCE3 1 + angle_coeff @angle:p2-os-p2 harmonic 112.427 120.020 # SOURCE3 1 + angle_coeff @angle:p2-os-p5 harmonic 117.003 107.860 # SOURCE3 1 + angle_coeff @angle:p3-os-p3 harmonic 105.094 121.220 # SOURCE3 1 + angle_coeff @angle:p3-os-py harmonic 114.455 105.580 # SOURCE3 1 + angle_coeff @angle:p5-os-p5 harmonic 106.787 126.250 # SOURCE3 1 + angle_coeff @angle:s4-os-s4 harmonic 65.797 111.630 # SOURCE3 1 + angle_coeff @angle:s6-os-s6 harmonic 66.445 119.070 # SOURCE3 2 0.4318 + angle_coeff @angle:sh-os-sh harmonic 64.549 118.950 # SOURCE3 1 + angle_coeff @angle:s-os-s harmonic 60.143 118.080 # SOURCE3 1 + angle_coeff @angle:ss-os-ss harmonic 64.198 115.640 # SOURCE3 1 + angle_coeff @angle:br-p2-br harmonic 50.367 108.600 # SOURCE3 1 + angle_coeff @angle:br-p2-c2 harmonic 49.320 102.320 # SOURCE3 2 0.0146 + angle_coeff @angle:br-p2-n2 harmonic 61.779 103.330 # SOURCE3 1 + angle_coeff @angle:br-p2-o harmonic 59.925 110.870 # SOURCE3 1 + angle_coeff @angle:br-p2-p2 harmonic 63.559 115.460 # SOURCE3 4 7.8622 + angle_coeff @angle:br-p2-s harmonic 50.714 110.520 # SOURCE3 1 + angle_coeff @angle:c1-p2-c1 harmonic 49.523 99.040 # SOURCE3 1 + angle_coeff @angle:c1-p2-c2 harmonic 50.326 101.290 # SOURCE3 1 + angle_coeff @angle:c1-p2-n2 harmonic 63.856 101.790 # SOURCE3 1 + angle_coeff @angle:c1-p2-o harmonic 63.431 107.620 # SOURCE3 1 + angle_coeff @angle:c1-p2-p2 harmonic 68.223 99.540 # SOURCE3 1 + angle_coeff @angle:c1-p2-s harmonic 51.746 105.900 # SOURCE3 1 + angle_coeff @angle:c2-p2-c2 harmonic 51.141 104.500 # SOURCE3 1 + angle_coeff @angle:c2-p2-c3 harmonic 48.776 101.900 # SOURCE3 4 0.1132 + angle_coeff @angle:c2-p2-ca harmonic 49.013 101.950 # SOURCE3 1 + angle_coeff @angle:c2-p2-cl harmonic 54.318 102.720 # SOURCE3 2 + angle_coeff @angle:c2-p2-f harmonic 67.755 103.470 # SOURCE3 2 0.0136 + angle_coeff @angle:c2-p2-hp harmonic 37.280 97.190 # SOURCE3 3 0.0216 + angle_coeff @angle:c2-p2-i harmonic 44.010 101.940 # SOURCE3 2 0.0368 + angle_coeff @angle:c2-p2-n2 harmonic 66.728 99.880 # SOURCE3 1 + angle_coeff @angle:c2-p2-n3 harmonic 64.858 101.800 # SOURCE3 1 + angle_coeff @angle:c2-p2-n4 harmonic 60.347 98.260 # SOURCE3 6 0.1522 + angle_coeff @angle:c2-p2-n harmonic 63.154 103.280 # SOURCE3 4 3.3113 + angle_coeff @angle:c2-p2-na harmonic 62.619 103.990 # SOURCE3 8 1.6834 + angle_coeff @angle:c2-p2-nh harmonic 63.638 105.170 # SOURCE3 8 0.8263 + angle_coeff @angle:c2-p2-no harmonic 64.740 97.970 # SOURCE3 3 0.4175 + angle_coeff @angle:c2-p2-o harmonic 63.763 115.160 # SOURCE3 1 + angle_coeff @angle:c2-p2-oh harmonic 65.278 102.890 # SOURCE3 3 0.8191 + angle_coeff @angle:c2-p2-os harmonic 66.578 102.120 # SOURCE3 4 0.8783 + angle_coeff @angle:c2-p2-p2 harmonic 70.059 99.560 # SOURCE3 1 + angle_coeff @angle:c2-p2-p3 harmonic 61.583 99.270 # SOURCE3 4 1.1590 + angle_coeff @angle:c2-p2-p4 harmonic 61.685 96.940 # SOURCE3 1 + angle_coeff @angle:c2-p2-p5 harmonic 61.450 97.610 # SOURCE3 1 + angle_coeff @angle:c2-p2-s4 harmonic 48.314 95.150 # SOURCE3 1 + angle_coeff @angle:c2-p2-s6 harmonic 48.407 95.510 # SOURCE3 1 + angle_coeff @angle:c2-p2-s harmonic 53.268 105.530 # SOURCE3 1 + angle_coeff @angle:c2-p2-sh harmonic 50.735 101.490 # SOURCE3 3 0.0057 + angle_coeff @angle:c2-p2-ss harmonic 50.746 101.810 # SOURCE3 4 0.5883 + angle_coeff @angle:c3-p2-c3 harmonic 47.191 99.300 # SOURCE3 1 + angle_coeff @angle:c3-p2-n2 harmonic 62.233 100.820 # SOURCE3 1 + angle_coeff @angle:c3-p2-o harmonic 61.561 106.720 # SOURCE3 1 + angle_coeff @angle:c3-p2-os harmonic 62.459 101.340 # SOURCE3 1 + angle_coeff @angle:c3-p2-p2 harmonic 66.273 100.480 # SOURCE3 1 + angle_coeff @angle:c3-p2-s harmonic 50.533 105.680 # SOURCE3 1 + angle_coeff @angle:ca-p2-ca harmonic 47.481 99.700 # SOURCE3 1 + angle_coeff @angle:ca-p2-n2 harmonic 62.575 100.820 # SOURCE3 1 + angle_coeff @angle:ca-p2-n harmonic 64.349 89.970 # SOURCE3 1 + angle_coeff @angle:ca-p2-na harmonic 64.367 89.210 # SOURCE3 1 + angle_coeff @angle:ca-p2-o harmonic 61.891 106.880 # SOURCE3 1 + angle_coeff @angle:ca-p2-s harmonic 50.228 107.930 # SOURCE3 1 + angle_coeff @angle:c-p2-c2 harmonic 49.148 97.300 # SOURCE3 1 + angle_coeff @angle:c-p2-c harmonic 48.369 90.100 # SOURCE3 1 + angle_coeff @angle:ce-p2-o harmonic 62.381 107.440 # SOURCE3 1 + angle_coeff @angle:ce-p2-s harmonic 51.184 105.540 # SOURCE3 1 + angle_coeff @angle:cf-p2-o harmonic 62.381 107.440 # SOURCE3 1 + angle_coeff @angle:cf-p2-s harmonic 51.184 105.540 # SOURCE3 1 + angle_coeff @angle:cl-p2-cl harmonic 58.906 108.700 # SOURCE3 1 + angle_coeff @angle:cl-p2-n2 harmonic 68.360 103.380 # SOURCE3 1 + angle_coeff @angle:cl-p2-o harmonic 66.726 110.570 # SOURCE3 1 + angle_coeff @angle:cl-p2-p2 harmonic 73.823 103.110 # SOURCE3 1 + angle_coeff @angle:cl-p2-s harmonic 55.803 110.110 # SOURCE3 1 + angle_coeff @angle:f-p2-f harmonic 88.550 107.100 # SOURCE3 1 + angle_coeff @angle:f-p2-n2 harmonic 86.735 103.570 # SOURCE3 1 + angle_coeff @angle:f-p2-o harmonic 86.673 110.610 # SOURCE3 1 + angle_coeff @angle:f-p2-p2 harmonic 89.962 103.480 # SOURCE3 1 + angle_coeff @angle:f-p2-s harmonic 66.939 114.710 # SOURCE3 2 5.2794 + angle_coeff @angle:hp-p2-hp harmonic 27.644 98.760 # SOURCE3 1 + angle_coeff @angle:hp-p2-n1 harmonic 46.969 95.180 # SOURCE3 2 1.5708 + angle_coeff @angle:hp-p2-n2 harmonic 48.480 95.540 # SOURCE3 19 4.7352 + angle_coeff @angle:hp-p2-ne harmonic 48.264 100.100 # SOURCE3 14 6.1290 + angle_coeff @angle:hp-p2-nf harmonic 48.264 100.100 # SOURCE3 14 + angle_coeff @angle:hp-p2-o harmonic 48.141 105.580 # SOURCE3 1 + angle_coeff @angle:hp-p2-p2 harmonic 47.796 101.880 # SOURCE3 27 12.9535 + angle_coeff @angle:hp-p2-p4 harmonic 40.954 94.510 # SOURCE3 1 + angle_coeff @angle:hp-p2-p5 harmonic 42.165 89.070 # SOURCE3 1 + angle_coeff @angle:hp-p2-pe harmonic 47.048 97.250 # SOURCE3 16 8.8916 + angle_coeff @angle:hp-p2-pf harmonic 47.048 97.250 # SOURCE3 16 + angle_coeff @angle:hp-p2-s4 harmonic 32.527 89.990 # SOURCE3 1 + angle_coeff @angle:hp-p2-s harmonic 37.377 102.520 # SOURCE3 1 + angle_coeff @angle:hp-p2-s6 harmonic 33.031 88.130 # SOURCE3 1 + angle_coeff @angle:i-p2-i harmonic 47.836 104.160 # SOURCE3 1 + angle_coeff @angle:i-p2-n2 harmonic 55.025 101.770 # SOURCE3 1 + angle_coeff @angle:i-p2-o harmonic 52.674 109.510 # SOURCE3 1 + angle_coeff @angle:i-p2-p2 harmonic 60.877 102.630 # SOURCE3 1 + angle_coeff @angle:i-p2-s harmonic 45.705 110.600 # SOURCE3 1 + angle_coeff @angle:n1-p2-n1 harmonic 87.795 86.220 # HF/6-31G* 1 + angle_coeff @angle:n2-p2-n2 harmonic 86.095 98.000 # SOURCE3 1 + angle_coeff @angle:n2-p2-n3 harmonic 83.297 100.420 # SOURCE3 1 + angle_coeff @angle:n2-p2-n4 harmonic 78.374 93.420 # SOURCE3 1 + angle_coeff @angle:n2-p2-na harmonic 80.458 102.030 # SOURCE3 1 + angle_coeff @angle:n2-p2-nh harmonic 82.457 101.870 # SOURCE3 2 0.8491 + angle_coeff @angle:n2-p2-no harmonic 82.358 98.120 # SOURCE3 1 + angle_coeff @angle:n2-p2-o harmonic 81.674 115.340 # SOURCE3 1 + angle_coeff @angle:n2-p2-oh harmonic 80.728 109.720 # SOURCE3 1 + angle_coeff @angle:n2-p2-os harmonic 85.101 102.290 # SOURCE3 1 + angle_coeff @angle:n2-p2-p3 harmonic 77.520 99.510 # SOURCE3 1 + angle_coeff @angle:n2-p2-p4 harmonic 75.847 101.730 # SOURCE3 1 + angle_coeff @angle:n2-p2-p5 harmonic 79.007 93.680 # SOURCE3 1 + angle_coeff @angle:n2-p2-s4 harmonic 60.003 97.830 # SOURCE3 1 + angle_coeff @angle:n2-p2-s6 harmonic 60.149 98.140 # SOURCE3 1 + angle_coeff @angle:n2-p2-s harmonic 65.491 112.940 # SOURCE3 1 + angle_coeff @angle:n2-p2-sh harmonic 64.416 100.820 # SOURCE3 1 + angle_coeff @angle:n2-p2-ss harmonic 64.240 101.760 # SOURCE3 1 + angle_coeff @angle:n3-p2-n3 harmonic 79.448 106.300 # SOURCE3 1 + angle_coeff @angle:n3-p2-o harmonic 82.859 106.830 # SOURCE3 1 + angle_coeff @angle:n3-p2-p2 harmonic 87.256 100.580 # SOURCE3 1 + angle_coeff @angle:n3-p2-s harmonic 66.611 105.750 # SOURCE3 1 + angle_coeff @angle:n4-p2-n4 harmonic 74.750 88.800 # SOURCE3 1 + angle_coeff @angle:n4-p2-o harmonic 76.313 101.360 # SOURCE3 1 + angle_coeff @angle:n4-p2-p2 harmonic 82.466 96.530 # SOURCE3 1 + angle_coeff @angle:n4-p2-s harmonic 61.808 104.980 # SOURCE3 1 + angle_coeff @angle:na-p2-na harmonic 75.931 106.100 # SOURCE3 1 + angle_coeff @angle:na-p2-o harmonic 80.149 107.460 # SOURCE3 1 + angle_coeff @angle:na-p2-s harmonic 64.498 108.150 # SOURCE3 1 + angle_coeff @angle:ne-p2-o harmonic 85.784 107.710 # SOURCE3 1 + angle_coeff @angle:ne-p2-s harmonic 68.411 105.500 # SOURCE3 1 + angle_coeff @angle:nf-p2-o harmonic 85.784 107.710 # SOURCE3 1 + angle_coeff @angle:nf-p2-s harmonic 68.411 105.500 # SOURCE3 1 + angle_coeff @angle:nh-p2-nh harmonic 79.891 104.000 # SOURCE3 1 + angle_coeff @angle:nh-p2-o harmonic 82.088 108.110 # SOURCE3 2 0.6773 + angle_coeff @angle:nh-p2-p2 harmonic 84.120 107.730 # SOURCE3 3 3.1678 + angle_coeff @angle:nh-p2-s harmonic 65.274 109.620 # SOURCE3 2 1.7725 + angle_coeff @angle:n-p2-n2 harmonic 82.195 98.850 # SOURCE3 1 + angle_coeff @angle:n-p2-o harmonic 81.559 105.080 # SOURCE3 1 + angle_coeff @angle:no-p2-no harmonic 79.425 98.200 # SOURCE3 1 + angle_coeff @angle:no-p2-o harmonic 81.482 104.870 # SOURCE3 1 + angle_coeff @angle:no-p2-p2 harmonic 82.518 108.570 # SOURCE3 3 8.2121 + angle_coeff @angle:no-p2-s harmonic 64.423 109.060 # SOURCE3 2 5.4074 + angle_coeff @angle:n-p2-p2 harmonic 85.198 102.120 # SOURCE3 1 + angle_coeff @angle:n-p2-s harmonic 63.562 112.340 # SOURCE3 1 + angle_coeff @angle:oh-p2-oh harmonic 83.880 100.100 # SOURCE3 1 + angle_coeff @angle:oh-p2-p2 harmonic 85.099 107.820 # SOURCE3 2 2.6708 + angle_coeff @angle:oh-p2-s harmonic 66.041 109.750 # SOURCE3 1 + angle_coeff @angle:o-p2-o harmonic 82.822 119.960 # SOURCE3 1 + angle_coeff @angle:o-p2-oh harmonic 82.704 110.460 # SOURCE3 1 + angle_coeff @angle:o-p2-os harmonic 85.052 108.810 # SOURCE3 1 + angle_coeff @angle:o-p2-p2 harmonic 84.879 114.230 # SOURCE3 1 + angle_coeff @angle:o-p2-p3 harmonic 75.364 106.690 # SOURCE3 1 + angle_coeff @angle:o-p2-p4 harmonic 75.313 104.370 # SOURCE3 1 + angle_coeff @angle:o-p2-p5 harmonic 75.237 104.490 # SOURCE3 1 + angle_coeff @angle:o-p2-pe harmonic 72.675 145.960 # SOURCE3 1 + angle_coeff @angle:o-p2-pf harmonic 72.675 145.960 # SOURCE3 1 + angle_coeff @angle:o-p2-s4 harmonic 57.795 106.590 # SOURCE3 1 + angle_coeff @angle:o-p2-s6 harmonic 58.473 105.040 # SOURCE3 1 + angle_coeff @angle:o-p2-s harmonic 65.598 117.420 # SOURCE3 1 + angle_coeff @angle:o-p2-sh harmonic 62.592 109.600 # SOURCE3 1 + angle_coeff @angle:os-p2-os harmonic 87.712 98.300 # SOURCE3 1 + angle_coeff @angle:os-p2-p2 harmonic 88.869 101.460 # SOURCE3 1 + angle_coeff @angle:o-p2-ss harmonic 62.723 109.600 # SOURCE3 1 + angle_coeff @angle:os-p2-s harmonic 67.319 108.470 # SOURCE3 3 1.7065 + angle_coeff @angle:p2-p2-n2 harmonic 90.057 97.400 # SOURCE3 1 + angle_coeff @angle:p2-p2-p3 harmonic 83.101 101.730 # SOURCE3 1 + angle_coeff @angle:p2-p2-p4 harmonic 82.238 101.980 # SOURCE3 1 + angle_coeff @angle:p2-p2-p5 harmonic 83.299 99.330 # SOURCE3 1 + angle_coeff @angle:p2-p2-s4 harmonic 65.891 95.730 # SOURCE3 1 + angle_coeff @angle:p2-p2-s6 harmonic 66.042 95.950 # SOURCE3 1 + angle_coeff @angle:p2-p2-s harmonic 69.717 111.280 # SOURCE3 1 + angle_coeff @angle:p2-p2-sh harmonic 64.935 113.940 # SOURCE3 3 8.5009 + angle_coeff @angle:p3-p2-p3 harmonic 77.638 101.000 # SOURCE3 1 + angle_coeff @angle:p3-p2-s harmonic 61.492 113.280 # SOURCE3 2 6.7035 + angle_coeff @angle:p4-p2-s harmonic 63.615 103.890 # SOURCE3 1 + angle_coeff @angle:p5-p2-p5 harmonic 81.461 89.400 # SOURCE3 1 + angle_coeff @angle:p5-p2-s harmonic 64.429 101.210 # SOURCE3 1 + angle_coeff @angle:pe-p2-s harmonic 69.635 106.350 # SOURCE3 1 + angle_coeff @angle:pf-p2-s harmonic 69.635 106.350 # SOURCE3 1 + angle_coeff @angle:s4-p2-s4 harmonic 50.406 85.300 # SOURCE3 1 + angle_coeff @angle:s6-p2-s6 harmonic 47.194 98.200 # SOURCE3 1 + angle_coeff @angle:sh-p2-sh harmonic 52.119 98.500 # SOURCE3 1 + angle_coeff @angle:s-p2-s harmonic 55.726 106.600 # SOURCE3 1 + angle_coeff @angle:s-p2-s4 harmonic 49.051 105.290 # SOURCE3 1 + angle_coeff @angle:s-p2-s6 harmonic 48.843 106.930 # SOURCE3 1 + angle_coeff @angle:s-p2-sh harmonic 51.478 110.730 # SOURCE3 2 0.0232 + angle_coeff @angle:s-p2-ss harmonic 50.784 114.140 # SOURCE3 4 5.9223 + angle_coeff @angle:ss-p2-ss harmonic 52.411 97.900 # SOURCE3 1 + angle_coeff @angle:br-p3-br harmonic 51.098 103.540 # SOURCE3 1 + angle_coeff @angle:br-p3-hp harmonic 32.984 96.360 # SOURCE3 4 0.6701 + angle_coeff @angle:c1-p3-c1 harmonic 48.612 100.500 # SOURCE3 1 + angle_coeff @angle:c1-p3-f harmonic 66.318 96.900 # SOURCE2 1 + angle_coeff @angle:c1-p3-hp harmonic 34.779 97.670 # SOURCE3 2 + angle_coeff @angle:c2-p3-c2 harmonic 47.149 101.770 # SOURCE3 3 + angle_coeff @angle:c2-p3-hp harmonic 34.073 97.850 # SOURCE3 4 + angle_coeff @angle:c3-p3-c3 harmonic 47.098 99.350 # SOURCE3_SOURCE5 108 0.9814 + angle_coeff @angle:c3-p3-ca harmonic 46.899 101.940 # SOURCE3 2 + angle_coeff @angle:c3-p3-cl harmonic 54.343 99.890 # SOURCE3 1 + angle_coeff @angle:c3-p3-f harmonic 64.355 97.800 # SOURCE2 1 + angle_coeff @angle:c3-p3-hp harmonic 33.769 97.480 # SOURCE3_SOURCE5 20 0.3444 + angle_coeff @angle:c3-p3-n2 harmonic 61.301 96.550 # SOURCE3 2 + angle_coeff @angle:c3-p3-n3 harmonic 60.308 101.410 # SOURCE3_SOURCE5 22 1.5604 + angle_coeff @angle:c3-p3-n4 harmonic 59.355 96.940 # SOURCE3 6 0.4815 + angle_coeff @angle:c3-p3-n harmonic 59.620 101.770 # SOURCE3 12 2.4449 + angle_coeff @angle:c3-p3-na harmonic 60.213 100.170 # SOURCE3 4 0.0554 + angle_coeff @angle:c3-p3-nh harmonic 59.410 104.500 # SOURCE3 2 + angle_coeff @angle:c3-p3-no harmonic 59.922 96.980 # SOURCE3 2 + angle_coeff @angle:c3-p3-o harmonic 60.035 111.670 # SOURCE3 28 5.3387 + angle_coeff @angle:c3-p3-oh harmonic 62.034 98.210 # SOURCE3 2 + angle_coeff @angle:c3-p3-os harmonic 61.657 99.530 # SOURCE3 3 1.7678 + angle_coeff @angle:c3-p3-p3 harmonic 58.575 99.880 # SOURCE3_SOURCE5 26 1.6230 + angle_coeff @angle:c3-p3-p5 harmonic 58.297 100.900 # SOURCE3 10 2.7070 + angle_coeff @angle:c3-p3-s4 harmonic 47.756 98.880 # SOURCE3 8 6.2235 + angle_coeff @angle:c3-p3-s6 harmonic 47.355 101.180 # SOURCE3 12 6.4536 + angle_coeff @angle:c3-p3-sh harmonic 47.131 98.710 # SOURCE3 2 + angle_coeff @angle:c3-p3-ss harmonic 47.137 99.370 # SOURCE3 2 + angle_coeff @angle:ca-p3-ca harmonic 47.814 99.860 # SOURCE3 1 + angle_coeff @angle:ca-p3-hp harmonic 34.261 97.500 # SOURCE3 2 + angle_coeff @angle:c-p3-c3 harmonic 47.331 97.060 # SOURCE3 3 1.1490 + angle_coeff @angle:c-p3-c harmonic 46.120 100.900 # SOURCE3 1 + angle_coeff @angle:c-p3-hp harmonic 33.554 96.550 # SOURCE3 6 0.5223 + angle_coeff @angle:cl-p3-cl harmonic 62.437 102.820 # SOURCE3 1 + angle_coeff @angle:cl-p3-f harmonic 72.784 99.200 # SOURCE2 1 + angle_coeff @angle:cl-p3-hp harmonic 38.308 96.300 # SOURCE3 3 0.6203 + angle_coeff @angle:c-p3-os harmonic 67.637 81.320 # SOURCE3 1 + angle_coeff @angle:cx-p3-hp harmonic 34.036 95.200 # SOURCE2 1 + angle_coeff @angle:f-p3-f harmonic 90.383 97.400 # SOURCE2 8 1.6636 + angle_coeff @angle:f-p3-hp harmonic 48.664 96.410 # SOURCE3 2 + angle_coeff @angle:f-p3-n3 harmonic 83.292 100.600 # SOURCE2 1 + angle_coeff @angle:f-p3-os harmonic 85.509 99.230 # SOURCE2_SOURCE5 5 0.5316 + angle_coeff @angle:f-p3-p3 harmonic 77.745 97.200 # SOURCE2 1 + angle_coeff @angle:hp-p3-hp harmonic 26.638 95.220 # SOURCE3_SOURCE5 51 2.1059 + angle_coeff @angle:hp-p3-i harmonic 29.813 96.190 # SOURCE3 4 0.6454 + angle_coeff @angle:hp-p3-n1 harmonic 47.221 92.980 # HF/6-31G* 1 + angle_coeff @angle:hp-p3-n2 harmonic 43.917 98.280 # SOURCE3 10 1.8860 + angle_coeff @angle:hp-p3-n3 harmonic 45.466 94.460 # SOURCE3 2 + angle_coeff @angle:hp-p3-n4 harmonic 42.822 93.210 # SOURCE3 2 + angle_coeff @angle:hp-p3-n harmonic 44.516 95.150 # SOURCE3 2 + angle_coeff @angle:hp-p3-na harmonic 44.183 97.270 # SOURCE3 12 0.9318 + angle_coeff @angle:hp-p3-nh harmonic 45.553 94.100 # SOURCE3 2 + angle_coeff @angle:hp-p3-no harmonic 43.557 93.060 # SOURCE3 2 + angle_coeff @angle:hp-p3-o harmonic 48.052 101.020 # SOURCE3 2 + angle_coeff @angle:hp-p3-oh harmonic 46.151 95.950 # SOURCE3 2 + angle_coeff @angle:hp-p3-os harmonic 45.868 97.350 # SOURCE3 6 2.8326 + angle_coeff @angle:hp-p3-p2 harmonic 40.595 99.110 # SOURCE3 16 4.3022 + angle_coeff @angle:hp-p3-p3 harmonic 40.175 95.520 # SOURCE3 4 0.0844 + angle_coeff @angle:hp-p3-p4 harmonic 40.047 95.950 # SOURCE3 6 0.0489 + angle_coeff @angle:hp-p3-p5 harmonic 40.189 95.540 # SOURCE3 2 + angle_coeff @angle:hp-p3-s4 harmonic 33.215 95.490 # SOURCE3 2 + angle_coeff @angle:hp-p3-s6 harmonic 33.822 92.950 # SOURCE3 2 + angle_coeff @angle:hp-p3-sh harmonic 32.748 94.210 # SOURCE3 2 + angle_coeff @angle:hp-p3-ss harmonic 32.846 94.610 # SOURCE3 2 + angle_coeff @angle:i-p3-i harmonic 49.016 105.250 # SOURCE3 1 + angle_coeff @angle:n1-p3-n1 harmonic 86.652 90.440 # HF/6-31G* 1 + angle_coeff @angle:n2-p3-n2 harmonic 76.240 103.460 # SOURCE3 1 + angle_coeff @angle:n3-p3-n3 harmonic 74.122 113.800 # SOURCE3 1 + angle_coeff @angle:n3-p3-o harmonic 80.756 107.100 # SOURCE3 4 + angle_coeff @angle:n3-p3-oh harmonic 80.929 98.360 # SOURCE3 1 + angle_coeff @angle:n4-p3-n4 harmonic 72.570 100.530 # SOURCE3 1 + angle_coeff @angle:na-p3-na harmonic 75.328 106.220 # SOURCE3 1 + angle_coeff @angle:nh-p3-nh harmonic 75.698 109.110 # SOURCE3 1 + angle_coeff @angle:n-p3-n harmonic 75.573 104.580 # SOURCE3 1 + angle_coeff @angle:n-p3-o harmonic 80.307 104.990 # SOURCE3 4 + angle_coeff @angle:no-p3-no harmonic 74.810 98.330 # SOURCE3 1 + angle_coeff @angle:oh-p3-oh harmonic 79.802 104.480 # SOURCE3 1 + angle_coeff @angle:o-p3-o harmonic 81.687 122.180 # SOURCE3 2 7.8556 + angle_coeff @angle:o-p3-p3 harmonic 70.126 116.740 # SOURCE3 14 0.7525 + angle_coeff @angle:o-p3-p5 harmonic 73.068 107.620 # SOURCE3 4 + angle_coeff @angle:o-p3-s4 harmonic 59.257 110.700 # SOURCE3 4 0.7259 + angle_coeff @angle:o-p3-s6 harmonic 60.626 106.660 # SOURCE3 6 3.4017 + angle_coeff @angle:os-p3-os harmonic 81.795 99.760 # SOURCE3_SOURCE5 8 1.2613 + angle_coeff @angle:p2-p3-p2 harmonic 76.665 103.580 # SOURCE3 1 + angle_coeff @angle:p3-p3-p3 harmonic 73.903 105.310 # SOURCE3 4 3.5864 + angle_coeff @angle:p4-p3-p4 harmonic 76.119 99.090 # SOURCE3 1 + angle_coeff @angle:p5-p3-p5 harmonic 76.218 99.100 # SOURCE3 1 + angle_coeff @angle:s4-p3-s4 harmonic 49.282 98.260 # SOURCE3 1 + angle_coeff @angle:s6-p3-s6 harmonic 49.641 97.780 # SOURCE3 1 + angle_coeff @angle:sh-p3-sh harmonic 46.105 107.580 # SOURCE3 1 + angle_coeff @angle:s-p3-s harmonic 42.980 131.320 # SOURCE3 1 + angle_coeff @angle:ss-p3-ss harmonic 45.990 109.240 # SOURCE3 1 + angle_coeff @angle:br-p4-br harmonic 50.850 110.410 # SOURCE3 1 + angle_coeff @angle:br-p4-o harmonic 57.453 124.800 # SOURCE3 1 + angle_coeff @angle:c2-p4-c2 harmonic 46.901 104.210 # SOURCE3 1 + angle_coeff @angle:c2-p4-hp harmonic 34.221 99.500 # SOURCE3 2 + angle_coeff @angle:c2-p4-o harmonic 60.517 113.590 # SOURCE3 1 + angle_coeff @angle:c3-p4-c3 harmonic 46.849 102.550 # SOURCE3 4 0.0192 + angle_coeff @angle:c3-p4-n2 harmonic 60.249 103.170 # SOURCE3 1 + angle_coeff @angle:c3-p4-n3 harmonic 60.876 102.370 # SOURCE3 1 + angle_coeff @angle:c3-p4-n4 harmonic 57.893 99.570 # SOURCE3 1 + angle_coeff @angle:c3-p4-n harmonic 60.075 103.260 # SOURCE3 1 + angle_coeff @angle:c3-p4-na harmonic 58.423 117.670 # SOURCE3 5 19.0404 + angle_coeff @angle:c3-p4-nh harmonic 60.622 102.790 # SOURCE3 1 + angle_coeff @angle:c3-p4-no harmonic 58.960 99.800 # SOURCE3 3 0.2151 + angle_coeff @angle:c3-p4-o harmonic 59.565 115.670 # SOURCE3_SOURCE5 41 1.9882 + angle_coeff @angle:c3-p4-oh harmonic 62.836 98.560 # SOURCE3 2 0.4558 + angle_coeff @angle:c3-p4-os harmonic 63.080 98.010 # SOURCE3 2 0.0931 + angle_coeff @angle:c3-p4-p2 harmonic 56.813 109.270 # SOURCE3 1 + angle_coeff @angle:c3-p4-p3 harmonic 57.663 103.530 # SOURCE3 1 + angle_coeff @angle:c3-p4-p4 harmonic 61.536 102.120 # SOURCE3 1 + angle_coeff @angle:c3-p4-p5 harmonic 57.093 104.150 # SOURCE3 1 + angle_coeff @angle:c3-p4-sh harmonic 47.201 100.170 # SOURCE3 2 0.0815 + angle_coeff @angle:c3-p4-ss harmonic 47.127 101.190 # SOURCE3 1 + angle_coeff @angle:ca-p4-ca harmonic 46.528 107.770 # SOURCE3 1 + angle_coeff @angle:ca-p4-o harmonic 61.439 111.640 # SOURCE3 1 + angle_coeff @angle:cl-p4-cl harmonic 62.229 103.510 # SOURCE3 1 + angle_coeff @angle:cl-p4-o harmonic 66.762 116.530 # SOURCE3 2 + angle_coeff @angle:hp-p4-hp harmonic 27.316 99.210 # SOURCE3 4 6.4572 + angle_coeff @angle:hp-p4-n1 harmonic 45.702 99.910 # HF/6-31G* 1 + angle_coeff @angle:hp-p4-o harmonic 47.223 109.350 # SOURCE3 6 10.8284 + angle_coeff @angle:hp-p4-p3 harmonic 39.333 98.960 # SOURCE3 4 + angle_coeff @angle:hp-p4-s harmonic 30.046 110.240 # SOURCE3 4 4.1081 + angle_coeff @angle:i-p4-i harmonic 51.559 113.220 # SOURCE3 2 6.7916 + angle_coeff @angle:i-p4-o harmonic 59.585 110.220 # SOURCE3 4 9.7726 + angle_coeff @angle:n1-p4-n1 harmonic 81.177 100.610 # HF/6-31G* 1 + angle_coeff @angle:n1-p4-o harmonic 79.782 114.590 # HF/6-31G* 1 + angle_coeff @angle:n2-p4-n2 harmonic 78.358 102.540 # SOURCE3 1 + angle_coeff @angle:n2-p4-o harmonic 76.567 120.280 # SOURCE3 1 + angle_coeff @angle:n3-p4-o harmonic 79.727 113.270 # SOURCE3 1 + angle_coeff @angle:n4-p4-o harmonic 74.226 107.610 # SOURCE3 1 + angle_coeff @angle:na-p4-o harmonic 84.731 110.600 # SOURCE3 5 1.3133 + angle_coeff @angle:nh-p4-nh harmonic 82.137 95.300 # SOURCE3 1 + angle_coeff @angle:nh-p4-o harmonic 78.559 115.860 # SOURCE3 3 3.2712 + angle_coeff @angle:n-p4-o harmonic 77.006 117.990 # SOURCE3 1 + angle_coeff @angle:no-p4-o harmonic 73.956 114.690 # SOURCE3 3 0.1070 + angle_coeff @angle:oh-p4-oh harmonic 85.208 95.710 # SOURCE3 1 + angle_coeff @angle:o-p4-o harmonic 84.013 117.220 # SOURCE3 6 2.7792 + angle_coeff @angle:o-p4-oh harmonic 79.987 117.390 # SOURCE3 4 1.0083 + angle_coeff @angle:o-p4-os harmonic 80.383 116.670 # SOURCE3 4 0.6923 + angle_coeff @angle:o-p4-p2 harmonic 69.856 121.350 # SOURCE3 1 + angle_coeff @angle:o-p4-p3 harmonic 70.923 114.000 # SOURCE3 3 0.6663 + angle_coeff @angle:o-p4-p4 harmonic 75.914 116.430 # SOURCE3 1 + angle_coeff @angle:o-p4-p5 harmonic 71.622 109.760 # SOURCE3 1 + angle_coeff @angle:o-p4-s4 harmonic 54.866 112.190 # SOURCE3 1 + angle_coeff @angle:o-p4-s6 harmonic 54.029 113.890 # SOURCE3 1 + angle_coeff @angle:o-p4-s harmonic 57.277 112.780 # SOURCE3 2 + angle_coeff @angle:o-p4-sh harmonic 56.730 118.090 # SOURCE3 1 + angle_coeff @angle:os-p4-os harmonic 83.473 100.340 # SOURCE3 1 + angle_coeff @angle:o-p4-ss harmonic 57.476 116.140 # SOURCE3 4 1.0636 + angle_coeff @angle:p2-p4-p2 harmonic 73.236 110.710 # SOURCE3 1 + angle_coeff @angle:p3-p4-p3 harmonic 70.664 114.980 # SOURCE3 1 + angle_coeff @angle:p4-p4-p4 harmonic 79.664 107.380 # SOURCE3 1 + angle_coeff @angle:p5-p4-p5 harmonic 72.301 107.780 # SOURCE3 1 + angle_coeff @angle:s4-p4-s4 harmonic 46.168 96.240 # SOURCE3 1 + angle_coeff @angle:s6-p4-s6 harmonic 44.412 102.360 # SOURCE3 1 + angle_coeff @angle:sh-p4-sh harmonic 48.494 98.810 # SOURCE3 1 + angle_coeff @angle:s-p4-s harmonic 46.079 106.300 # SOURCE3 2 25.0119 + angle_coeff @angle:ss-p4-ss harmonic 47.422 104.410 # SOURCE3 1 + angle_coeff @angle:br-p5-br harmonic 51.952 103.380 # SOURCE3 1 + angle_coeff @angle:br-p5-o harmonic 59.322 114.650 # SOURCE3 3 1.0910 + angle_coeff @angle:br-p5-oh harmonic 62.204 102.920 # SOURCE3 4 0.5468 + angle_coeff @angle:c1-p5-c1 harmonic 49.058 102.890 # SOURCE3 1 + angle_coeff @angle:c1-p5-o harmonic 61.836 115.770 # SOURCE3 2 + angle_coeff @angle:c1-p5-oh harmonic 63.769 102.790 # SOURCE3 2 + angle_coeff @angle:c2-p5-c2 harmonic 45.370 106.560 # SOURCE3 1 + angle_coeff @angle:c2-p5-o harmonic 60.781 109.520 # SOURCE4_SOURCE5 15 2.0293 + angle_coeff @angle:c2-p5-oh harmonic 61.672 101.690 # SOURCE3 1 + angle_coeff @angle:c2-p5-os harmonic 63.109 97.120 # SOURCE3_SOURCE5 6 0.9178 + angle_coeff @angle:c3-p5-c3 harmonic 46.061 106.000 # SOURCE3_SOURCE5 107 1.6965 + angle_coeff @angle:c3-p5-hp harmonic 33.063 103.260 # SOURCE4_SOURCE5 20 1.3795 + angle_coeff @angle:c3-p5-n3 harmonic 60.649 104.400 # SOURCE3_SOURCE5 10 1.8148 + angle_coeff @angle:c3-p5-o harmonic 60.550 112.500 # SOURCE3 23 4.4203 + angle_coeff @angle:c3-p5-oh harmonic 61.886 102.690 # SOURCE3_SOURCE5 389 1.5370 + angle_coeff @angle:c3-p5-os harmonic 62.476 100.770 # SOURCE4 51 2.0928 + angle_coeff @angle:c3-p5-p4 harmonic 56.514 106.270 # SOURCE3 1 + angle_coeff @angle:c3-p5-s harmonic 46.672 114.400 # SOURCE3_SOURCE5 36 1.0844 + angle_coeff @angle:c3-p5-ss harmonic 45.854 105.940 # SOURCE3_SOURCE5 24 1.6358 + angle_coeff @angle:ca-p5-ca harmonic 46.780 107.900 # SOURCE3_SOURCE5 5 0.5519 + angle_coeff @angle:ca-p5-o harmonic 61.263 113.980 # SOURCE3 1 + angle_coeff @angle:ca-p5-oh harmonic 63.154 101.770 # SOURCE3 1 + angle_coeff @angle:ca-p5-os harmonic 62.551 103.750 # SOURCE3 1 + angle_coeff @angle:c-p5-c harmonic 45.421 104.160 # SOURCE3 1 + angle_coeff @angle:cl-p5-cl harmonic 62.172 103.700 # SOURCE2 1 + angle_coeff @angle:cl-p5-o harmonic 68.012 112.650 # SOURCE3_SOURCE5 7 1.0635 + angle_coeff @angle:cl-p5-oh harmonic 70.253 102.440 # SOURCE3 2 + angle_coeff @angle:c-p5-o harmonic 60.972 107.100 # SOURCE4_SOURCE5 37 0.4646 + angle_coeff @angle:c-p5-oh harmonic 61.112 102.120 # SOURCE3 1 + angle_coeff @angle:f-p5-f harmonic 92.407 92.220 # SOURCE2_SOURCE5 19 1.3661 + angle_coeff @angle:f-p5-o harmonic 85.135 112.070 # SOURCE4_SOURCE5 15 0.5195 + angle_coeff @angle:f-p5-oh harmonic 85.837 101.980 # SOURCE3 2 + angle_coeff @angle:f-p5-os harmonic 85.720 102.270 # SOURCE4_SOURCE5 16 1.0230 + angle_coeff @angle:f-p5-s harmonic 61.598 117.400 # SOURCE2 1 + angle_coeff @angle:hp-p5-hp harmonic 25.816 100.550 # SOURCE3_SOURCE5 11 0.5508 + angle_coeff @angle:hp-p5-n1 harmonic 46.858 101.320 # HF/6-31G* 1 + angle_coeff @angle:hp-p5-o harmonic 45.433 115.080 # SOURCE3_SOURCE5 27 1.7749 + angle_coeff @angle:hp-p5-oh harmonic 45.976 101.570 # SOURCE3_SOURCE5 16 1.3736 + angle_coeff @angle:hp-p5-s harmonic 31.882 119.200 # SOURCE2 1 + angle_coeff @angle:i-p5-i harmonic 48.013 107.170 # SOURCE3 1 + angle_coeff @angle:i-p5-o harmonic 52.148 115.930 # SOURCE3 3 0.0415 + angle_coeff @angle:i-p5-oh harmonic 55.980 102.260 # SOURCE3 4 1.9577 + angle_coeff @angle:n1-p5-n1 harmonic 86.407 101.550 # HF/6-31G* 1 + angle_coeff @angle:n1-p5-o harmonic 83.757 113.780 # HF/6-31G* 1 + angle_coeff @angle:n2-p5-n2 harmonic 82.960 106.340 # SOURCE3 1 + angle_coeff @angle:n2-p5-o harmonic 82.994 113.530 # SOURCE3 1 + angle_coeff @angle:n2-p5-oh harmonic 84.118 102.400 # SOURCE3 1 + angle_coeff @angle:n3-p5-n3 harmonic 80.585 103.370 # SOURCE4 47 2.1009 + angle_coeff @angle:n3-p5-nh harmonic 80.369 103.840 # SOURCE4_SOURCE5 11 1.8670 + angle_coeff @angle:n3-p5-o harmonic 80.416 114.640 # SOURCE4 76 2.2728 + angle_coeff @angle:n3-p5-oh harmonic 81.248 104.990 # SOURCE3_SOURCE5 18 0.6974 + angle_coeff @angle:n3-p5-os harmonic 82.342 102.230 # SOURCE4_SOURCE5 90 2.1717 + angle_coeff @angle:n3-p5-s harmonic 60.056 116.560 # SOURCE4_SOURCE5 28 0.9342 + angle_coeff @angle:n4-p5-n4 harmonic 73.942 102.200 # SOURCE3 1 + angle_coeff @angle:n4-p5-o harmonic 77.060 109.780 # SOURCE3 5 2.7519 + angle_coeff @angle:n4-p5-oh harmonic 79.407 98.480 # SOURCE3 6 0.4104 + angle_coeff @angle:n4-p5-os harmonic 81.044 94.550 # SOURCE3 2 + angle_coeff @angle:na-p5-na harmonic 76.550 108.570 # SOURCE3 1 + angle_coeff @angle:na-p5-o harmonic 79.422 113.430 # SOURCE3 11 0.8968 + angle_coeff @angle:na-p5-oh harmonic 81.176 102.070 # SOURCE3 16 1.4144 + angle_coeff @angle:na-p5-os harmonic 80.790 103.060 # SOURCE3 4 0.7463 + angle_coeff @angle:nh-p5-nh harmonic 82.064 99.510 # SOURCE3 1 + angle_coeff @angle:nh-p5-o harmonic 80.296 114.860 # SOURCE3_SOURCE5 11 1.6006 + angle_coeff @angle:nh-p5-oh harmonic 82.027 102.910 # SOURCE3_SOURCE5 6 0.9034 + angle_coeff @angle:nh-p5-os harmonic 81.134 105.200 # SOURCE3_SOURCE5 6 2.0688 + angle_coeff @angle:n-p5-n3 harmonic 79.065 104.310 # SOURCE4_SOURCE5 28 1.2397 + angle_coeff @angle:n-p5-n harmonic 78.462 103.090 # SOURCE3 1 + angle_coeff @angle:n-p5-o harmonic 79.797 112.180 # SOURCE4_SOURCE5 14 1.5068 + angle_coeff @angle:n-p5-oh harmonic 80.973 102.440 # SOURCE3 4 0.0999 + angle_coeff @angle:no-p5-no harmonic 76.253 95.680 # SOURCE3 1 + angle_coeff @angle:no-p5-o harmonic 75.912 112.750 # SOURCE3 4 3.3684 + angle_coeff @angle:no-p5-oh harmonic 78.162 101.350 # SOURCE3 2 + angle_coeff @angle:no-p5-os harmonic 78.031 101.700 # SOURCE3 4 0.0565 + angle_coeff @angle:n-p5-os harmonic 81.763 100.480 # SOURCE3 2 + angle_coeff @angle:oh-p5-oh harmonic 83.590 102.690 # SOURCE3_SOURCE5 359 1.1644 + angle_coeff @angle:oh-p5-os harmonic 83.902 101.940 # SOURCE3_SOURCE5 591 1.1251 + angle_coeff @angle:oh-p5-p2 harmonic 75.094 103.530 # SOURCE3 1 + angle_coeff @angle:oh-p5-p3 harmonic 74.007 103.830 # SOURCE3 13 0.4303 + angle_coeff @angle:oh-p5-p4 harmonic 74.032 101.790 # SOURCE3 1 + angle_coeff @angle:oh-p5-p5 harmonic 80.103 100.450 # SOURCE3 1 + angle_coeff @angle:oh-p5-s4 harmonic 61.903 103.240 # SOURCE3 1 + angle_coeff @angle:oh-p5-s6 harmonic 62.438 101.480 # SOURCE3 1 + angle_coeff @angle:oh-p5-s harmonic 62.070 111.300 # SOURCE3_SOURCE5 8 1.1112 + angle_coeff @angle:oh-p5-sh harmonic 61.449 101.410 # SOURCE3 2 + angle_coeff @angle:oh-p5-ss harmonic 59.814 104.090 # SOURCE3_SOURCE5 23 1.4682 + angle_coeff @angle:o-p5-o harmonic 85.510 115.800 # SOURCE3 17 5.7902 + angle_coeff @angle:o-p5-oh harmonic 81.901 115.210 # SOURCE4_SOURCE5 1716 1.3221 + angle_coeff @angle:o-p5-os harmonic 81.819 115.460 # SOURCE3_SOURCE5 843 2.3835 + angle_coeff @angle:o-p5-p2 harmonic 71.892 114.600 # SOURCE3 1 + angle_coeff @angle:o-p5-p3 harmonic 70.584 115.480 # SOURCE3 9 2.1084 + angle_coeff @angle:o-p5-p4 harmonic 70.090 114.660 # SOURCE3 1 + angle_coeff @angle:o-p5-p5 harmonic 76.354 113.440 # SOURCE3 1 + angle_coeff @angle:o-p5-s4 harmonic 60.725 110.230 # SOURCE3 1 + angle_coeff @angle:o-p5-s6 harmonic 60.311 111.750 # SOURCE3 1 + angle_coeff @angle:o-p5-s harmonic 61.702 116.940 # SOURCE3 3 2.9506 + angle_coeff @angle:o-p5-sh harmonic 58.488 114.560 # SOURCE3 3 1.7645 + angle_coeff @angle:os-p5-os harmonic 83.949 101.840 # SOURCE4_SOURCE5 608 1.9896 + angle_coeff @angle:os-p5-p3 harmonic 74.065 103.670 # SOURCE3 2 + angle_coeff @angle:os-p5-p5 harmonic 78.545 104.480 # SOURCE3 1 + angle_coeff @angle:os-p5-s4 harmonic 62.122 102.520 # SOURCE3 1 + angle_coeff @angle:os-p5-s6 harmonic 62.313 101.890 # SOURCE3 1 + angle_coeff @angle:o-p5-ss harmonic 57.641 114.340 # SOURCE3_SOURCE5 37 1.7416 + angle_coeff @angle:os-p5-s harmonic 60.508 117.130 # SOURCE4_SOURCE5 200 0.8203 + angle_coeff @angle:os-p5-sh harmonic 61.258 102.050 # SOURCE3_SOURCE5 7 0.5915 + angle_coeff @angle:os-p5-ss harmonic 60.283 102.480 # SOURCE4_SOURCE5 70 1.4633 + angle_coeff @angle:p2-p5-p2 harmonic 74.412 107.140 # SOURCE3 1 + angle_coeff @angle:p3-p5-p3 harmonic 73.965 105.230 # SOURCE3 3 5.1024 + angle_coeff @angle:p4-p5-p4 harmonic 74.460 101.620 # SOURCE3 1 + angle_coeff @angle:p5-p5-p5 harmonic 76.997 112.720 # SOURCE3 1 + angle_coeff @angle:s6-p5-s6 harmonic 48.731 105.180 # SOURCE3 1 + angle_coeff @angle:sh-p5-sh harmonic 47.889 104.560 # SOURCE3 1 + angle_coeff @angle:sh-p5-ss harmonic 46.903 107.130 # SOURCE3 1 + angle_coeff @angle:s-p5-s harmonic 49.342 114.130 # SOURCE3 1 + angle_coeff @angle:ss-p5-ss harmonic 45.986 109.610 # SOURCE3 1 + angle_coeff @angle:cd-pc-n harmonic 66.016 90.800 # SOURCE3 3 2.3423 + angle_coeff @angle:cd-pc-na harmonic 66.396 90.180 # SOURCE3 81 2.7619 + angle_coeff @angle:cc-pd-n harmonic 66.016 90.800 # SOURCE3 3 + angle_coeff @angle:cc-pd-na harmonic 66.396 90.180 # SOURCE3 81 + angle_coeff @angle:c2-pe-ca harmonic 49.088 101.440 # SOURCE3 3 0.7177 + angle_coeff @angle:c2-pe-ce harmonic 48.888 103.010 # SOURCE3 4 1.4470 + angle_coeff @angle:c2-pe-cg harmonic 51.641 104.030 # SOURCE3 3 3.8740 + angle_coeff @angle:c2-pe-n2 harmonic 69.448 94.140 # SOURCE3 1 + angle_coeff @angle:c2-pe-ne harmonic 64.662 98.700 # SOURCE3 12 5.3383 + angle_coeff @angle:c2-pe-o harmonic 63.086 115.160 # SOURCE3 2 0.0149 + angle_coeff @angle:c2-pe-p2 harmonic 65.232 107.820 # SOURCE3 1 + angle_coeff @angle:c2-pe-pe harmonic 61.668 102.990 # SOURCE3 9 8.2860 + angle_coeff @angle:c2-pe-px harmonic 65.444 97.370 # SOURCE3 4 0.6655 + angle_coeff @angle:c2-pe-py harmonic 65.200 96.710 # SOURCE3 4 1.2755 + angle_coeff @angle:c2-pe-s harmonic 51.862 111.160 # SOURCE3 2 + angle_coeff @angle:c2-pe-sx harmonic 48.622 95.110 # SOURCE3 4 0.2676 + angle_coeff @angle:c2-pe-sy harmonic 47.698 95.560 # SOURCE3 2 0.0462 + angle_coeff @angle:ca-pe-n2 harmonic 63.263 102.030 # SOURCE3 1 + angle_coeff @angle:ca-pe-o harmonic 62.025 106.880 # SOURCE3 2 0.0018 + angle_coeff @angle:ca-pe-p2 harmonic 65.219 100.790 # SOURCE3 1 + angle_coeff @angle:ca-pe-pf harmonic 61.993 99.700 # SOURCE3 2 + angle_coeff @angle:ca-pe-s harmonic 50.574 107.930 # SOURCE3 1 + angle_coeff @angle:c-pe-c2 harmonic 48.762 97.300 # SOURCE3 3 0.0335 + angle_coeff @angle:ce-pe-n2 harmonic 64.000 100.550 # SOURCE3 1 + angle_coeff @angle:ce-pe-o harmonic 62.134 107.440 # SOURCE3 1 + angle_coeff @angle:ce-pe-p2 harmonic 65.808 99.560 # SOURCE3 1 + angle_coeff @angle:ce-pe-s harmonic 51.312 105.540 # SOURCE3 1 + angle_coeff @angle:cg-pe-n2 harmonic 68.416 101.790 # SOURCE3 1 + angle_coeff @angle:cg-pe-o harmonic 66.891 107.620 # SOURCE3 1 + angle_coeff @angle:cg-pe-p2 harmonic 67.155 104.680 # SOURCE3 2 5.1435 + angle_coeff @angle:cg-pe-s harmonic 53.387 108.600 # SOURCE3 4 2.6981 + angle_coeff @angle:n2-pe-n2 harmonic 85.418 108.140 # SOURCE3 1 + angle_coeff @angle:n2-pe-ne harmonic 80.952 106.800 # SOURCE3 6 4.5981 + angle_coeff @angle:n2-pe-o harmonic 83.198 115.390 # SOURCE3 1 + angle_coeff @angle:n2-pe-p2 harmonic 82.679 111.600 # SOURCE3 1 + angle_coeff @angle:n2-pe-pe harmonic 76.187 109.400 # SOURCE3 1 + angle_coeff @angle:n2-pe-px harmonic 78.660 110.300 # SOURCE3 3 6.0548 + angle_coeff @angle:n2-pe-py harmonic 84.653 93.680 # SOURCE3 1 + angle_coeff @angle:n2-pe-s harmonic 66.247 114.840 # SOURCE3 3 3.6512 + angle_coeff @angle:n2-pe-sx harmonic 60.809 97.830 # SOURCE3 1 + angle_coeff @angle:n2-pe-sy harmonic 59.570 98.140 # SOURCE3 1 + angle_coeff @angle:ne-pe-o harmonic 80.037 110.240 # SOURCE3 3 3.8478 + angle_coeff @angle:ne-pe-p2 harmonic 82.546 104.480 # SOURCE3 2 7.1207 + angle_coeff @angle:ne-pe-s harmonic 65.116 109.190 # SOURCE3 5 3.6708 + angle_coeff @angle:o-pe-o harmonic 82.114 119.960 # SOURCE3 1 + angle_coeff @angle:o-pe-p2 harmonic 81.980 114.230 # SOURCE3 1 + angle_coeff @angle:o-pe-pe harmonic 66.057 145.960 # SOURCE3 1 + angle_coeff @angle:o-pe-px harmonic 81.034 104.370 # SOURCE3 1 + angle_coeff @angle:o-pe-py harmonic 80.312 104.490 # SOURCE3 1 + angle_coeff @angle:o-pe-s harmonic 65.783 117.420 # SOURCE3 2 0.0426 + angle_coeff @angle:o-pe-sx harmonic 58.314 106.590 # SOURCE3 1 + angle_coeff @angle:o-pe-sy harmonic 57.621 105.040 # SOURCE3 1 + angle_coeff @angle:p2-pe-pe harmonic 85.030 98.240 # SOURCE3 1 + angle_coeff @angle:p2-pe-px harmonic 83.137 108.280 # SOURCE3 2 6.2959 + angle_coeff @angle:p2-pe-py harmonic 81.676 110.870 # SOURCE3 3 8.1645 + angle_coeff @angle:p2-pe-s harmonic 68.307 111.280 # SOURCE3 1 + angle_coeff @angle:p2-pe-sx harmonic 65.549 95.730 # SOURCE3 1 + angle_coeff @angle:p2-pe-sy harmonic 64.541 95.950 # SOURCE3 1 + angle_coeff @angle:pe-pe-s harmonic 64.452 107.910 # SOURCE3 2 1.5577 + angle_coeff @angle:px-pe-s harmonic 66.458 107.620 # SOURCE3 2 3.7266 + angle_coeff @angle:py-pe-s harmonic 65.679 108.730 # SOURCE3 3 5.3201 + angle_coeff @angle:s-pe-s harmonic 43.414 178.440 # SOURCE3 1 + angle_coeff @angle:s-pe-sx harmonic 48.826 108.320 # SOURCE3 2 3.0318 + angle_coeff @angle:s-pe-sy harmonic 48.370 106.930 # SOURCE3 1 + angle_coeff @angle:c2-pf-ca harmonic 49.088 101.440 # SOURCE3 3 + angle_coeff @angle:c2-pf-cf harmonic 48.888 103.010 # SOURCE3 4 + angle_coeff @angle:c2-pf-ch harmonic 51.641 104.030 # SOURCE3 3 + angle_coeff @angle:c2-pf-n2 harmonic 69.448 94.140 # SOURCE3 1 + angle_coeff @angle:c2-pf-nf harmonic 64.662 98.700 # SOURCE3 12 + angle_coeff @angle:c2-pf-o harmonic 63.086 115.160 # SOURCE3 2 + angle_coeff @angle:c2-pf-p2 harmonic 65.232 107.820 # SOURCE3 1 + angle_coeff @angle:c2-pf-pf harmonic 61.668 102.990 # SOURCE3 9 + angle_coeff @angle:c2-pf-px harmonic 65.444 97.370 # SOURCE3 4 + angle_coeff @angle:c2-pf-py harmonic 65.200 96.710 # SOURCE3 4 + angle_coeff @angle:c2-pf-s harmonic 51.862 111.160 # SOURCE3 2 + angle_coeff @angle:c2-pf-sx harmonic 48.622 95.110 # SOURCE3 4 + angle_coeff @angle:c2-pf-sy harmonic 47.698 95.560 # SOURCE3 2 + angle_coeff @angle:ca-pf-n2 harmonic 63.263 102.030 # SOURCE3 1 + angle_coeff @angle:ca-pf-o harmonic 62.025 106.880 # SOURCE3 2 + angle_coeff @angle:ca-pf-p2 harmonic 65.219 100.790 # SOURCE3 1 + angle_coeff @angle:ca-pf-pe harmonic 61.993 99.700 # SOURCE3 2 + angle_coeff @angle:ca-pf-s harmonic 50.574 107.930 # SOURCE3 1 + angle_coeff @angle:c-pf-c2 harmonic 48.762 97.300 # SOURCE3 3 + angle_coeff @angle:cf-pf-n2 harmonic 64.000 100.550 # SOURCE3 1 + angle_coeff @angle:cf-pf-o harmonic 62.134 107.440 # SOURCE3 1 + angle_coeff @angle:cf-pf-p2 harmonic 65.808 99.560 # SOURCE3 1 + angle_coeff @angle:cf-pf-s harmonic 51.312 105.540 # SOURCE3 1 + angle_coeff @angle:ch-pf-n2 harmonic 68.416 101.790 # SOURCE3 1 + angle_coeff @angle:ch-pf-o harmonic 66.891 107.620 # SOURCE3 1 + angle_coeff @angle:ch-pf-p2 harmonic 67.155 104.680 # SOURCE3 2 + angle_coeff @angle:ch-pf-s harmonic 53.387 108.600 # SOURCE3 4 + angle_coeff @angle:n2-pf-n2 harmonic 85.418 108.140 # SOURCE3 1 + angle_coeff @angle:n2-pf-nf harmonic 80.952 106.800 # SOURCE3 6 + angle_coeff @angle:n2-pf-o harmonic 83.198 115.390 # SOURCE3 1 + angle_coeff @angle:n2-pf-p2 harmonic 82.679 111.600 # SOURCE3 1 + angle_coeff @angle:n2-pf-pf harmonic 76.187 109.400 # SOURCE3 1 + angle_coeff @angle:n2-pf-px harmonic 78.660 110.300 # SOURCE3 3 + angle_coeff @angle:n2-pf-py harmonic 84.653 93.680 # SOURCE3 1 + angle_coeff @angle:n2-pf-s harmonic 66.247 114.840 # SOURCE3 3 + angle_coeff @angle:n2-pf-sx harmonic 60.809 97.830 # SOURCE3 1 + angle_coeff @angle:n2-pf-sy harmonic 59.570 98.140 # SOURCE3 1 + angle_coeff @angle:nf-pf-o harmonic 80.037 110.240 # SOURCE3 3 + angle_coeff @angle:nf-pf-p2 harmonic 82.546 104.480 # SOURCE3 2 + angle_coeff @angle:nf-pf-s harmonic 65.116 109.190 # SOURCE3 5 + angle_coeff @angle:o-pf-o harmonic 82.114 119.960 # SOURCE3 1 + angle_coeff @angle:o-pf-p2 harmonic 81.980 114.230 # SOURCE3 1 + angle_coeff @angle:o-pf-pf harmonic 66.057 145.960 # SOURCE3 1 + angle_coeff @angle:o-pf-px harmonic 81.034 104.370 # SOURCE3 1 + angle_coeff @angle:o-pf-py harmonic 80.312 104.490 # SOURCE3 1 + angle_coeff @angle:o-pf-s harmonic 65.783 117.420 # SOURCE3 2 + angle_coeff @angle:o-pf-sx harmonic 58.314 106.590 # SOURCE3 1 + angle_coeff @angle:o-pf-sy harmonic 57.621 105.040 # SOURCE3 1 + angle_coeff @angle:p2-pf-pf harmonic 85.030 98.240 # SOURCE3 1 + angle_coeff @angle:p2-pf-px harmonic 83.137 108.280 # SOURCE3 2 + angle_coeff @angle:p2-pf-py harmonic 81.676 110.870 # SOURCE3 3 + angle_coeff @angle:p2-pf-s harmonic 68.307 111.280 # SOURCE3 1 + angle_coeff @angle:p2-pf-sx harmonic 65.549 95.730 # SOURCE3 1 + angle_coeff @angle:p2-pf-sy harmonic 64.541 95.950 # SOURCE3 1 + angle_coeff @angle:pf-pf-s harmonic 64.452 107.910 # SOURCE3 2 + angle_coeff @angle:px-pf-s harmonic 66.458 107.620 # SOURCE3 2 + angle_coeff @angle:py-pf-s harmonic 65.679 108.730 # SOURCE3 3 + angle_coeff @angle:s-pf-s harmonic 43.414 178.440 # SOURCE3 1 + angle_coeff @angle:s-pf-sx harmonic 48.826 108.320 # SOURCE3 2 + angle_coeff @angle:s-pf-sy harmonic 48.370 106.930 # SOURCE3 1 + angle_coeff @angle:c3-px-ca harmonic 46.648 104.790 # SOURCE3 1 + angle_coeff @angle:c3-px-ce harmonic 46.683 104.860 # SOURCE3 4 0.6354 + angle_coeff @angle:c3-px-cf harmonic 46.683 104.860 # SOURCE3 4 + angle_coeff @angle:c3-px-ne harmonic 60.976 102.460 # SOURCE3 7 1.8685 + angle_coeff @angle:c3-px-nf harmonic 60.976 102.460 # SOURCE3 7 + angle_coeff @angle:c3-px-o harmonic 60.307 113.790 # SOURCE3_SOURCE5 33 4.2352 + angle_coeff @angle:c3-px-pe harmonic 61.145 105.730 # SOURCE3 10 4.4059 + angle_coeff @angle:c3-px-pf harmonic 61.145 105.730 # SOURCE3 10 + angle_coeff @angle:c3-px-py harmonic 58.192 103.110 # SOURCE3 3 0.8680 + angle_coeff @angle:c3-px-sx harmonic 45.492 99.550 # SOURCE3 1 + angle_coeff @angle:c3-px-sy harmonic 44.530 103.410 # SOURCE3 1 + angle_coeff @angle:ca-px-ca harmonic 46.837 104.150 # SOURCE3 2 3.6168 + angle_coeff @angle:ca-px-o harmonic 62.137 107.500 # SOURCE3 5 5.7355 + angle_coeff @angle:c-px-c3 harmonic 46.307 101.720 # SOURCE3 1 + angle_coeff @angle:ce-px-ce harmonic 46.926 104.210 # SOURCE3 1 + angle_coeff @angle:ce-px-o harmonic 60.493 113.790 # SOURCE3 6 0.3877 + angle_coeff @angle:cf-px-cf harmonic 46.926 104.210 # SOURCE3 1 + angle_coeff @angle:cf-px-o harmonic 60.493 113.790 # SOURCE3 6 + angle_coeff @angle:c-px-o harmonic 58.294 114.470 # SOURCE3 1 + angle_coeff @angle:ne-px-ne harmonic 79.109 103.220 # SOURCE3 2 0.6807 + angle_coeff @angle:ne-px-o harmonic 79.281 114.130 # SOURCE3 11 8.9737 + angle_coeff @angle:nf-px-nf harmonic 79.109 103.220 # SOURCE3 2 + angle_coeff @angle:nf-px-o harmonic 79.281 114.130 # SOURCE3 11 + angle_coeff @angle:o-px-pe harmonic 76.837 116.500 # SOURCE3 12 8.2925 + angle_coeff @angle:o-px-pf harmonic 76.837 116.500 # SOURCE3 12 + angle_coeff @angle:o-px-py harmonic 71.388 114.200 # SOURCE3 5 1.7165 + angle_coeff @angle:o-px-sx harmonic 54.930 112.810 # SOURCE3 3 0.8799 + angle_coeff @angle:o-px-sy harmonic 54.586 113.540 # SOURCE3 3 0.5010 + angle_coeff @angle:pe-px-pe harmonic 79.592 110.710 # SOURCE3 1 + angle_coeff @angle:pf-px-pf harmonic 79.592 110.710 # SOURCE3 1 + angle_coeff @angle:py-px-py harmonic 73.550 107.780 # SOURCE3 1 + angle_coeff @angle:sx-px-sx harmonic 46.354 96.240 # SOURCE3 1 + angle_coeff @angle:sy-px-sy harmonic 44.807 102.360 # SOURCE3 1 + angle_coeff @angle:c3-py-n4 harmonic 57.271 103.830 # SOURCE3 4 + angle_coeff @angle:c3-py-na harmonic 59.344 106.890 # SOURCE3 2 + angle_coeff @angle:c3-py-o harmonic 59.442 116.680 # SOURCE3_SOURCE5 22 1.9051 + angle_coeff @angle:c3-py-oh harmonic 62.641 100.160 # SOURCE3 2 + angle_coeff @angle:c3-py-os harmonic 61.038 105.390 # SOURCE3 1 + angle_coeff @angle:c3-py-px harmonic 57.225 106.270 # SOURCE3 2 + angle_coeff @angle:c3-py-py harmonic 56.530 109.830 # SOURCE3_SOURCE5 16 1.4525 + angle_coeff @angle:c3-py-sx harmonic 43.696 106.360 # SOURCE3 4 + angle_coeff @angle:ca-py-ca harmonic 46.314 107.550 # SOURCE3 1 + angle_coeff @angle:ca-py-o harmonic 60.635 114.330 # SOURCE3_SOURCE5 20 1.3895 + angle_coeff @angle:ca-py-oh harmonic 62.332 102.870 # SOURCE4_SOURCE5 16 1.4519 + angle_coeff @angle:ca-py-os harmonic 62.763 101.360 # SOURCE3_SOURCE5 12 1.6676 + angle_coeff @angle:c-py-c3 harmonic 44.799 110.360 # SOURCE3 1 + angle_coeff @angle:c-py-c harmonic 45.772 104.200 # SOURCE3 1 + angle_coeff @angle:ce-py-ce harmonic 46.806 106.540 # SOURCE3 1 + angle_coeff @angle:ce-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 17 2.0725 + angle_coeff @angle:ce-py-oh harmonic 61.997 104.770 # SOURCE3 6 2.1852 + angle_coeff @angle:ce-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 + angle_coeff @angle:cf-py-cf harmonic 46.806 106.540 # SOURCE3 1 + angle_coeff @angle:cf-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 12 1.5779 + angle_coeff @angle:cf-py-oh harmonic 61.997 104.770 # SOURCE3 6 + angle_coeff @angle:cf-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 + angle_coeff @angle:c-py-o harmonic 59.457 114.000 # SOURCE3_SOURCE5 17 1.4765 + angle_coeff @angle:c-py-oh harmonic 61.100 103.220 # SOURCE3_SOURCE5 16 1.4543 + angle_coeff @angle:c-py-os harmonic 62.044 100.010 # SOURCE3_SOURCE5 14 3.2269 + angle_coeff @angle:n3-py-ne harmonic 79.409 108.760 # SOURCE4_SOURCE5 30 1.0660 + angle_coeff @angle:n4-py-o harmonic 72.867 115.580 # SOURCE3 4 + angle_coeff @angle:n4-py-py harmonic 98.929 55.100 # SOURCE3 4 + angle_coeff @angle:na-py-o harmonic 76.532 122.400 # SOURCE3 2 + angle_coeff @angle:na-py-py harmonic 105.838 50.880 # SOURCE3 2 + angle_coeff @angle:ne-py-ne harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 + angle_coeff @angle:ne-py-o harmonic 82.910 113.210 # SOURCE3 15 3.8894 + angle_coeff @angle:ne-py-oh harmonic 83.005 104.700 # SOURCE3 26 2.7513 + angle_coeff @angle:ne-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 + angle_coeff @angle:nf-py-nf harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 + angle_coeff @angle:nf-py-o harmonic 82.910 113.210 # SOURCE3 15 + angle_coeff @angle:nf-py-oh harmonic 83.005 104.700 # SOURCE3 26 + angle_coeff @angle:nf-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 + angle_coeff @angle:oh-py-oh harmonic 83.937 101.680 # SOURCE3_SOURCE5 49 1.9218 + angle_coeff @angle:oh-py-pe harmonic 79.277 104.840 # SOURCE3 22 2.0337 + angle_coeff @angle:oh-py-pf harmonic 79.277 104.840 # SOURCE3 22 + angle_coeff @angle:oh-py-px harmonic 74.246 104.300 # SOURCE3 8 1.2772 + angle_coeff @angle:oh-py-py harmonic 76.047 100.450 # SOURCE3 6 + angle_coeff @angle:oh-py-sx harmonic 57.417 100.940 # SOURCE3 4 + angle_coeff @angle:oh-py-sy harmonic 59.053 101.470 # SOURCE3 6 0.2490 + angle_coeff @angle:o-py-oh harmonic 81.623 115.830 # SOURCE3_SOURCE5 105 1.8918 + angle_coeff @angle:o-py-os harmonic 81.496 115.990 # SOURCE3_SOURCE5 47 1.2146 + angle_coeff @angle:o-py-pe harmonic 76.936 114.560 # SOURCE3 12 3.6114 + angle_coeff @angle:o-py-pf harmonic 76.936 114.560 # SOURCE3 12 + angle_coeff @angle:o-py-px harmonic 72.318 111.370 # SOURCE3 5 0.3803 + angle_coeff @angle:o-py-py harmonic 69.944 120.430 # SOURCE3 16 6.0629 + angle_coeff @angle:os-py-os harmonic 83.760 101.820 # SOURCE3_SOURCE5 27 1.5502 + angle_coeff @angle:os-py-py harmonic 74.513 104.590 # SOURCE3_SOURCE5 5 0.4023 + angle_coeff @angle:os-py-sx harmonic 56.596 103.860 # SOURCE3 2 + angle_coeff @angle:os-py-sy harmonic 58.853 102.120 # SOURCE3 2 + angle_coeff @angle:o-py-sx harmonic 53.190 118.560 # SOURCE3 7 6.2976 + angle_coeff @angle:o-py-sy harmonic 56.689 111.710 # SOURCE3 5 1.1937 + angle_coeff @angle:pe-py-pe harmonic 80.108 107.140 # SOURCE3 1 + angle_coeff @angle:pf-py-pf harmonic 80.108 107.140 # SOURCE3 1 + angle_coeff @angle:py-py-py harmonic 72.354 112.700 # SOURCE3 1 + angle_coeff @angle:py-py-sx harmonic 75.004 61.540 # SOURCE3 4 + angle_coeff @angle:sy-py-sy harmonic 45.561 105.170 # SOURCE3 1 + angle_coeff @angle:c1-s2-o harmonic 94.269 117.250 # SOURCE3 1 + angle_coeff @angle:c2-s2-n2 harmonic 98.098 110.840 # SOURCE3 1 + angle_coeff @angle:c2-s2-o harmonic 94.864 114.700 # SOURCE2 1 + angle_coeff @angle:cl-s2-n1 harmonic 92.974 117.700 # SOURCE2 1 + angle_coeff @angle:f-s2-n1 harmonic 122.911 116.900 # SOURCE2 1 + angle_coeff @angle:n1-s2-o harmonic 127.997 108.460 # HF/6-31G* 1 + angle_coeff @angle:n2-s2-o harmonic 117.918 121.200 # SOURCE2 2 0.8000 + angle_coeff @angle:o-s2-o harmonic 118.448 116.170 # SOURCE3 1 + angle_coeff @angle:o-s2-s harmonic 91.358 118.300 # SOURCE2 1 + angle_coeff @angle:s-s2-s harmonic 74.776 115.040 # SOURCE3 1 + angle_coeff @angle:br-s4-br harmonic 74.689 98.020 # SOURCE3 1 + angle_coeff @angle:br-s4-c3 harmonic 72.437 92.980 # SOURCE3 1 + angle_coeff @angle:br-s4-o harmonic 84.014 112.070 # SOURCE3 1 + angle_coeff @angle:c1-s4-c1 harmonic 77.086 93.550 # SOURCE3 1 + angle_coeff @angle:c1-s4-o harmonic 94.436 110.360 # SOURCE3 2 + angle_coeff @angle:c2-s4-c2 harmonic 73.133 102.290 # SOURCE3 1 + angle_coeff @angle:c2-s4-c3 harmonic 74.359 94.950 # SOURCE3 1 + angle_coeff @angle:c2-s4-o harmonic 95.340 107.090 # SOURCE3 1 + angle_coeff @angle:c3-s4-c3 harmonic 72.538 96.120 # SOURCE3_SOURCE5 72 1.2506 + angle_coeff @angle:c3-s4-ca harmonic 73.801 95.000 # SOURCE3 1 + angle_coeff @angle:c3-s4-f harmonic 99.956 91.700 # SOURCE3 1 + angle_coeff @angle:c3-s4-hs harmonic 53.159 90.600 # SOURCE3 1 + angle_coeff @angle:c3-s4-i harmonic 64.204 90.530 # SOURCE3 1 + angle_coeff @angle:c3-s4-n2 harmonic 98.749 90.590 # SOURCE3 1 + angle_coeff @angle:c3-s4-n3 harmonic 92.849 95.770 # SOURCE3_SOURCE5 10 1.8721 + angle_coeff @angle:c3-s4-n harmonic 92.379 96.070 # SOURCE3 4 1.0354 + angle_coeff @angle:c3-s4-n4 harmonic 88.918 92.470 # SOURCE3 1 + angle_coeff @angle:c3-s4-na harmonic 93.247 93.070 # SOURCE3 10 1.8813 + angle_coeff @angle:c3-s4-nh harmonic 92.347 97.080 # SOURCE3 1 + angle_coeff @angle:c3-s4-no harmonic 89.712 89.530 # SOURCE3 1 + angle_coeff @angle:c3-s4-o harmonic 92.851 106.710 # SOURCE3_SOURCE5 233 1.1391 + angle_coeff @angle:c3-s4-oh harmonic 97.024 90.280 # SOURCE4_SOURCE5 21 0.2709 + angle_coeff @angle:c3-s4-os harmonic 97.226 90.060 # SOURCE3 4 0.4484 + angle_coeff @angle:c3-s4-p2 harmonic 91.018 94.370 # SOURCE3 1 + angle_coeff @angle:c3-s4-p3 harmonic 93.042 96.540 # SOURCE3 4 1.3634 + angle_coeff @angle:c3-s4-p4 harmonic 87.791 97.400 # SOURCE3 1 + angle_coeff @angle:c3-s4-p5 harmonic 93.163 99.180 # SOURCE3 1 + angle_coeff @angle:c3-s4-s4 harmonic 75.465 89.500 # SOURCE3 1 + angle_coeff @angle:c3-s4-s harmonic 71.946 98.720 # SOURCE3 2 0.0185 + angle_coeff @angle:c3-s4-s6 harmonic 72.311 97.480 # SOURCE3 1 + angle_coeff @angle:c3-s4-sh harmonic 71.328 94.660 # SOURCE3 1 + angle_coeff @angle:c3-s4-ss harmonic 71.131 95.310 # SOURCE3 3 1.4101 + angle_coeff @angle:ca-s4-ca harmonic 74.616 95.210 # SOURCE3 1 + angle_coeff @angle:ca-s4-o harmonic 94.489 106.630 # SOURCE3 1 + angle_coeff @angle:c-s4-c3 harmonic 72.142 95.070 # SOURCE3 1 + angle_coeff @angle:c-s4-c harmonic 74.707 86.830 # SOURCE3 1 + angle_coeff @angle:cl-s4-cl harmonic 92.643 97.680 # SOURCE3 1 + angle_coeff @angle:cl-s4-o harmonic 100.538 108.340 # SOURCE3 2 + angle_coeff @angle:c-s4-o harmonic 91.597 106.170 # SOURCE3 1 + angle_coeff @angle:cx-s4-cx harmonic 102.278 48.800 # SOURCE2 1 + angle_coeff @angle:cx-s4-o harmonic 91.767 110.000 # SOURCE2 1 + angle_coeff @angle:f-s4-f harmonic 137.119 92.710 # SOURCE2 3 0.1490 + angle_coeff @angle:f-s4-o harmonic 129.265 106.810 # SOURCE2 2 0.0100 + angle_coeff @angle:f-s4-s harmonic 90.806 107.500 # SOURCE2 1 + angle_coeff @angle:hs-s4-hs harmonic 42.707 87.000 # SOURCE3 2 0.0202 + angle_coeff @angle:hs-s4-n1 harmonic 72.280 90.510 # HF/6-31G* 1 + angle_coeff @angle:hs-s4-o harmonic 69.666 110.270 # SOURCE3 5 0.1908 + angle_coeff @angle:i-s4-i harmonic 68.021 97.290 # SOURCE3 1 + angle_coeff @angle:i-s4-o harmonic 69.889 113.910 # SOURCE3 1 + angle_coeff @angle:n1-s4-n1 harmonic 127.594 94.020 # HF/6-31G* 1 + angle_coeff @angle:n1-s4-o harmonic 122.838 110.090 # HF/6-31G* 1 + angle_coeff @angle:n2-s4-n2 harmonic 133.526 90.170 # SOURCE3 1 + angle_coeff @angle:n2-s4-o harmonic 126.113 107.570 # SOURCE3 1 + angle_coeff @angle:n3-s4-n3 harmonic 121.849 91.190 # SOURCE3 1 + angle_coeff @angle:n3-s4-o harmonic 117.831 110.430 # SOURCE3_SOURCE5 13 1.9165 + angle_coeff @angle:n4-s4-n4 harmonic 106.426 94.610 # SOURCE3 1 + angle_coeff @angle:n4-s4-o harmonic 110.589 104.910 # SOURCE3 3 0.4370 + angle_coeff @angle:na-s4-na harmonic 112.128 103.100 # SOURCE3 1 + angle_coeff @angle:na-s4-o harmonic 116.397 109.750 # SOURCE3 10 2.6919 + angle_coeff @angle:nh-s4-nh harmonic 121.527 92.240 # SOURCE3 1 + angle_coeff @angle:nh-s4-o harmonic 119.657 107.540 # SOURCE3 3 0.0401 + angle_coeff @angle:n-s4-n harmonic 120.832 91.300 # SOURCE3 1 + angle_coeff @angle:n-s4-o harmonic 118.814 107.440 # SOURCE3_SOURCE5 9 1.2433 + angle_coeff @angle:no-s4-no harmonic 111.990 83.400 # SOURCE3 1 + angle_coeff @angle:no-s4-o harmonic 110.173 103.580 # SOURCE3 3 1.5109 + angle_coeff @angle:oh-s4-oh harmonic 120.174 100.340 # SOURCE3 1 + angle_coeff @angle:o-s4-o harmonic 127.045 114.110 # SOURCE3_SOURCE5 14 2.6371 + angle_coeff @angle:o-s4-oh harmonic 120.725 110.100 # SOURCE4_SOURCE5 30 0.8834 + angle_coeff @angle:o-s4-os harmonic 121.937 108.220 # SOURCE3_SOURCE5 19 1.5128 + angle_coeff @angle:o-s4-p2 harmonic 110.606 106.770 # SOURCE3 1 + angle_coeff @angle:o-s4-p3 harmonic 115.784 106.510 # SOURCE3 8 4.0943 + angle_coeff @angle:o-s4-p4 harmonic 109.471 103.360 # SOURCE3 1 + angle_coeff @angle:o-s4-p5 harmonic 123.827 96.950 # SOURCE3 1 + angle_coeff @angle:o-s4-s4 harmonic 91.337 104.550 # SOURCE3 1 + angle_coeff @angle:o-s4-s harmonic 88.312 112.220 # SOURCE3 4 2.8682 + angle_coeff @angle:o-s4-s6 harmonic 92.094 102.840 # SOURCE3 1 + angle_coeff @angle:o-s4-sh harmonic 86.714 107.510 # SOURCE3 3 0.7511 + angle_coeff @angle:os-s4-os harmonic 124.379 94.070 # SOURCE3_SOURCE5 7 2.3843 + angle_coeff @angle:o-s4-ss harmonic 86.001 109.490 # SOURCE3 5 1.8509 + angle_coeff @angle:p2-s4-p2 harmonic 118.888 92.620 # SOURCE3 1 + angle_coeff @angle:p3-s4-p3 harmonic 122.725 95.710 # SOURCE3 2 1.2239 + angle_coeff @angle:p5-s4-p5 harmonic 126.784 93.860 # SOURCE3 1 + angle_coeff @angle:s4-s4-s4 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s4-s4-s6 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s4-s6 harmonic 75.638 93.520 # SOURCE3 1 + angle_coeff @angle:sh-s4-sh harmonic 69.229 102.760 # SOURCE3 1 + angle_coeff @angle:sh-s4-ss harmonic 69.301 102.640 # SOURCE3 1 + angle_coeff @angle:s-s4-s harmonic 70.495 108.080 # SOURCE3 1 + angle_coeff @angle:ss-s4-ss harmonic 71.889 95.470 # SOURCE3 1 + angle_coeff @angle:br-s6-br harmonic 77.581 101.570 # SOURCE3 1 + angle_coeff @angle:br-s6-c3 harmonic 73.519 98.990 # SOURCE3 1 + angle_coeff @angle:br-s6-f harmonic 94.581 100.600 # SOURCE2 1 + angle_coeff @angle:br-s6-o harmonic 90.691 107.580 # SOURCE3 6 0.3000 + angle_coeff @angle:c1-s6-c1 harmonic 75.601 99.990 # SOURCE3 1 + angle_coeff @angle:c1-s6-o harmonic 97.406 107.980 # SOURCE3_SOURCE5 7 0.4450 + angle_coeff @angle:c2-s6-c2 harmonic 72.969 102.750 # SOURCE3 1 + angle_coeff @angle:c2-s6-c3 harmonic 71.521 104.050 # SOURCE3 1 + angle_coeff @angle:c2-s6-o harmonic 96.507 106.580 # SOURCE3 1 + angle_coeff @angle:c3-s6-c3 harmonic 70.681 103.830 # SOURCE3_SOURCE5 74 2.0698 + angle_coeff @angle:c3-s6-ca harmonic 71.693 103.170 # SOURCE3 1 + angle_coeff @angle:c3-s6-cy harmonic 73.114 94.680 # SOURCE4_SOURCE5 19 0.4776 + angle_coeff @angle:c3-s6-f harmonic 98.119 95.900 # SOURCE3_SOURCE5 9 2.4171 + angle_coeff @angle:c3-s6-hs harmonic 51.078 100.620 # SOURCE3 1 + angle_coeff @angle:c3-s6-i harmonic 61.761 97.740 # SOURCE3 1 + angle_coeff @angle:c3-s6-n2 harmonic 90.421 112.480 # SOURCE4_SOURCE5 27 1.7086 + angle_coeff @angle:c3-s6-n3 harmonic 92.504 101.970 # SOURCE4_SOURCE5 162 1.1030 + angle_coeff @angle:c3-s6-n harmonic 90.797 103.440 # SOURCE3_SOURCE5 15 0.8616 + angle_coeff @angle:c3-s6-n4 harmonic 87.728 99.400 # SOURCE3 3 0.4695 + angle_coeff @angle:c3-s6-na harmonic 90.979 102.810 # SOURCE3 10 3.1256 + angle_coeff @angle:c3-s6-nh harmonic 90.894 104.320 # SOURCE4_SOURCE5 92 1.5234 + angle_coeff @angle:c3-s6-no harmonic 86.016 99.570 # SOURCE3 1 + angle_coeff @angle:c3-s6-o harmonic 93.703 108.610 # SOURCE3_SOURCE5 1062 1.0758 + angle_coeff @angle:c3-s6-oh harmonic 94.842 98.740 # SOURCE4_SOURCE5 121 0.7363 + angle_coeff @angle:c3-s6-os harmonic 96.240 96.420 # SOURCE4_SOURCE5 70 0.5868 + angle_coeff @angle:c3-s6-p2 harmonic 86.273 106.470 # SOURCE3 1 + angle_coeff @angle:c3-s6-p3 harmonic 90.571 103.400 # SOURCE3 3 0.8516 + angle_coeff @angle:c3-s6-p4 harmonic 84.641 104.120 # SOURCE3 1 + angle_coeff @angle:c3-s6-p5 harmonic 91.629 103.460 # SOURCE3 1 + angle_coeff @angle:c3-s6-s4 harmonic 72.386 98.100 # SOURCE3 1 + angle_coeff @angle:c3-s6-s harmonic 71.088 104.500 # SOURCE3 1 + angle_coeff @angle:c3-s6-s6 harmonic 71.006 101.950 # SOURCE3 1 + angle_coeff @angle:c3-s6-sh harmonic 70.399 101.840 # SOURCE3 1 + angle_coeff @angle:c3-s6-ss harmonic 69.952 102.470 # SOURCE3 3 1.7451 + angle_coeff @angle:ca-s6-ca harmonic 72.567 103.080 # SOURCE3 1 + angle_coeff @angle:ca-s6-o harmonic 97.373 104.090 # SOURCE4_SOURCE5 137 0.5743 + angle_coeff @angle:c-s6-c3 harmonic 70.322 101.240 # SOURCE3 1 + angle_coeff @angle:c-s6-c harmonic 69.677 99.820 # SOURCE3 1 + angle_coeff @angle:cc-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 24 0.8201 + angle_coeff @angle:cl-s6-cl harmonic 90.995 101.250 # SOURCE3 1 + angle_coeff @angle:cl-s6-f harmonic 105.577 99.000 # SOURCE2 1 + angle_coeff @angle:cl-s6-o harmonic 101.239 107.520 # SOURCE3_SOURCE5 6 0.2106 + angle_coeff @angle:c-s6-o harmonic 91.492 107.970 # SOURCE3 1 + angle_coeff @angle:c-s6-os harmonic 91.455 102.120 # SOURCE3 1 + angle_coeff @angle:cx-s6-cx harmonic 101.683 54.700 # SOURCE2 1 + angle_coeff @angle:cy-s6-o harmonic 91.172 110.520 # SOURCE4_SOURCE5 71 0.9427 + angle_coeff @angle:f-s6-f harmonic 137.577 89.710 # SOURCE2_SOURCE5 22 1.8574 + angle_coeff @angle:f-s6-o harmonic 130.197 106.540 # SOURCE3_SOURCE5 7 0.0793 + angle_coeff @angle:hs-s6-hs harmonic 40.502 99.020 # SOURCE3 2 0.0595 + angle_coeff @angle:hs-s6-n1 harmonic 77.206 97.270 # HF/6-31G* 1 + angle_coeff @angle:hs-s6-o harmonic 72.305 107.680 # SOURCE3_SOURCE5 17 0.0882 + angle_coeff @angle:i-s6-i harmonic 67.346 99.250 # SOURCE3 1 + angle_coeff @angle:i-s6-o harmonic 70.931 108.820 # SOURCE3_SOURCE5 6 0.6545 + angle_coeff @angle:n1-s6-n1 harmonic 147.507 95.520 # HF/6-31G* 1 + angle_coeff @angle:n1-s6-o harmonic 137.179 107.520 # HF/6-31G* 1 + angle_coeff @angle:n2-s6-n2 harmonic 132.302 98.610 # SOURCE3 1 + angle_coeff @angle:n2-s6-o harmonic 124.131 119.100 # SOURCE3_SOURCE5 11 3.0533 + angle_coeff @angle:n2-s6-oh harmonic 123.655 106.960 # SOURCE3 2 + angle_coeff @angle:n2-s6-os harmonic 126.381 103.250 # SOURCE3 1 + angle_coeff @angle:n3-s6-n3 harmonic 123.034 98.440 # SOURCE4_SOURCE5 16 0.3984 + angle_coeff @angle:n3-s6-o harmonic 124.794 107.430 # SOURCE3_SOURCE5 319 1.1452 + angle_coeff @angle:n3-s6-os harmonic 124.070 99.660 # SOURCE4_SOURCE5 27 0.8063 + angle_coeff @angle:n4-s6-n4 harmonic 105.682 101.850 # SOURCE3 1 + angle_coeff @angle:n4-s6-o harmonic 115.123 102.920 # SOURCE3 10 1.5434 + angle_coeff @angle:na-s6-na harmonic 119.677 98.040 # SOURCE3 1 + angle_coeff @angle:na-s6-o harmonic 123.180 105.820 # SOURCE3_SOURCE5 31 0.6987 + angle_coeff @angle:nh-s6-nh harmonic 123.669 94.560 # SOURCE3 1 + angle_coeff @angle:nh-s6-o harmonic 123.651 107.210 # SOURCE3_SOURCE5 106 1.3795 + angle_coeff @angle:n-s6-n harmonic 116.385 104.160 # SOURCE3 1 + angle_coeff @angle:n-s6-o harmonic 122.694 107.020 # SOURCE3_SOURCE5 63 1.7044 + angle_coeff @angle:no-s6-no harmonic 107.924 91.630 # SOURCE3 1 + angle_coeff @angle:no-s6-o harmonic 109.649 107.430 # SOURCE3 6 1.5494 + angle_coeff @angle:n-s6-os harmonic 122.468 99.230 # SOURCE4_SOURCE5 10 0.9794 + angle_coeff @angle:oh-s6-oh harmonic 124.674 100.340 # SOURCE3 6 0.0076 + angle_coeff @angle:oh-s6-os harmonic 127.394 96.810 # SOURCE4_SOURCE5 74 0.8201 + angle_coeff @angle:oh-s6-p2 harmonic 108.695 109.670 # SOURCE3 2 + angle_coeff @angle:o-s6-o harmonic 128.200 120.050 # SOURCE4_SOURCE5 971 1.8153 + angle_coeff @angle:o-s6-oh harmonic 126.323 108.050 # SOURCE3_SOURCE5 306 0.8954 + angle_coeff @angle:o-s6-os harmonic 126.629 108.560 # SOURCE3_SOURCE5 346 1.4469 + angle_coeff @angle:o-s6-p2 harmonic 111.304 106.610 # SOURCE3 1 + angle_coeff @angle:o-s6-p3 harmonic 116.333 107.070 # SOURCE3 22 1.0550 + angle_coeff @angle:o-s6-p4 harmonic 107.389 105.670 # SOURCE3 1 + angle_coeff @angle:o-s6-p5 harmonic 118.512 106.640 # SOURCE3 1 + angle_coeff @angle:o-s6-s4 harmonic 90.199 107.850 # SOURCE3 1 + angle_coeff @angle:o-s6-s harmonic 90.887 110.290 # SOURCE3 6 2.2405 + angle_coeff @angle:o-s6-s6 harmonic 90.953 106.070 # SOURCE3 1 + angle_coeff @angle:o-s6-sh harmonic 89.506 106.810 # SOURCE3 6 0.6292 + angle_coeff @angle:os-s6-os harmonic 126.643 98.700 # SOURCE3 1 + angle_coeff @angle:o-s6-ss harmonic 88.847 107.430 # SOURCE3 10 1.1423 + angle_coeff @angle:p3-s6-p3 harmonic 114.939 110.170 # SOURCE3 4 5.3678 + angle_coeff @angle:p5-s6-p5 harmonic 120.162 104.490 # SOURCE3 1 + angle_coeff @angle:s4-s6-s4 harmonic 72.429 101.990 # SOURCE3 1 + angle_coeff @angle:s4-s6-s6 harmonic 77.030 90.170 # SOURCE3 1 + angle_coeff @angle:s6-s6-s6 harmonic 71.972 103.290 # SOURCE3 1 + angle_coeff @angle:sh-s6-sh harmonic 69.961 106.430 # SOURCE3 1 + angle_coeff @angle:sh-s6-ss harmonic 71.071 102.640 # SOURCE3 1 + angle_coeff @angle:s-s6-s harmonic 71.394 109.340 # SOURCE3 1 + angle_coeff @angle:ss-s6-ss harmonic 71.189 101.820 # SOURCE3 1 + angle_coeff @angle:br-sh-hs harmonic 49.791 95.640 # SOURCE3 1 + angle_coeff @angle:c1-sh-hs harmonic 55.580 95.990 # calculated_based_on_C#C-SH 0 + angle_coeff @angle:c2-sh-hs harmonic 52.778 96.790 # SOURCE4_SOURCE5 12 0.5703 + angle_coeff @angle:c3-sh-hs harmonic 51.361 96.400 # SOURCE3_SOURCE5 191 0.6428 + angle_coeff @angle:ca-sh-hs harmonic 53.161 95.500 # SOURCE4_SOURCE5 44 0.8350 + angle_coeff @angle:cc-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 23 1.3099 + angle_coeff @angle:c-sh-hs harmonic 53.042 94.470 # SOURCE3_SOURCE5 41 0.9733 + angle_coeff @angle:f-sh-hs harmonic 71.420 96.500 # SOURCE3 1 + angle_coeff @angle:hs-sh-hs harmonic 42.155 93.000 # SOURCE3_SOURCE5 3 0.4777 + angle_coeff @angle:hs-sh-i harmonic 44.148 96.440 # SOURCE3 1 + angle_coeff @angle:hs-sh-n1 harmonic 72.794 93.510 # HF/6-31G* 1 + angle_coeff @angle:hs-sh-n2 harmonic 67.814 95.820 # SOURCE3 5 3.1495 + angle_coeff @angle:hs-sh-n harmonic 68.213 95.590 # SOURCE3 4 3.9065 + angle_coeff @angle:hs-sh-n3 harmonic 67.725 95.980 # SOURCE3 3 1.1735 + angle_coeff @angle:hs-sh-n4 harmonic 66.458 93.130 # SOURCE3 3 0.1675 + angle_coeff @angle:hs-sh-na harmonic 67.804 97.380 # SOURCE3 9 1.0223 + angle_coeff @angle:hs-sh-nh harmonic 66.944 101.110 # SOURCE3 1 + angle_coeff @angle:hs-sh-no harmonic 66.751 92.930 # SOURCE3 1 + angle_coeff @angle:hs-sh-o harmonic 67.503 109.230 # SOURCE3 2 0.0068 + angle_coeff @angle:hs-sh-oh harmonic 68.281 98.640 # SOURCE3 2 0.0605 + angle_coeff @angle:hs-sh-os harmonic 69.115 98.150 # SOURCE3 3 0.1661 + angle_coeff @angle:hs-sh-p2 harmonic 66.084 99.120 # SOURCE3 10 5.4110 + angle_coeff @angle:hs-sh-p3 harmonic 62.144 95.810 # SOURCE3 3 0.4396 + angle_coeff @angle:hs-sh-p4 harmonic 63.188 94.220 # SOURCE3 4 0.7605 + angle_coeff @angle:hs-sh-p5 harmonic 64.112 94.520 # SOURCE3 3 0.5589 + angle_coeff @angle:hs-sh-s harmonic 47.237 102.870 # SOURCE3 2 + angle_coeff @angle:hs-sh-s4 harmonic 48.513 92.160 # SOURCE3 3 1.6519 + angle_coeff @angle:hs-sh-s6 harmonic 49.509 93.830 # SOURCE3 3 1.2561 + angle_coeff @angle:hs-sh-sh harmonic 49.372 99.070 # SOURCE3 2 + angle_coeff @angle:hs-sh-ss harmonic 49.131 99.170 # SOURCE3 3 0.2457 + angle_coeff @angle:br-ss-br harmonic 77.455 102.920 # SOURCE3 1 + angle_coeff @angle:br-ss-c3 harmonic 73.438 99.030 # SOURCE3 1 + angle_coeff @angle:c1-ss-c1 harmonic 77.701 98.300 # SOURCE2 1 + angle_coeff @angle:c1-ss-c3 harmonic 72.838 101.860 # SOURCE2_SOURCE5 24 1.0923 + angle_coeff @angle:c2-ss-c2 harmonic 75.153 99.560 # SOURCE3 1 + angle_coeff @angle:c2-ss-c3 harmonic 72.568 100.370 # SOURCE4 100 2.3280 + angle_coeff @angle:c2-ss-cy harmonic 76.860 88.910 # SOURCE4_SOURCE5 51 0.4794 + angle_coeff @angle:c2-ss-n2 harmonic 92.922 106.760 # SOURCE3 1 + angle_coeff @angle:c2-ss-na harmonic 93.759 100.510 # SOURCE3 6 6.9702 + angle_coeff @angle:c2-ss-os harmonic 100.020 89.760 # SOURCE3 1 + angle_coeff @angle:c2-ss-ss harmonic 75.743 92.260 # SOURCE3 1 + angle_coeff @angle:c3-ss-c3 harmonic 71.051 99.240 # SOURCE3_SOURCE5 443 1.3973 + angle_coeff @angle:c3-ss-ca harmonic 71.145 102.100 # SOURCE4_SOURCE5 393 1.3148 + angle_coeff @angle:c3-ss-cc harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 + angle_coeff @angle:c3-ss-cd harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 + angle_coeff @angle:c3-ss-cl harmonic 80.033 99.400 # SOURCE2 1 + angle_coeff @angle:c3-ss-cy harmonic 72.699 94.270 # SOURCE4_SOURCE5 150 0.4649 + angle_coeff @angle:c3-ss-f harmonic 95.769 97.490 # SOURCE3 1 + angle_coeff @angle:c3-ss-i harmonic 67.953 100.000 # SOURCE3 1 + angle_coeff @angle:c3-ss-n1 harmonic 94.433 98.440 # HF/6-31G* 1 + angle_coeff @angle:c3-ss-n2 harmonic 94.643 96.080 # SOURCE3_SOURCE5 11 1.2317 + angle_coeff @angle:c3-ss-n3 harmonic 91.857 98.830 # SOURCE3 3 0.2909 + angle_coeff @angle:c3-ss-n harmonic 91.130 100.300 # SOURCE3 4 0.6579 + angle_coeff @angle:c3-ss-n4 harmonic 90.288 97.790 # SOURCE3 3 0.2002 + angle_coeff @angle:c3-ss-na harmonic 92.714 96.590 # SOURCE3_SOURCE5 21 1.0132 + angle_coeff @angle:c3-ss-nh harmonic 91.350 100.630 # SOURCE3 1 + angle_coeff @angle:c3-ss-no harmonic 89.523 98.620 # SOURCE3 1 + angle_coeff @angle:c3-ss-o harmonic 92.362 106.990 # SOURCE3_SOURCE5 11 1.0097 + angle_coeff @angle:c3-ss-oh harmonic 92.897 98.280 # SOURCE3 2 1.4326 + angle_coeff @angle:c3-ss-os harmonic 92.581 98.210 # SOURCE3 4 1.7097 + angle_coeff @angle:c3-ss-p2 harmonic 95.479 98.410 # SOURCE3 8 0.9454 + angle_coeff @angle:c3-ss-p3 harmonic 90.885 98.700 # SOURCE3 3 0.0356 + angle_coeff @angle:c3-ss-p4 harmonic 91.629 98.160 # SOURCE3 4 0.1361 + angle_coeff @angle:c3-ss-p5 harmonic 90.364 100.060 # SOURCE4_SOURCE5 62 1.0141 + angle_coeff @angle:c3-ss-s4 harmonic 70.640 96.370 # SOURCE3 3 0.0202 + angle_coeff @angle:c3-ss-s harmonic 70.410 101.900 # SOURCE3 1 + angle_coeff @angle:c3-ss-s6 harmonic 71.595 96.760 # SOURCE3 3 1.5680 + angle_coeff @angle:c3-ss-sh harmonic 70.887 101.930 # SOURCE3 1 + angle_coeff @angle:c3-ss-ss harmonic 70.258 103.390 # SOURCE4_SOURCE5 237 1.0715 + angle_coeff @angle:ca-ss-ca harmonic 73.541 98.830 # SOURCE4_SOURCE5 225 1.3938 + angle_coeff @angle:ca-ss-cc harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 + angle_coeff @angle:ca-ss-cd harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 + angle_coeff @angle:ca-ss-cl harmonic 80.234 101.050 # SOURCE3 1 + angle_coeff @angle:ca-ss-n harmonic 97.427 90.990 # SOURCE3_SOURCE5 5 0.5202 + angle_coeff @angle:ca-ss-na harmonic 93.087 99.320 # SOURCE3 1 + angle_coeff @angle:ca-ss-nc harmonic 97.913 94.760 # SOURCE3 1 + angle_coeff @angle:ca-ss-nd harmonic 97.913 94.760 # SOURCE3 1 + angle_coeff @angle:ca-ss-ss harmonic 70.425 105.130 # SOURCE4_SOURCE5 69 1.0007 + angle_coeff @angle:c-ss-c2 harmonic 76.536 92.430 # SOURCE3 1 + angle_coeff @angle:c-ss-c3 harmonic 71.828 99.160 # SOURCE3_SOURCE5 108 1.2072 + angle_coeff @angle:c-ss-c harmonic 71.820 101.400 # SOURCE3 1 + angle_coeff @angle:c-ss-cc harmonic 75.135 94.890 # SOURCE4_SOURCE5 32 1.7205 + angle_coeff @angle:cc-ss-cc harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 + angle_coeff @angle:cc-ss-cd harmonic 77.807 90.760 # SOURCE4_SOURCE5 157 1.7485 + angle_coeff @angle:cc-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 + angle_coeff @angle:cc-ss-na harmonic 93.760 99.330 # SOURCE3 18 + angle_coeff @angle:cc-ss-nc harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 + angle_coeff @angle:cc-ss-os harmonic 94.746 98.810 # SOURCE3 2 2.1583 + angle_coeff @angle:cc-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 + angle_coeff @angle:cd-ss-cd harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 + angle_coeff @angle:cd-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 + angle_coeff @angle:cd-ss-na harmonic 93.760 99.330 # SOURCE3 18 2.5847 + angle_coeff @angle:cd-ss-nd harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 + angle_coeff @angle:cd-ss-os harmonic 94.746 98.810 # SOURCE3 2 + angle_coeff @angle:cd-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 + angle_coeff @angle:cl-ss-cl harmonic 90.057 103.370 # SOURCE3 1 + angle_coeff @angle:cx-ss-cx harmonic 102.217 48.300 # SOURCE2 1 + angle_coeff @angle:f-ss-f harmonic 129.659 98.300 # SOURCE2 1 + angle_coeff @angle:f-ss-ss harmonic 90.124 108.300 # SOURCE2 1 + angle_coeff @angle:i-ss-i harmonic 72.646 106.290 # SOURCE3 1 + angle_coeff @angle:n1-ss-n1 harmonic 128.766 96.960 # HF/6-31G* 1 + angle_coeff @angle:n2-ss-n2 harmonic 125.325 96.750 # SOURCE3 1 + angle_coeff @angle:n3-ss-n3 harmonic 117.075 102.340 # SOURCE3 1 + angle_coeff @angle:n4-ss-n4 harmonic 111.994 101.190 # SOURCE3 1 + angle_coeff @angle:na-ss-na harmonic 116.207 102.810 # SOURCE3 1 + angle_coeff @angle:nc-ss-nc harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 + angle_coeff @angle:nd-ss-nd harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 + angle_coeff @angle:nh-ss-nh harmonic 114.991 107.890 # SOURCE3 1 + angle_coeff @angle:n-ss-n harmonic 116.487 103.100 # SOURCE3 1 + angle_coeff @angle:no-ss-no harmonic 108.247 106.430 # SOURCE3 1 + angle_coeff @angle:oh-ss-oh harmonic 118.444 104.250 # SOURCE3 1 + angle_coeff @angle:o-ss-o harmonic 124.036 119.300 # SOURCE2 1 + angle_coeff @angle:o-ss-p5 harmonic 114.305 106.410 # SOURCE3 1 + angle_coeff @angle:o-ss-s6 harmonic 89.483 105.390 # SOURCE3 1 + angle_coeff @angle:os-ss-os harmonic 118.047 102.990 # SOURCE3 1 + angle_coeff @angle:o-ss-ss harmonic 88.228 112.700 # SOURCE2 1 + angle_coeff @angle:p2-ss-p2 harmonic 127.760 99.520 # SOURCE3 1 + angle_coeff @angle:p3-ss-p3 harmonic 117.165 101.670 # SOURCE3 1 + angle_coeff @angle:p5-ss-p5 harmonic 126.593 87.370 # SOURCE3_SOURCE5 11 1.2491 + angle_coeff @angle:s4-ss-s4 harmonic 71.661 96.080 # SOURCE3 1 + angle_coeff @angle:s4-ss-s6 harmonic 70.568 101.260 # SOURCE3 1 + angle_coeff @angle:s6-ss-s6 harmonic 71.193 101.810 # SOURCE3 1 + angle_coeff @angle:sh-ss-sh harmonic 70.979 107.540 # SOURCE3 1 + angle_coeff @angle:sh-ss-ss harmonic 71.215 106.530 # SOURCE3 1 + angle_coeff @angle:s-ss-s harmonic 67.904 115.040 # SOURCE3 1 + angle_coeff @angle:ss-ss-ss harmonic 70.653 107.930 # SOURCE4_SOURCE5 72 1.6368 + angle_coeff @angle:c3-sx-ca harmonic 72.223 96.640 # SOURCE4_SOURCE5 41 0.4942 + angle_coeff @angle:c3-sx-cc harmonic 73.054 95.180 # SOURCE4_SOURCE5 41 0.6549 + angle_coeff @angle:c3-sx-ce harmonic 72.861 95.290 # SOURCE3_SOURCE5 10 0.5723 + angle_coeff @angle:c3-sx-cf harmonic 72.861 95.290 # SOURCE3_SOURCE5 7 0.8172 + angle_coeff @angle:c3-sx-ne harmonic 93.362 90.060 # SOURCE3 5 1.9627 + angle_coeff @angle:c3-sx-nf harmonic 93.362 90.060 # SOURCE3 5 + angle_coeff @angle:c3-sx-o harmonic 91.942 107.520 # SOURCE3_SOURCE5 84 0.7996 + angle_coeff @angle:c3-sx-pe harmonic 91.537 94.320 # SOURCE3 7 0.5547 + angle_coeff @angle:c3-sx-pf harmonic 91.537 94.320 # SOURCE3 7 + angle_coeff @angle:c3-sx-px harmonic 88.346 96.460 # SOURCE3 3 1.3351 + angle_coeff @angle:c3-sx-py harmonic 88.211 95.670 # SOURCE3 1 + angle_coeff @angle:c3-sx-sx harmonic 67.226 91.470 # SOURCE3 4 1.9919 + angle_coeff @angle:c3-sx-sy harmonic 68.899 95.470 # SOURCE3 3 2.8422 + angle_coeff @angle:ca-sx-ca harmonic 72.893 95.750 # SOURCE3_SOURCE5 14 1.8607 + angle_coeff @angle:ca-sx-o harmonic 92.722 107.150 # SOURCE4_SOURCE5 86 0.9103 + angle_coeff @angle:c-sx-c3 harmonic 72.536 92.710 # SOURCE3 3 0.3095 + angle_coeff @angle:c-sx-c harmonic 74.104 86.850 # SOURCE3 1 + angle_coeff @angle:cc-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 45 1.5594 + angle_coeff @angle:ce-sx-ce harmonic 73.461 94.960 # SOURCE3 1 + angle_coeff @angle:ce-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 27 0.8358 + angle_coeff @angle:cf-sx-cf harmonic 73.461 94.960 # SOURCE3 1 + angle_coeff @angle:cf-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 22 0.9547 + angle_coeff @angle:c-sx-o harmonic 90.915 106.170 # SOURCE3 5 0.9477 + angle_coeff @angle:ne-sx-ne harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 + angle_coeff @angle:ne-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 13 1.0385 + angle_coeff @angle:nf-sx-nf harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 + angle_coeff @angle:nf-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 6 0.5536 + angle_coeff @angle:o-sx-pe harmonic 111.805 106.430 # SOURCE3 9 2.8345 + angle_coeff @angle:o-sx-pf harmonic 111.805 106.430 # SOURCE3 9 + angle_coeff @angle:o-sx-px harmonic 109.143 104.770 # SOURCE3 3 1.9810 + angle_coeff @angle:o-sx-py harmonic 106.155 109.130 # SOURCE3 7 5.6840 + angle_coeff @angle:o-sx-sx harmonic 79.764 104.650 # SOURCE3 6 3.0524 + angle_coeff @angle:o-sx-sy harmonic 85.123 103.410 # SOURCE3 5 0.9618 + angle_coeff @angle:pe-sx-pe harmonic 120.095 92.620 # SOURCE3 1 + angle_coeff @angle:pf-sx-pf harmonic 120.095 92.620 # SOURCE3 1 + angle_coeff @angle:py-sx-py harmonic 133.313 69.230 # SOURCE3 3 17.4143 + angle_coeff @angle:sx-sx-sx harmonic 69.059 84.900 # SOURCE3 1 + angle_coeff @angle:sy-sx-sy harmonic 69.768 93.520 # SOURCE3 1 + angle_coeff @angle:c3-sy-ca harmonic 70.945 103.930 # SOURCE4_SOURCE5 136 0.4172 + angle_coeff @angle:c3-sy-cc harmonic 71.767 101.950 # SOURCE4_SOURCE5 32 1.4362 + angle_coeff @angle:c3-sy-ce harmonic 71.136 103.530 # SOURCE3_SOURCE5 11 1.3594 + angle_coeff @angle:c3-sy-cf harmonic 71.136 103.530 # SOURCE3_SOURCE5 8 1.7429 + angle_coeff @angle:c3-sy-ne harmonic 92.368 102.190 # SOURCE3_SOURCE5 11 3.1966 + angle_coeff @angle:c3-sy-nf harmonic 92.368 102.190 # SOURCE3_SOURCE5 6 2.3703 + angle_coeff @angle:c3-sy-o harmonic 93.792 107.850 # SOURCE3_SOURCE5 283 0.5690 + angle_coeff @angle:c3-sy-pe harmonic 85.480 106.030 # SOURCE3 6 2.6117 + angle_coeff @angle:c3-sy-pf harmonic 85.480 106.030 # SOURCE3 6 + angle_coeff @angle:c3-sy-px harmonic 85.416 103.620 # SOURCE3 3 0.7078 + angle_coeff @angle:c3-sy-py harmonic 87.474 103.390 # SOURCE3 3 0.4563 + angle_coeff @angle:c3-sy-sx harmonic 66.097 104.640 # SOURCE3 3 4.6276 + angle_coeff @angle:c3-sy-sy harmonic 67.466 100.780 # SOURCE3 4 1.1633 + angle_coeff @angle:ca-sy-ca harmonic 71.127 104.440 # SOURCE4_SOURCE5 55 1.7845 + angle_coeff @angle:ca-sy-cc harmonic 71.045 105.090 # SOURCE4_SOURCE5 10 0.3628 + angle_coeff @angle:ca-sy-n3 harmonic 92.241 102.440 # SOURCE4_SOURCE5 407 1.1038 + angle_coeff @angle:ca-sy-n harmonic 90.479 105.370 # SOURCE4_SOURCE5 122 1.2203 + angle_coeff @angle:ca-sy-ne harmonic 92.539 103.010 # SOURCE4_SOURCE5 36 2.1672 + angle_coeff @angle:ca-sy-nh harmonic 90.475 105.500 # SOURCE4_SOURCE5 205 1.5936 + angle_coeff @angle:ca-sy-o harmonic 94.276 108.350 # SOURCE3_SOURCE5 1362 0.6985 + angle_coeff @angle:ca-sy-oh harmonic 93.834 101.300 # SOURCE4_SOURCE5 94 0.8210 + angle_coeff @angle:ca-sy-os harmonic 96.750 92.980 # SOURCE3 1 + angle_coeff @angle:c-sy-c3 harmonic 70.399 101.250 # SOURCE3 3 1.1850 + angle_coeff @angle:c-sy-c harmonic 69.867 99.810 # SOURCE3 1 + angle_coeff @angle:cc-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 + angle_coeff @angle:cc-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 + angle_coeff @angle:cd-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 + angle_coeff @angle:cd-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 12 0.2429 + angle_coeff @angle:cd-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 + angle_coeff @angle:ce-sy-ce harmonic 71.811 102.780 # SOURCE3 1 + angle_coeff @angle:ce-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 66 0.9753 + angle_coeff @angle:cf-sy-cf harmonic 71.811 102.780 # SOURCE3 1 + angle_coeff @angle:cf-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 56 1.0516 + angle_coeff @angle:c-sy-o harmonic 91.740 107.480 # SOURCE3_SOURCE5 16 0.7996 + angle_coeff @angle:n2-sy-o harmonic 121.876 123.530 # SOURCE4 6 1.2388 + angle_coeff @angle:n3-sy-ne harmonic 120.039 101.930 # SOURCE4_SOURCE5 15 1.4395 + angle_coeff @angle:n3-sy-o harmonic 123.426 107.130 # SOURCE4_SOURCE5 863 1.1609 + angle_coeff @angle:na-sy-na harmonic 119.379 98.040 # SOURCE3 1 + angle_coeff @angle:nc-sy-nc harmonic 132.584 98.040 # SOURCE3 2 + angle_coeff @angle:nd-sy-nd harmonic 132.584 98.040 # SOURCE3 2 + angle_coeff @angle:ne-sy-ne harmonic 122.921 98.620 # SOURCE3 1 + angle_coeff @angle:ne-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 101 1.9902 + angle_coeff @angle:nf-sy-nf harmonic 122.921 98.620 # SOURCE3 1 + angle_coeff @angle:nf-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 87 1.9451 + angle_coeff @angle:nh-sy-o harmonic 123.056 106.230 # SOURCE4_SOURCE5 319 1.7353 + angle_coeff @angle:n-sy-o harmonic 122.195 107.540 # SOURCE4_SOURCE5 155 1.8699 + angle_coeff @angle:o-sy-o harmonic 126.375 121.410 # SOURCE3_SOURCE5 734 0.8526 + angle_coeff @angle:o-sy-oh harmonic 125.990 106.680 # SOURCE3_SOURCE5 166 0.5588 + angle_coeff @angle:o-sy-os harmonic 123.063 107.520 # SOURCE4_SOURCE5 38 1.6656 + angle_coeff @angle:o-sy-pe harmonic 109.504 106.900 # SOURCE3 12 1.4524 + angle_coeff @angle:o-sy-pf harmonic 109.504 106.900 # SOURCE3 12 + angle_coeff @angle:o-sy-px harmonic 108.122 106.170 # SOURCE3 6 0.7059 + angle_coeff @angle:o-sy-py harmonic 111.153 106.670 # SOURCE3 10 0.6478 + angle_coeff @angle:o-sy-sx harmonic 83.961 106.330 # SOURCE3 10 2.0456 + angle_coeff @angle:o-sy-sy harmonic 84.205 106.190 # SOURCE3 12 0.1754 + angle_coeff @angle:py-sy-py harmonic 112.342 104.490 # SOURCE3 1 + angle_coeff @angle:sx-sy-sx harmonic 66.808 101.990 # SOURCE3 1 + angle_coeff @angle:sy-sy-sy harmonic 66.534 103.290 # SOURCE3 1 + angle_coeff @angle:c2-c1-cf harmonic 60.047 179.050 # SOURCE4_SOURCE5 9 0.3913 + angle_coeff @angle:c3-c1-ch harmonic 57.725 178.430 # SOURCE4_SOURCE5 95 0.5682 + angle_coeff @angle:nf-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 15 0.2067 + angle_coeff @angle:br-c2-cf harmonic 64.279 121.530 # SOURCE4_SOURCE5 11 0.7009 + angle_coeff @angle:cd-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 16 0.8001 + angle_coeff @angle:cd-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 17 1.2171 + angle_coeff @angle:cd-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 6 0.0560 + angle_coeff @angle:cf-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 30 1.0225 + angle_coeff @angle:cf-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 145 1.6214 + angle_coeff @angle:cf-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 6 1.9423 + angle_coeff @angle:cf-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 150 2.3947 + angle_coeff @angle:cf-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 5 0.9817 + angle_coeff @angle:cf-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 9 1.0481 + angle_coeff @angle:cf-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 62 1.7479 + angle_coeff @angle:cf-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 98 2.2743 + angle_coeff @angle:h4-c2-nf harmonic 64.858 119.510 # SOURCE4_SOURCE5 42 1.6302 + angle_coeff @angle:h5-c2-nf harmonic 64.691 119.850 # SOURCE4_SOURCE5 27 1.3790 + angle_coeff @angle:nf-c2-os harmonic 114.213 118.760 # SOURCE4 5 + angle_coeff @angle:nf-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 23 2.4188 + angle_coeff @angle:n-c2-nf harmonic 109.323 125.340 # SOURCE4_SOURCE5 15 1.5591 + angle_coeff @angle:ca-c3-cf harmonic 65.618 112.210 # SOURCE4_SOURCE5 93 1.2595 + angle_coeff @angle:cd-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 7 1.7201 + angle_coeff @angle:c-c3-cf harmonic 65.527 111.890 # SOURCE4_SOURCE5 59 1.5769 + angle_coeff @angle:cd-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 10 0.7123 + angle_coeff @angle:cd-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 21 0.5628 + angle_coeff @angle:cd-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 6 1.1723 + angle_coeff @angle:cd-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 10 0.6466 + angle_coeff @angle:cd-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 6 0.7766 + angle_coeff @angle:cf-c3-cf harmonic 65.833 111.470 # SOURCE4_SOURCE5 35 0.5985 + angle_coeff @angle:cf-c3-n harmonic 84.349 110.220 # SOURCE4_SOURCE5 10 1.0919 + angle_coeff @angle:cf-c3-oh harmonic 84.971 111.190 # SOURCE4_SOURCE5 57 1.5702 + angle_coeff @angle:cf-c3-os harmonic 85.412 109.500 # SOURCE4_SOURCE5 55 1.8883 + angle_coeff @angle:cf-c3-ss harmonic 63.337 110.720 # SOURCE4_SOURCE5 12 1.7025 + angle_coeff @angle:cd-ca-cq harmonic 66.010 124.300 # SOURCE4_SOURCE5 10 0.6423 + angle_coeff @angle:cf-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 29 0.5242 + angle_coeff @angle:ch-ca-cq harmonic 67.320 121.530 # SOURCE4_SOURCE5 12 0.1831 + angle_coeff @angle:cl-ca-cq harmonic 71.726 120.390 # SOURCE4_SOURCE5 34 0.5366 + angle_coeff @angle:cq-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 30 0.2799 + angle_coeff @angle:cq-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 35 0.4098 + angle_coeff @angle:cq-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 349 0.5003 + angle_coeff @angle:cq-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 79 0.8527 + angle_coeff @angle:cq-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 19 0.6123 + angle_coeff @angle:cq-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 29 1.4592 + angle_coeff @angle:cq-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 16 2.4162 + angle_coeff @angle:ca-c-nf harmonic 85.290 114.710 # SOURCE4_SOURCE5 9 0.7464 + angle_coeff @angle:br-cd-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 24 1.3164 + angle_coeff @angle:br-cd-cd harmonic 63.389 124.050 # SOURCE4_SOURCE5 23 1.9356 + angle_coeff @angle:br-cd-cc harmonic 63.686 124.230 # SOURCE4_SOURCE5 84 2.2845 + angle_coeff @angle:br-cd-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 13 0.9881 + angle_coeff @angle:ca-cd-cf harmonic 64.258 127.010 # SOURCE4_SOURCE5 27 1.6430 + angle_coeff @angle:ca-cd-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 11 2.0536 + angle_coeff @angle:cd-c-cf harmonic 66.433 115.570 # SOURCE4_SOURCE5 8 1.2130 + angle_coeff @angle:cd-cd-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 19 1.0481 + angle_coeff @angle:c-cd-ch harmonic 67.046 117.880 # SOURCE4_SOURCE5 19 0.6396 + angle_coeff @angle:cd-cd-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 12 0.8482 + angle_coeff @angle:cc-cd-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 54 0.6386 + angle_coeff @angle:cc-cd-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 197 1.4212 + angle_coeff @angle:c-cd-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 33 0.4384 + angle_coeff @angle:ch-cd-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 7 1.0826 + angle_coeff @angle:ch-cd-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 15 0.9326 + angle_coeff @angle:cd-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 20 0.4400 + angle_coeff @angle:cl-cd-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 25 0.9015 + angle_coeff @angle:cl-cd-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 16 0.8775 + angle_coeff @angle:c-cd-nf harmonic 84.503 119.880 # SOURCE4 6 + angle_coeff @angle:cd-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 57 2.2083 + angle_coeff @angle:cd-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 32 1.0830 + angle_coeff @angle:cx-cd-nc harmonic 83.147 127.820 # SOURCE4_SOURCE5 15 1.5594 + angle_coeff @angle:cx-cd-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 13 0.0898 + angle_coeff @angle:cc-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 24 0.1441 + angle_coeff @angle:cc-c-nc harmonic 86.534 113.750 # SOURCE4_SOURCE5 14 0.0860 + angle_coeff @angle:cf-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 13 0.7631 + angle_coeff @angle:cf-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 94 0.4993 + angle_coeff @angle:cf-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 8 0.5728 + angle_coeff @angle:na-cd-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 114 0.8160 + angle_coeff @angle:na-cd-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 23 1.0304 + angle_coeff @angle:na-cd-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 19 0.3766 + angle_coeff @angle:na-cd-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 8 1.7069 + angle_coeff @angle:nd-cd-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 10 0.8384 + angle_coeff @angle:nc-cd-nc harmonic 110.827 128.070 # SOURCE4_SOURCE5 10 0.4198 + angle_coeff @angle:nc-cd-nf harmonic 107.796 129.010 # SOURCE4_SOURCE5 13 1.6879 + angle_coeff @angle:nc-cd-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 64 0.2909 + angle_coeff @angle:nc-cd-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 13 0.8081 + angle_coeff @angle:nc-cd-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 19 0.3234 + angle_coeff @angle:nc-cd-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 20 1.2273 + angle_coeff @angle:nf-cd-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 10 0.2421 + angle_coeff @angle:n-cd-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 13 0.1189 + angle_coeff @angle:no-cd-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 82 0.2764 + angle_coeff @angle:no-cd-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 23 0.2526 + angle_coeff @angle:ca-cc-cf harmonic 66.694 124.900 # SOURCE4_SOURCE5 32 1.6591 + angle_coeff @angle:ca-cc-na harmonic 83.626 123.450 # SOURCE4 39 + angle_coeff @angle:cd-cc-cg harmonic 67.080 125.790 # SOURCE4_SOURCE5 54 1.7418 + angle_coeff @angle:cd-cc-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 12 0.8462 + angle_coeff @angle:cd-cc-nd harmonic 88.069 123.820 # SOURCE4_SOURCE5 14 0.3678 + angle_coeff @angle:cc-cc-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 7 0.2293 + angle_coeff @angle:cf-cc-nc harmonic 86.641 123.980 # SOURCE4_SOURCE5 5 2.4219 + angle_coeff @angle:c-cc-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 8 0.2226 + angle_coeff @angle:na-cc-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 54 1.7570 + angle_coeff @angle:na-cc-ss harmonic 83.703 111.460 # SOURCE4 20 + angle_coeff @angle:nc-cc-nc harmonic 107.603 125.700 # SOURCE4_SOURCE5 18 0.6787 + angle_coeff @angle:oh-cc-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 6 1.1909 + angle_coeff @angle:c2-cf-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 38 1.3369 + angle_coeff @angle:c2-cf-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 32 1.8945 + angle_coeff @angle:c2-cf-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 11 1.2780 + angle_coeff @angle:c2-cf-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 5 0.8452 + angle_coeff @angle:c2-cf-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 17 1.7138 + angle_coeff @angle:c3-cf-ch harmonic 66.013 117.220 # SOURCE4_SOURCE5 26 1.7890 + angle_coeff @angle:c3-cf-ne harmonic 84.378 120.680 # SOURCE4_SOURCE5 7 2.0560 + angle_coeff @angle:c3-cf-nh harmonic 82.733 119.560 # SOURCE4_SOURCE5 5 1.0524 + angle_coeff @angle:ca-cf-cf harmonic 65.684 119.540 # SOURCE4_SOURCE5 18 1.9239 + angle_coeff @angle:ca-cf-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 8 0.9719 + angle_coeff @angle:ca-cf-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 181 1.0407 + angle_coeff @angle:ca-cf-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 147 1.1060 + angle_coeff @angle:ca-cf-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 17 1.5899 + angle_coeff @angle:ca-cf-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 9 1.2901 + angle_coeff @angle:c-cf-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 17 1.7879 + angle_coeff @angle:cd-cf-cc harmonic 65.259 130.610 # SOURCE4_SOURCE5 19 0.8270 + angle_coeff @angle:c-cf-cf harmonic 65.150 120.980 # SOURCE4_SOURCE5 37 2.3876 + angle_coeff @angle:c-cf-ch harmonic 66.500 118.420 # SOURCE4_SOURCE5 34 1.0602 + angle_coeff @angle:cd-cf-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 48 0.8279 + angle_coeff @angle:c-cf-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 19 1.2383 + angle_coeff @angle:cd-cf-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 13 1.6005 + angle_coeff @angle:c-cf-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 34 1.2419 + angle_coeff @angle:cf-cf-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 23 1.1321 + angle_coeff @angle:cf-cf-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 19 1.5331 + angle_coeff @angle:ce-cf-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 18 1.4229 + angle_coeff @angle:ce-cf-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 18 1.1766 + angle_coeff @angle:ce-cf-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 7 1.8420 + angle_coeff @angle:ce-cf-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 27 1.6583 + angle_coeff @angle:ch-cf-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 8 0.9418 + angle_coeff @angle:c-cf-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 15 2.2145 + angle_coeff @angle:c-cf-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 26 2.3740 + angle_coeff @angle:h4-cf-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 12 0.5604 + angle_coeff @angle:h4-cf-nf harmonic 62.153 115.650 # SOURCE4_SOURCE5 12 1.7190 + angle_coeff @angle:n2-cf-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 13 0.4519 + angle_coeff @angle:n2-cf-ss harmonic 81.512 117.230 # SOURCE4 6 + angle_coeff @angle:nf-cf-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 29 1.5167 + angle_coeff @angle:ne-cf-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 17 1.8891 + angle_coeff @angle:ca-ce-cd harmonic 64.611 130.880 # SOURCE4_SOURCE5 29 1.2258 + angle_coeff @angle:c-ce-cc harmonic 66.092 117.820 # SOURCE4_SOURCE5 19 0.9022 + angle_coeff @angle:c-ce-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 8 1.4615 + angle_coeff @angle:h4-ce-nf harmonic 64.320 120.560 # SOURCE4_SOURCE5 33 0.8495 + angle_coeff @angle:c1-ch-cd harmonic 58.883 178.610 # SOURCE4_SOURCE5 7 0.3553 + angle_coeff @angle:ch-cg-cg harmonic 60.571 179.580 # SOURCE4_SOURCE5 48 0.3197 + angle_coeff @angle:n-c-nf harmonic 113.600 110.260 # SOURCE4_SOURCE5 15 1.6743 + angle_coeff @angle:ca-cq-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 38 0.8587 + angle_coeff @angle:nb-cq-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 6 0.6645 + angle_coeff @angle:cd-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 29 0.6832 + angle_coeff @angle:cf-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 21 0.5798 + angle_coeff @angle:cf-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 24 0.2234 + angle_coeff @angle:cf-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 21 2.1971 + angle_coeff @angle:cd-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 14 1.5712 + angle_coeff @angle:cd-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 7 1.6660 + angle_coeff @angle:c3-n4-cd harmonic 64.438 111.040 # SOURCE4_SOURCE5 11 1.9847 + angle_coeff @angle:c3-na-cq harmonic 65.414 119.620 # SOURCE4_SOURCE5 10 0.5495 + angle_coeff @angle:ca-na-cq harmonic 67.035 120.860 # SOURCE4_SOURCE5 38 1.4370 + angle_coeff @angle:cd-na-cf harmonic 64.694 126.610 # SOURCE4_SOURCE5 8 0.5158 + angle_coeff @angle:cq-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 20 0.6372 + angle_coeff @angle:c-n-cf harmonic 63.457 131.380 # SOURCE4_SOURCE5 225 1.7874 + angle_coeff @angle:ca-nc-nd harmonic 92.520 108.340 # SOURCE4_SOURCE5 14 0.2755 + angle_coeff @angle:c2-nf-ch harmonic 70.178 123.230 # SOURCE4_SOURCE5 27 1.1966 + angle_coeff @angle:c-nf-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 10 2.0084 + angle_coeff @angle:c3-nh-ce harmonic 65.126 120.120 # SOURCE4_SOURCE5 32 2.1639 + angle_coeff @angle:cd-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 16 0.9182 + angle_coeff @angle:cd-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 37 1.3342 + angle_coeff @angle:cf-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 8 1.1060 + angle_coeff @angle:hn-n-nd harmonic 62.278 115.420 # SOURCE4_SOURCE5 24 0.7584 + angle_coeff @angle:cd-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 426 0.5387 + angle_coeff @angle:n3-py-nf harmonic 79.409 108.760 # SOURCE4_SOURCE5 18 1.1434 + angle_coeff @angle:cd-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 15 0.9562 + angle_coeff @angle:cd-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 15 1.4000 + angle_coeff @angle:c-ss-cd harmonic 75.135 94.890 # SOURCE4_SOURCE5 18 1.2231 + angle_coeff @angle:c3-sx-cd harmonic 73.054 95.180 # SOURCE4_SOURCE5 24 0.6543 + angle_coeff @angle:cd-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 28 1.4279 + angle_coeff @angle:c3-sy-cd harmonic 71.767 101.950 # SOURCE4_SOURCE5 20 1.3784 + angle_coeff @angle:ca-sy-cd harmonic 71.045 105.090 # SOURCE4_SOURCE5 5 0.3628 + angle_coeff @angle:ca-sy-nf harmonic 92.539 103.010 # SOURCE4_SOURCE5 25 2.4137 + angle_coeff @angle:cc-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 6 0.2429 + angle_coeff @angle:n3-sy-nf harmonic 120.039 101.930 # SOURCE4_SOURCE5 10 1.4898 + angle_coeff @angle:cl-py-ne harmonic 67.181 109.160 # SOURCE5 79 0.9726 + angle_coeff @angle:ce-ce-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 + angle_coeff @angle:cp-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 + angle_coeff @angle:ca-cc-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 + angle_coeff @angle:h1-c3-i harmonic 39.280 103.880 # SOURCE5 43 0.8359 + angle_coeff @angle:h4-c2-h4 harmonic 37.559 117.920 # SOURCE5 46 1.0787 + angle_coeff @angle:c-ss-ss harmonic 72.810 97.680 # SOURCE5 29 1.7788 + angle_coeff @angle:f-py-ne harmonic 83.682 108.600 # SOURCE5 47 0.7739 + angle_coeff @angle:ca-nh-ce harmonic 65.017 127.740 # SOURCE5 32 0.9569 + angle_coeff @angle:ce-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 + angle_coeff @angle:py-ne-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 + angle_coeff @angle:c-cd-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 + angle_coeff @angle:s-p5-ss harmonic 46.401 116.670 # SOURCE5 27 1.1060 + angle_coeff @angle:cx-c3-nh harmonic 86.752 103.860 # SOURCE5 29 2.2522 + angle_coeff @angle:cc-cc-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 + angle_coeff @angle:cd-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 + angle_coeff @angle:h1-cy-nh harmonic 59.704 113.860 # SOURCE5 31 0.8499 + angle_coeff @angle:h5-c-os harmonic 63.962 113.090 # SOURCE5 20 0.1826 + angle_coeff @angle:c2-c3-n4 harmonic 81.944 113.640 # SOURCE5 18 2.3563 + angle_coeff @angle:c2-cx-c3 harmonic 65.275 115.480 # SOURCE5 22 1.1986 + angle_coeff @angle:c3-c2-cx harmonic 64.810 117.870 # SOURCE5 20 2.2886 + angle_coeff @angle:br-cx-cx harmonic 62.999 119.040 # SOURCE5 21 0.7114 + angle_coeff @angle:cc-cf-ch harmonic 68.168 122.270 # SOURCE5 30 0.9028 + angle_coeff @angle:c3-c3-sx harmonic 63.092 110.500 # SOURCE5 14 1.4461 + angle_coeff @angle:ca-cy-hc harmonic 46.450 114.530 # SOURCE5 17 1.6221 + angle_coeff @angle:cx-c1-n1 harmonic 74.188 178.250 # SOURCE5 17 0.8798 + angle_coeff @angle:cl-py-cl harmonic 61.568 101.950 # SOURCE5 12 0.7596 + angle_coeff @angle:c2-ce-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 + angle_coeff @angle:c3-c-cx harmonic 64.715 116.040 # SOURCE5 14 1.1793 + angle_coeff @angle:cf-cc-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 + angle_coeff @angle:cd-cd-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 + angle_coeff @angle:c3-py-ca harmonic 46.073 107.270 # SOURCE5 20 1.8136 + angle_coeff @angle:c3-c3-py harmonic 80.645 111.570 # SOURCE5 14 1.9142 + angle_coeff @angle:c3-py-s harmonic 46.250 113.850 # SOURCE5 14 0.3847 + angle_coeff @angle:ca-c-cx harmonic 64.997 117.660 # SOURCE5 20 1.5268 + angle_coeff @angle:ce-ce-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 + angle_coeff @angle:c3-n4-cx harmonic 62.636 117.290 # SOURCE5 15 0.3164 + angle_coeff @angle:h4-ce-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 + angle_coeff @angle:hx-cy-n4 harmonic 58.977 110.620 # SOURCE5 14 1.8211 + angle_coeff @angle:cy-no-o harmonic 84.157 116.830 # SOURCE5 17 1.1181 + angle_coeff @angle:cc-cd-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 + angle_coeff @angle:ca-nb-na harmonic 87.254 118.780 # SOURCE5 10 0.6408 + angle_coeff @angle:cl-c3-cy harmonic 71.118 111.890 # SOURCE5 12 0.7377 + angle_coeff @angle:f-c2-h4 harmonic 66.183 112.050 # SOURCE5 13 0.7763 + angle_coeff @angle:ca-py-s harmonic 45.997 116.310 # SOURCE5 11 1.2602 + angle_coeff @angle:cl-c3-cx harmonic 71.664 110.760 # SOURCE5 9 1.3315 + angle_coeff @angle:ca-nh-cy harmonic 63.219 126.620 # SOURCE5 12 1.1353 + angle_coeff @angle:cy-cy-no harmonic 79.836 115.430 # SOURCE5 15 1.0848 + angle_coeff @angle:ce-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 + angle_coeff @angle:cy-cy-hx harmonic 45.080 115.920 # SOURCE5 9 1.5918 + angle_coeff @angle:ce-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 + angle_coeff @angle:c3-cx-cu harmonic 63.779 120.910 # SOURCE5 11 0.4272 + angle_coeff @angle:cf-cf-ne harmonic 86.585 120.790 # SOURCE5 9 1.8014 + angle_coeff @angle:f-p5-na harmonic 88.711 89.260 # SOURCE5 12 1.2991 + angle_coeff @angle:h4-ce-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 + angle_coeff @angle:ne-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 + angle_coeff @angle:ca-os-py harmonic 83.011 123.310 # SOURCE5 12 0.8994 + angle_coeff @angle:cf-ce-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 + angle_coeff @angle:cy-cy-n4 harmonic 90.361 89.940 # SOURCE5 10 0.7009 + angle_coeff @angle:na-cc-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 + angle_coeff @angle:nb-na-o harmonic 113.391 118.130 # SOURCE5 11 0.6838 + angle_coeff @angle:c-cx-n3 harmonic 82.187 116.960 # SOURCE5 11 1.3298 + angle_coeff @angle:cd-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 + angle_coeff @angle:f-c3-no harmonic 111.081 107.760 # SOURCE5 11 0.3179 + angle_coeff @angle:ce-cd-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 + angle_coeff @angle:cq-cp-cq harmonic 69.705 108.020 # SOURCE5 24 0.5633 + angle_coeff @angle:os-py-s harmonic 59.825 116.220 # SOURCE5 11 0.4580 + angle_coeff @angle:c-c3-cy harmonic 65.476 110.880 # SOURCE5 9 1.4172 + angle_coeff @angle:cy-c2-ha harmonic 45.849 118.590 # SOURCE5 5 1.8406 + angle_coeff @angle:cp-cq-cp harmonic 69.705 108.020 # SOURCE5 24 0.5633 + angle_coeff @angle:cx-cu-cx harmonic 89.228 63.190 # SOURCE5 12 0.2140 + angle_coeff @angle:cu-c2-ha harmonic 50.414 121.490 # SOURCE5 12 0.1524 + angle_coeff @angle:cd-ce-cg harmonic 68.168 122.270 # SOURCE5 30 0.9028 + angle_coeff @angle:cf-ne-ne harmonic 87.949 113.170 # SOURCE5 15 1.6715 + angle_coeff @angle:c3-c2-no harmonic 82.781 115.940 # SOURCE5 9 0.9963 + angle_coeff @angle:f-cy-f harmonic 120.355 108.560 # SOURCE5 9 1.2393 + angle_coeff @angle:c2-cy-hc harmonic 46.979 112.800 # SOURCE5 10 0.5936 + angle_coeff @angle:c3-c2-cy harmonic 64.260 117.990 # SOURCE5 10 1.8958 + angle_coeff @angle:c-ce-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 + angle_coeff @angle:cf-cc-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 + angle_coeff @angle:cd-cc-i harmonic 60.056 124.280 # SOURCE5 14 1.7120 + angle_coeff @angle:ce-cf-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 + angle_coeff @angle:cl-c3-p5 harmonic 92.521 109.520 # SOURCE5 9 0.8307 + angle_coeff @angle:c2-c3-no harmonic 83.742 107.190 # SOURCE5 9 0.5470 + angle_coeff @angle:ce-nf-nf harmonic 87.949 113.170 # SOURCE5 15 1.6715 + angle_coeff @angle:c1-c3-cx harmonic 66.544 112.350 # SOURCE5 11 0.3186 + angle_coeff @angle:ce-c3-h2 harmonic 46.896 112.270 # SOURCE5 9 0.2011 + angle_coeff @angle:na-cd-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 + angle_coeff @angle:cx-cx-n4 harmonic 113.255 60.300 # SOURCE5 10 0.1253 + angle_coeff @angle:c1-cx-hc harmonic 48.408 114.860 # SOURCE5 6 0.1269 + angle_coeff @angle:cg-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 + angle_coeff @angle:ce-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 + angle_coeff @angle:cp-ca-cq harmonic 70.964 111.520 # SOURCE5 8 0.0849 + angle_coeff @angle:cl-py-nf harmonic 67.181 109.160 # SOURCE5 79 0.9726 + angle_coeff @angle:ca-c3-cy harmonic 65.233 112.320 # SOURCE5 7 0.8064 + angle_coeff @angle:ch-cd-nd harmonic 85.036 123.030 # SOURCE5 7 0.2371 + angle_coeff @angle:h1-cy-ss harmonic 41.667 111.560 # SOURCE5 6 1.1376 + angle_coeff @angle:h5-cc-n2 harmonic 63.976 123.280 # SOURCE5 5 1.2554 + angle_coeff @angle:cc-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 + angle_coeff @angle:c-c3-no harmonic 83.428 106.990 # SOURCE5 8 1.0618 + angle_coeff @angle:c3-py-c3 harmonic 46.116 105.720 # SOURCE5 10 2.4094 + angle_coeff @angle:hx-c3-n3 harmonic 60.702 111.730 # SOURCE5 10 0.1463 + angle_coeff @angle:cf-cf-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 + angle_coeff @angle:c3-n3-py harmonic 81.527 118.270 # SOURCE5 8 1.5513 + angle_coeff @angle:h5-c2-os harmonic 64.726 110.950 # SOURCE5 9 1.4177 + angle_coeff @angle:cc-c3-ce harmonic 66.308 110.890 # SOURCE5 7 2.0183 + angle_coeff @angle:n4-c3-p5 harmonic 104.054 106.090 # SOURCE5 10 1.7975 + angle_coeff @angle:ne-cd-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 + angle_coeff @angle:na-cd-ne harmonic 111.251 122.470 # SOURCE5 7 2.4448 + angle_coeff @angle:cl-c3-h3 harmonic 48.652 107.660 # SOURCE5 10 0.1942 + angle_coeff @angle:h5-c-s harmonic 44.037 123.510 # SOURCE5 6 0.5125 + angle_coeff @angle:cf-ce-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 + angle_coeff @angle:c3-c2-f harmonic 87.663 113.280 # SOURCE5 8 1.0861 + angle_coeff @angle:h4-c2-oh harmonic 64.512 114.610 # SOURCE5 8 1.2250 + angle_coeff @angle:ne-ce-nf harmonic 108.272 127.960 # SOURCE5 10 1.2321 + angle_coeff @angle:cc-n-cd harmonic 67.143 121.050 # SOURCE5 7 0.3580 + angle_coeff @angle:f-py-f harmonic 90.389 97.510 # SOURCE5 5 0.2281 + angle_coeff @angle:n-cc-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 + angle_coeff @angle:cq-cp-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 + angle_coeff @angle:c-c-s harmonic 64.027 121.310 # SOURCE5 8 0.9033 + angle_coeff @angle:cf-ce-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 + angle_coeff @angle:br-ce-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 + angle_coeff @angle:cp-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 + angle_coeff @angle:n-s6-oh harmonic 123.280 97.300 # SOURCE5 8 0.9381 + angle_coeff @angle:cd-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 + angle_coeff @angle:nb-ca-sy harmonic 81.256 115.730 # SOURCE5 6 0.4033 + angle_coeff @angle:na-sy-o harmonic 122.952 105.300 # SOURCE5 5 1.0811 + angle_coeff @angle:hx-cx-hx harmonic 37.969 115.770 # SOURCE5 9 0.0901 + angle_coeff @angle:cd-cf-ne harmonic 86.147 122.390 # SOURCE5 7 1.4919 + angle_coeff @angle:h5-c-oh harmonic 65.262 109.490 # SOURCE5 7 0.3600 + angle_coeff @angle:cy-n-cy harmonic 71.371 94.550 # SOURCE5 5 0.6286 + angle_coeff @angle:br-c3-no harmonic 81.143 106.960 # SOURCE5 6 2.2092 + angle_coeff @angle:c2-ss-s4 harmonic 73.233 92.420 # SOURCE5 8 0.4009 + angle_coeff @angle:c3-nh-o harmonic 85.477 117.530 # SOURCE5 7 1.0041 + angle_coeff @angle:br-cc-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 + angle_coeff @angle:c-ce-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 + angle_coeff @angle:c3-n-n3 harmonic 82.135 117.560 # SOURCE5 6 2.4546 + angle_coeff @angle:h5-ca-na harmonic 62.521 115.800 # SOURCE5 8 0.4738 + angle_coeff @angle:n2-nh-oh harmonic 106.301 117.890 # SOURCE5 6 0.2008 + angle_coeff @angle:c2-c3-p5 harmonic 80.813 112.220 # SOURCE5 6 0.6523 + angle_coeff @angle:c3-cx-nh harmonic 82.121 116.580 # SOURCE5 7 1.1795 + angle_coeff @angle:c2-cc-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 + angle_coeff @angle:c-ca-na harmonic 84.333 117.810 # SOURCE5 7 2.2477 + angle_coeff @angle:cl-c2-n2 harmonic 91.772 121.450 # SOURCE5 8 0.8251 + angle_coeff @angle:n2-s4-ne harmonic 122.203 104.290 # SOURCE5 8 0.9503 + angle_coeff @angle:nc-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 + angle_coeff @angle:o-sy-ss harmonic 85.092 107.590 # SOURCE5 7 2.0694 + angle_coeff @angle:c2-ce-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 + angle_coeff @angle:c3-cx-ca harmonic 64.734 117.010 # SOURCE5 6 1.1320 + angle_coeff @angle:cc-cc-nf harmonic 87.342 121.680 # SOURCE5 7 1.9093 + angle_coeff @angle:ca-nd-cd harmonic 73.420 104.240 # SOURCE5 8 0.2625 + angle_coeff @angle:cc-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 + angle_coeff @angle:ca-os-sy harmonic 63.798 118.010 # SOURCE5 8 2.0392 + angle_coeff @angle:hx-c3-p5 harmonic 54.750 107.590 # SOURCE5 7 1.8329 + angle_coeff @angle:ca-ce-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 + angle_coeff @angle:h4-ce-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 + angle_coeff @angle:c3-ce-ne harmonic 83.806 116.230 # SOURCE5 5 1.2988 + angle_coeff @angle:c1-n1-ce harmonic 61.729 176.870 # SOURCE5 7 0.6686 + angle_coeff @angle:c3-n2-cd harmonic 67.858 117.010 # SOURCE5 6 1.8279 + angle_coeff @angle:cc-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 + angle_coeff @angle:ca-ce-cg harmonic 67.208 116.470 # SOURCE5 5 1.0847 + angle_coeff @angle:c2-cc-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 + angle_coeff @angle:ca-c3-s4 harmonic 63.907 109.520 # SOURCE5 7 1.3239 + angle_coeff @angle:n2-cf-nf harmonic 111.801 120.690 # SOURCE5 6 1.4522 + angle_coeff @angle:ce-cf-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 + angle_coeff @angle:c3-cx-ss harmonic 62.514 114.160 # SOURCE5 7 0.1562 + angle_coeff @angle:nh-ce-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 + angle_coeff @angle:cd-c-ne harmonic 87.008 112.220 # SOURCE5 6 0.1806 + angle_coeff @angle:na-c3-ss harmonic 82.873 103.150 # SOURCE5 8 0.3361 + angle_coeff @angle:cf-cf-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 + angle_coeff @angle:cx-c3-h2 harmonic 46.468 114.010 # SOURCE5 8 0.8649 + angle_coeff @angle:cv-ss-cy harmonic 79.244 82.620 # SOURCE5 8 0.2654 + angle_coeff @angle:ss-cy-ss harmonic 68.296 95.040 # SOURCE5 6 0.9436 + angle_coeff @angle:ce-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 + angle_coeff @angle:nb-ca-ne harmonic 109.027 121.410 # SOURCE5 6 1.6965 + angle_coeff @angle:br-ca-nb harmonic 81.701 116.350 # SOURCE5 5 0.4508 + angle_coeff @angle:c3-nh-os harmonic 84.400 110.370 # SOURCE5 6 2.4123 + angle_coeff @angle:c2-nh-p5 harmonic 81.068 125.900 # SOURCE5 6 1.8594 + angle_coeff @angle:br-ca-cp harmonic 63.564 121.390 # SOURCE5 7 0.3403 + angle_coeff @angle:cc-ce-cc harmonic 67.224 116.170 # SOURCE5 6 0.4089 + angle_coeff @angle:c3-nh-s6 harmonic 63.928 116.490 # SOURCE5 6 0.5375 + angle_coeff @angle:cx-c3-na harmonic 82.551 114.780 # SOURCE5 7 1.7481 + angle_coeff @angle:ca-os-p3 harmonic 85.566 110.460 # SOURCE5 5 0.0025 + angle_coeff @angle:ce-cf-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 + angle_coeff @angle:ca-n2-n1 harmonic 92.483 118.480 # SOURCE5 5 0.1464 + angle_coeff @angle:cd-cd-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 + angle_coeff @angle:na-n2-os harmonic 113.058 104.340 # SOURCE5 6 0.3185 + angle_coeff @angle:ce-c3-f harmonic 88.332 110.310 # SOURCE5 6 0.9204 + angle_coeff @angle:cx-cc-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 + angle_coeff @angle:n-n2-na harmonic 113.870 106.040 # SOURCE5 6 0.3975 + angle_coeff @angle:c3-cf-cc harmonic 67.117 117.430 # SOURCE5 5 2.0116 + angle_coeff @angle:ca-na-cy harmonic 63.636 128.060 # SOURCE5 7 0.2603 + angle_coeff @angle:h1-c3-py harmonic 54.323 109.380 # SOURCE5 7 0.4767 + angle_coeff @angle:cy-s6-cy harmonic 75.496 86.770 # SOURCE5 5 1.5405 + angle_coeff @angle:ce-ce-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 + angle_coeff @angle:c3-p3-cy harmonic 45.442 103.850 # SOURCE5 6 0.6245 + angle_coeff @angle:h2-cx-os harmonic 60.942 114.700 # SOURCE5 7 1.4166 + angle_coeff @angle:c-c-ce harmonic 64.646 115.440 # SOURCE5 5 1.0373 + angle_coeff @angle:ce-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 + angle_coeff @angle:cx-c3-ss harmonic 64.879 105.420 # SOURCE5 7 0.4078 + angle_coeff @angle:cg-ce-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 + angle_coeff @angle:br-cy-cy harmonic 61.847 119.270 # SOURCE5 6 1.4624 + angle_coeff @angle:c-cy-cl harmonic 71.094 112.180 # SOURCE5 5 2.4165 + angle_coeff @angle:c-cx-n harmonic 81.704 120.510 # SOURCE5 7 1.7811 + angle_coeff @angle:br-c3-f harmonic 82.493 109.620 # SOURCE5 7 0.6251 + angle_coeff @angle:c3-n4-cy harmonic 63.514 112.130 # SOURCE5 5 0.7180 + angle_coeff @angle:ce-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 + angle_coeff @angle:cc-cd-i harmonic 60.200 124.280 # SOURCE5 14 1.7120 + angle_coeff @angle:c2-ss-ca harmonic 73.005 102.780 # SOURCE5 5 0.7426 + angle_coeff @angle:c-cx-ce harmonic 64.969 116.840 # SOURCE5 7 1.2393 + angle_coeff @angle:cy-nh-cy harmonic 71.537 93.310 # SOURCE5 6 0.3047 + angle_coeff @angle:cx-c-h4 harmonic 46.665 115.380 # SOURCE5 7 0.1819 + angle_coeff @angle:c-n4-c3 harmonic 63.969 108.760 # SOURCE5 7 1.5097 + angle_coeff @angle:f-cy-py harmonic 99.595 113.190 # SOURCE5 8 0.9744 + angle_coeff @angle:n2-c3-ss harmonic 80.436 109.390 # SOURCE5 5 1.4343 + angle_coeff @angle:c3-ss-cf harmonic 71.418 101.280 # SOURCE5 6 2.4411 + angle_coeff @angle:ce-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 + angle_coeff @angle:br-cc-nc harmonic 82.466 116.250 # SOURCE5 5 0.0824 + angle_coeff @angle:h3-c3-n harmonic 61.280 109.880 # SOURCE5 6 0.7497 + angle_coeff @angle:ca-ne-cd harmonic 67.557 123.670 # SOURCE5 5 2.0742 + angle_coeff @angle:cx-n-cy harmonic 64.984 116.210 # SOURCE5 6 0.4758 + angle_coeff @angle:cl-c3-s4 harmonic 71.477 111.990 # SOURCE5 6 1.5116 + angle_coeff @angle:cp-cq-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 + angle_coeff @angle:cc-cd-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 + angle_coeff @angle:hx-cy-hx harmonic 38.598 110.800 # SOURCE5 5 0.4155 + angle_coeff @angle:cc-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 + angle_coeff @angle:h1-cy-na harmonic 62.857 106.380 # SOURCE5 5 0.0918 + angle_coeff @angle:h4-cf-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 + angle_coeff @angle:c-p5-c3 harmonic 44.432 111.280 # SOURCE5 6 2.1227 + angle_coeff @angle:ca-c-nc harmonic 84.546 117.030 # SOURCE5 5 0.2959 + angle_coeff @angle:c3-os-sy harmonic 63.872 115.050 # SOURCE5 5 0.9975 + angle_coeff @angle:cd-ne-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 + angle_coeff @angle:cx-ca-nb harmonic 85.768 116.900 # SOURCE5 5 0.8439 + angle_coeff @angle:nc-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 + angle_coeff @angle:hp-p5-os harmonic 45.642 103.080 # SOURCE5 5 0.8064 + angle_coeff @angle:ca-n-oh harmonic 84.294 115.620 # SOURCE5 5 1.0474 + angle_coeff @angle:c3-s6-ne harmonic 91.348 108.190 # SOURCE5 5 0.2914 + angle_coeff @angle:c1-cx-h1 harmonic 48.407 114.800 # SOURCE5 5 0.4789 + angle_coeff @angle:na-c3-oh harmonic 109.816 108.590 # SOURCE5 6 1.4542 + angle_coeff @angle:n-nc-nd harmonic 109.773 119.880 # SOURCE5 5 0.1982 + angle_coeff @angle:c3-na-nb harmonic 85.173 113.140 # SOURCE5 5 0.4557 + angle_coeff @angle:ne-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 + angle_coeff @angle:br-ce-ce harmonic 64.975 115.220 # SOURCE5 6 0.2328 + angle_coeff @angle:cc-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 + angle_coeff @angle:c1-cx-os harmonic 84.507 117.430 # SOURCE5 5 0.5408 + angle_coeff @angle:nc-cc-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 + angle_coeff @angle:br-ce-cf harmonic 63.865 121.600 # SOURCE5 5 1.8246 + angle_coeff @angle:cy-c3-f harmonic 87.269 111.480 # SOURCE5 5 0.6981 + angle_coeff @angle:h5-ce-ne harmonic 62.727 113.650 # SOURCE5 5 0.5892 + angle_coeff @angle:n3-py-n3 harmonic 78.976 104.560 # SOURCE5 5 0.5659 + angle_coeff @angle:br-cc-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 + angle_coeff @angle:f-c3-na harmonic 113.041 110.410 # SOURCE5 5 0.7067 + angle_coeff @angle:cc-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 + angle_coeff @angle:ce-cf-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 + angle_coeff @angle:cc-cc-i harmonic 59.680 125.790 # SOURCE5 5 1.4784 + angle_coeff @angle:c-cg-ch harmonic 58.652 176.690 # SOURCE5 5 0.2913 + angle_coeff @angle:ce-c3-hx harmonic 47.212 110.880 # SOURCE5 5 0.3335 + angle_coeff @angle:cd-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 + angle_coeff @angle:br-c3-c2 harmonic 63.737 111.170 # SOURCE5 5 1.2445 + angle_coeff @angle:ce-ce-cg harmonic 68.210 114.640 # SOURCE5 5 0.4759 + angle_coeff @angle:cl-cd-nd harmonic 90.599 121.290 # SOURCE5 5 0.8123 + angle_coeff @angle:n-ca-na harmonic 109.145 117.170 # SOURCE5 5 0.3934 + angle_coeff @angle:cx-cd-nd harmonic 83.980 121.600 # SOURCE5 5 0.1341 + angle_coeff @angle:cl-p5-os harmonic 69.550 104.530 # SOURCE5 5 0.1303 + angle_coeff @angle:cx-ss-cy harmonic 73.867 91.640 # SOURCE5 5 0.0761 + angle_coeff @angle:cc-cg-ch harmonic 59.342 177.060 # SOURCE5 5 0.7516 + angle_coeff @angle:cc-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 + angle_coeff @angle:cq-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 + angle_coeff @angle:ca-cd-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 + angle_coeff @angle:f-py-nf harmonic 83.682 108.600 # SOURCE5 47 0.7739 + angle_coeff @angle:ca-nh-cf harmonic 65.017 127.740 # SOURCE5 32 0.9569 + angle_coeff @angle:cf-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 + angle_coeff @angle:py-nf-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 + angle_coeff @angle:c-cc-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 + angle_coeff @angle:cc-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 + angle_coeff @angle:c2-cf-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 + angle_coeff @angle:ce-cd-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 + angle_coeff @angle:cd-cc-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 + angle_coeff @angle:cf-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 + angle_coeff @angle:cf-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 + angle_coeff @angle:ce-ce-nf harmonic 86.585 120.790 # SOURCE5 9 1.8014 + angle_coeff @angle:cf-no-o harmonic 86.024 118.220 # SOURCE5 11 0.7792 + angle_coeff @angle:h4-cf-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 + angle_coeff @angle:nf-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 + angle_coeff @angle:na-cd-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 + angle_coeff @angle:cc-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 + angle_coeff @angle:cf-cc-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 + angle_coeff @angle:c-cf-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 + angle_coeff @angle:ce-cd-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 + angle_coeff @angle:cf-c3-h2 harmonic 46.902 112.270 # SOURCE5 9 0.2011 + angle_coeff @angle:na-cc-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 + angle_coeff @angle:ch-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 + angle_coeff @angle:cf-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 + angle_coeff @angle:cg-cc-nc harmonic 85.036 123.030 # SOURCE5 7 0.2371 + angle_coeff @angle:h5-cd-n2 harmonic 63.978 123.280 # SOURCE5 5 1.2554 + angle_coeff @angle:cd-c3-cf harmonic 66.313 110.890 # SOURCE5 7 2.0183 + angle_coeff @angle:nf-cc-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 + angle_coeff @angle:na-cc-nf harmonic 111.251 122.470 # SOURCE5 7 2.4448 + angle_coeff @angle:nf-cf-ne harmonic 108.272 127.960 # SOURCE5 10 1.2321 + angle_coeff @angle:n-cd-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 + angle_coeff @angle:ce-cf-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 + angle_coeff @angle:br-cf-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 + angle_coeff @angle:cq-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 + angle_coeff @angle:cc-ce-nf harmonic 86.147 122.390 # SOURCE5 7 1.4919 + angle_coeff @angle:cf-s4-ss harmonic 74.492 88.650 # SOURCE5 8 0.4156 + angle_coeff @angle:br-cd-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 + angle_coeff @angle:c-cf-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 + angle_coeff @angle:c2-cd-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 + angle_coeff @angle:n2-s4-nf harmonic 122.203 104.290 # SOURCE5 8 0.9503 + angle_coeff @angle:nd-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 + angle_coeff @angle:c2-cf-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 + angle_coeff @angle:cd-cd-ne harmonic 87.342 121.680 # SOURCE5 7 1.9093 + angle_coeff @angle:ca-nc-cc harmonic 73.420 104.240 # SOURCE5 8 0.2625 + angle_coeff @angle:cd-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 + angle_coeff @angle:ca-cf-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 + angle_coeff @angle:h4-cf-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 + angle_coeff @angle:c3-cf-nf harmonic 83.812 116.230 # SOURCE5 5 1.2988 + angle_coeff @angle:c1-n1-cf harmonic 61.729 176.870 # SOURCE5 7 0.6686 + angle_coeff @angle:c3-n2-cc harmonic 67.858 117.010 # SOURCE5 6 1.8279 + angle_coeff @angle:ca-cf-ch harmonic 67.208 116.470 # SOURCE5 5 1.0847 + angle_coeff @angle:c2-cd-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 + angle_coeff @angle:n2-ce-ne harmonic 111.801 120.690 # SOURCE5 6 1.4522 + angle_coeff @angle:nh-cf-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 + angle_coeff @angle:cc-c-nf harmonic 87.008 112.220 # SOURCE5 6 0.1806 + angle_coeff @angle:cf-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 + angle_coeff @angle:nb-ca-nf harmonic 109.027 121.410 # SOURCE5 6 1.6965 + angle_coeff @angle:br-ca-cq harmonic 63.564 121.390 # SOURCE5 7 0.3403 + angle_coeff @angle:cd-cf-cd harmonic 67.224 116.170 # SOURCE5 6 0.4089 + angle_coeff @angle:cf-ce-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 + angle_coeff @angle:cc-cc-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 + angle_coeff @angle:cf-c3-f harmonic 88.340 110.310 # SOURCE5 6 0.9204 + angle_coeff @angle:cx-cd-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 + angle_coeff @angle:c3-ce-cd harmonic 67.111 117.430 # SOURCE5 5 2.0116 + angle_coeff @angle:cf-cf-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 + angle_coeff @angle:c-c-cf harmonic 64.646 115.440 # SOURCE5 5 1.0373 + angle_coeff @angle:cf-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 + angle_coeff @angle:ch-cf-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 + angle_coeff @angle:cf-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 + angle_coeff @angle:c-cx-cf harmonic 64.969 116.840 # SOURCE5 7 1.2393 + angle_coeff @angle:c3-ss-ce harmonic 71.418 101.280 # SOURCE5 6 2.4411 + angle_coeff @angle:cf-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 + angle_coeff @angle:br-cd-nd harmonic 82.466 116.250 # SOURCE5 5 0.0824 + angle_coeff @angle:ca-nf-cc harmonic 67.557 123.670 # SOURCE5 5 2.0742 + angle_coeff @angle:cd-cc-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 + angle_coeff @angle:cd-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 + angle_coeff @angle:ca-c-nd harmonic 84.546 117.030 # SOURCE5 5 0.2959 + angle_coeff @angle:cc-nf-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 + angle_coeff @angle:nd-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 + angle_coeff @angle:c3-s6-nf harmonic 91.348 108.190 # SOURCE5 5 0.2914 + angle_coeff @angle:n-nd-nc harmonic 109.773 119.880 # SOURCE5 5 0.1982 + angle_coeff @angle:nf-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 + angle_coeff @angle:br-cf-cf harmonic 64.975 115.220 # SOURCE5 6 0.2328 + angle_coeff @angle:cd-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 + angle_coeff @angle:nd-cd-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 + angle_coeff @angle:br-cf-ce harmonic 63.865 121.600 # SOURCE5 5 1.8246 + angle_coeff @angle:h5-cf-nf harmonic 62.727 113.650 # SOURCE5 5 0.5892 + angle_coeff @angle:br-cd-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 + angle_coeff @angle:cd-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 + angle_coeff @angle:cf-ce-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 + angle_coeff @angle:cd-cd-i harmonic 59.818 125.790 # SOURCE5 5 1.4784 + angle_coeff @angle:c-ch-cg harmonic 58.652 176.690 # SOURCE5 5 0.2913 + angle_coeff @angle:cf-c3-hx harmonic 47.217 110.880 # SOURCE5 5 0.3335 + angle_coeff @angle:cf-cf-ch harmonic 68.210 114.640 # SOURCE5 5 0.4759 + angle_coeff @angle:cl-cc-nc harmonic 90.599 121.290 # SOURCE5 5 0.8123 + angle_coeff @angle:cx-cc-nc harmonic 83.980 121.600 # SOURCE5 5 0.1341 + angle_coeff @angle:cd-ch-cg harmonic 59.342 177.060 # SOURCE5 5 0.7516 + angle_coeff @angle:cd-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 + } # (end of angle_coeffs) + + write_once("Data Angles By Type") { + @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw + @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow + @angle:br-c1-br @atom:br @atom:c1 @atom:br + @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 + @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 + @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 + @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 + @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca + @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl + @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f + @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha + @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc + @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i + @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 + @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 + @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 + @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 + @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n + @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na + @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh + @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no + @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o + @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh + @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os + @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 + @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 + @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 + @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 + @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 + @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 + @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s + @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh + @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss + @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 + @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce + @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 + @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o + @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 + @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 + @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg + @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1 + @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca + @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1 + @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha + @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha + @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl + @angle:f-c1-f @atom:f @atom:c1 @atom:f + @angle:i-c1-i @atom:i @atom:c1 @atom:i + @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1 + @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3 + @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh + @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os + @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3 + @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss + @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2 + @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o + @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s + @angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3 + @angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4 + @angle:na-c1-na @atom:na @atom:c1 @atom:na + @angle:ne-c1-o @atom:ne @atom:c1 @atom:o + @angle:ne-c1-s @atom:ne @atom:c1 @atom:s + @angle:nf-c1-o @atom:nf @atom:c1 @atom:o + @angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh + @angle:n-c1-n @atom:n @atom:c1 @atom:n + @angle:no-c1-no @atom:no @atom:c1 @atom:no + @angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh + @angle:o-c1-o @atom:o @atom:c1 @atom:o + @angle:os-c1-os @atom:os @atom:c1 @atom:os + @angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2 + @angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3 + @angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4 + @angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5 + @angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2 + @angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4 + @angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6 + @angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh + @angle:s-c1-s @atom:s @atom:c1 @atom:s + @angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss + @angle:br-c2-br @atom:br @atom:c2 @atom:br + @angle:br-c2-c2 @atom:br @atom:c2 @atom:c2 + @angle:br-c2-c3 @atom:br @atom:c2 @atom:c3 + @angle:br-c2-ce @atom:br @atom:c2 @atom:ce + @angle:br-c2-h4 @atom:br @atom:c2 @atom:h4 + @angle:br-c2-ha @atom:br @atom:c2 @atom:ha + @angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1 + @angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2 + @angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3 + @angle:c1-c2-f @atom:c1 @atom:c2 @atom:f + @angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha + @angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2 + @angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3 + @angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca + @angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc + @angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd + @angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl + @angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx + @angle:c2-c2-cy @atom:c2 @atom:c2 @atom:cy + @angle:c2-c2-f @atom:c2 @atom:c2 @atom:f + @angle:c2-c2-h4 @atom:c2 @atom:c2 @atom:h4 + @angle:c2-c2-ha @atom:c2 @atom:c2 @atom:ha + @angle:c2-c2-hc @atom:c2 @atom:c2 @atom:hc + @angle:c2-c2-hx @atom:c2 @atom:c2 @atom:hx + @angle:c2-c2-i @atom:c2 @atom:c2 @atom:i + @angle:c2-c2-n1 @atom:c2 @atom:c2 @atom:n1 + @angle:c2-c2-n2 @atom:c2 @atom:c2 @atom:n2 + @angle:c2-c2-n3 @atom:c2 @atom:c2 @atom:n3 + @angle:c2-c2-n4 @atom:c2 @atom:c2 @atom:n4 + @angle:c2-c2-n @atom:c2 @atom:c2 @atom:n + @angle:c2-c2-na @atom:c2 @atom:c2 @atom:na + @angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh + @angle:c2-c2-no @atom:c2 @atom:c2 @atom:no + @angle:c2-c2-o @atom:c2 @atom:c2 @atom:o + @angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh + @angle:c2-c2-os @atom:c2 @atom:c2 @atom:os + @angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2 + @angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3 + @angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4 + @angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5 + @angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4 + @angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6 + @angle:c2-c2-s @atom:c2 @atom:c2 @atom:s + @angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh + @angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss + @angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3 + @angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc + @angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd + @angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce + @angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf + @angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4 + @angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha + @angle:c3-c2-hc @atom:c3 @atom:c2 @atom:hc + @angle:c3-c2-n2 @atom:c3 @atom:c2 @atom:n2 + @angle:c3-c2-n @atom:c3 @atom:c2 @atom:n + @angle:c3-c2-na @atom:c3 @atom:c2 @atom:na + @angle:c3-c2-ne @atom:c3 @atom:c2 @atom:ne + @angle:c3-c2-nf @atom:c3 @atom:c2 @atom:nf + @angle:c3-c2-nh @atom:c3 @atom:c2 @atom:nh + @angle:c3-c2-o @atom:c3 @atom:c2 @atom:o + @angle:c3-c2-oh @atom:c3 @atom:c2 @atom:oh + @angle:c3-c2-os @atom:c3 @atom:c2 @atom:os + @angle:c3-c2-p2 @atom:c3 @atom:c2 @atom:p2 + @angle:c3-c2-s @atom:c3 @atom:c2 @atom:s + @angle:c3-c2-ss @atom:c3 @atom:c2 @atom:ss + @angle:ca-c2-ca @atom:ca @atom:c2 @atom:ca + @angle:ca-c2-hc @atom:ca @atom:c2 @atom:hc + @angle:c-c2-c2 @atom:c @atom:c2 @atom:c2 + @angle:c-c2-c3 @atom:c @atom:c2 @atom:c3 + @angle:c-c2-c @atom:c @atom:c2 @atom:c + @angle:cc-c2-h4 @atom:cc @atom:c2 @atom:h4 + @angle:cc-c2-ha @atom:cc @atom:c2 @atom:ha + @angle:cc-c2-nh @atom:cc @atom:c2 @atom:nh + @angle:cc-c2-o @atom:cc @atom:c2 @atom:o + @angle:cd-c2-ha @atom:cd @atom:c2 @atom:ha + @angle:ce-c2-cl @atom:ce @atom:c2 @atom:cl + @angle:ce-c2-h4 @atom:ce @atom:c2 @atom:h4 + @angle:ce-c2-ha @atom:ce @atom:c2 @atom:ha + @angle:ce-c2-na @atom:ce @atom:c2 @atom:na + @angle:ce-c2-nh @atom:ce @atom:c2 @atom:nh + @angle:ce-c2-no @atom:ce @atom:c2 @atom:no + @angle:ce-c2-o @atom:ce @atom:c2 @atom:o + @angle:ce-c2-oh @atom:ce @atom:c2 @atom:oh + @angle:ce-c2-os @atom:ce @atom:c2 @atom:os + @angle:cf-c2-ha @atom:cf @atom:c2 @atom:ha + @angle:c-c2-ha @atom:c @atom:c2 @atom:ha + @angle:c-c2-hc @atom:c @atom:c2 @atom:hc + @angle:cl-c2-cl @atom:cl @atom:c2 @atom:cl + @angle:cl-c2-h4 @atom:cl @atom:c2 @atom:h4 + @angle:cl-c2-ha @atom:cl @atom:c2 @atom:ha + @angle:cx-c2-ha @atom:cx @atom:c2 @atom:ha + @angle:f-c2-f @atom:f @atom:c2 @atom:f + @angle:f-c2-ha @atom:f @atom:c2 @atom:ha + @angle:h4-c2-n2 @atom:h4 @atom:c2 @atom:n2 + @angle:h4-c2-n @atom:h4 @atom:c2 @atom:n + @angle:h4-c2-na @atom:h4 @atom:c2 @atom:na + @angle:h4-c2-ne @atom:h4 @atom:c2 @atom:ne + @angle:h4-c2-nh @atom:h4 @atom:c2 @atom:nh + @angle:h4-c2-no @atom:h4 @atom:c2 @atom:no + @angle:h4-c2-os @atom:h4 @atom:c2 @atom:os + @angle:h4-c2-ss @atom:h4 @atom:c2 @atom:ss + @angle:h5-c2-n2 @atom:h5 @atom:c2 @atom:n2 + @angle:h5-c2-na @atom:h5 @atom:c2 @atom:na + @angle:h5-c2-ne @atom:h5 @atom:c2 @atom:ne + @angle:h5-c2-nh @atom:h5 @atom:c2 @atom:nh + @angle:ha-c2-ha @atom:ha @atom:c2 @atom:ha + @angle:ha-c2-n1 @atom:ha @atom:c2 @atom:n1 + @angle:ha-c2-n2 @atom:ha @atom:c2 @atom:n2 + @angle:ha-c2-n3 @atom:ha @atom:c2 @atom:n3 + @angle:ha-c2-n @atom:ha @atom:c2 @atom:n + @angle:ha-c2-na @atom:ha @atom:c2 @atom:na + @angle:ha-c2-ne @atom:ha @atom:c2 @atom:ne + @angle:ha-c2-nf @atom:ha @atom:c2 @atom:nf + @angle:ha-c2-nh @atom:ha @atom:c2 @atom:nh + @angle:ha-c2-no @atom:ha @atom:c2 @atom:no + @angle:ha-c2-o @atom:ha @atom:c2 @atom:o + @angle:ha-c2-oh @atom:ha @atom:c2 @atom:oh + @angle:ha-c2-os @atom:ha @atom:c2 @atom:os + @angle:ha-c2-p2 @atom:ha @atom:c2 @atom:p2 + @angle:ha-c2-p3 @atom:ha @atom:c2 @atom:p3 + @angle:ha-c2-p4 @atom:ha @atom:c2 @atom:p4 + @angle:ha-c2-p5 @atom:ha @atom:c2 @atom:p5 + @angle:ha-c2-pe @atom:ha @atom:c2 @atom:pe + @angle:ha-c2-pf @atom:ha @atom:c2 @atom:pf + @angle:ha-c2-s2 @atom:ha @atom:c2 @atom:s2 + @angle:ha-c2-s4 @atom:ha @atom:c2 @atom:s4 + @angle:ha-c2-s @atom:ha @atom:c2 @atom:s + @angle:ha-c2-s6 @atom:ha @atom:c2 @atom:s6 + @angle:ha-c2-sh @atom:ha @atom:c2 @atom:sh + @angle:ha-c2-ss @atom:ha @atom:c2 @atom:ss + @angle:hc-c2-hc @atom:hc @atom:c2 @atom:hc + @angle:hc-c2-n2 @atom:hc @atom:c2 @atom:n2 + @angle:hc-c2-n @atom:hc @atom:c2 @atom:n + @angle:hc-c2-na @atom:hc @atom:c2 @atom:na + @angle:hc-c2-nh @atom:hc 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@atom:ss @atom:ca + @angle:c-cx-ce @atom:c @atom:cx @atom:ce + @angle:cy-nh-cy @atom:cy @atom:nh @atom:cy + @angle:cx-c-h4 @atom:cx @atom:c @atom:h4 + @angle:c-n4-c3 @atom:c @atom:n4 @atom:c3 + @angle:f-cy-py @atom:f @atom:cy @atom:py + @angle:n2-c3-ss @atom:n2 @atom:c3 @atom:ss + @angle:c3-ss-cf @atom:c3 @atom:ss @atom:cf + @angle:ce-cy-hc @atom:ce @atom:cy @atom:hc + @angle:br-cc-nc @atom:br @atom:cc @atom:nc + @angle:h3-c3-n @atom:h3 @atom:c3 @atom:n + @angle:ca-ne-cd @atom:ca @atom:ne @atom:cd + @angle:cx-n-cy @atom:cx @atom:n @atom:cy + @angle:cl-c3-s4 @atom:cl @atom:c3 @atom:s4 + @angle:cp-cq-nb @atom:cp @atom:cq @atom:nb + @angle:cc-cd-o @atom:cc @atom:cd @atom:o + @angle:hx-cy-hx @atom:hx @atom:cy @atom:hx + @angle:cc-na-sy @atom:cc @atom:na @atom:sy + @angle:h1-cy-na @atom:h1 @atom:cy @atom:na + @angle:h4-cf-sy @atom:h4 @atom:cf @atom:sy + @angle:c-p5-c3 @atom:c @atom:p5 @atom:c3 + @angle:ca-c-nc @atom:ca @atom:c @atom:nc + @angle:c3-os-sy @atom:c3 @atom:os @atom:sy + @angle:cd-ne-sy @atom:cd @atom:ne @atom:sy + @angle:cx-ca-nb @atom:cx @atom:ca @atom:nb + @angle:nc-ss-ss @atom:nc @atom:ss @atom:ss + @angle:hp-p5-os @atom:hp @atom:p5 @atom:os + @angle:ca-n-oh @atom:ca @atom:n @atom:oh + @angle:c3-s6-ne @atom:c3 @atom:s6 @atom:ne + @angle:c1-cx-h1 @atom:c1 @atom:cx @atom:h1 + @angle:na-c3-oh @atom:na @atom:c3 @atom:oh + @angle:n-nc-nd @atom:n @atom:nc @atom:nd + @angle:c3-na-nb @atom:c3 @atom:na @atom:nb + @angle:ne-c-os @atom:ne @atom:c @atom:os + @angle:br-ce-ce @atom:br @atom:ce @atom:ce + @angle:cc-c2-oh @atom:cc @atom:c2 @atom:oh + @angle:c1-cx-os @atom:c1 @atom:cx @atom:os + @angle:nc-cc-os @atom:nc @atom:cc @atom:os + @angle:br-ce-cf @atom:br @atom:ce @atom:cf + @angle:cy-c3-f @atom:cy @atom:c3 @atom:f + @angle:h5-ce-ne @atom:h5 @atom:ce @atom:ne + @angle:n3-py-n3 @atom:n3 @atom:py @atom:n3 + @angle:br-cc-ca @atom:br @atom:cc @atom:ca + @angle:f-c3-na @atom:f @atom:c3 @atom:na + @angle:cc-c3-s4 @atom:cc @atom:c3 @atom:s4 + @angle:ce-cf-sx @atom:ce @atom:cf @atom:sx + @angle:cc-cc-i @atom:cc @atom:cc @atom:i + @angle:c-cg-ch @atom:c @atom:cg @atom:ch + @angle:ce-c3-hx @atom:ce @atom:c3 @atom:hx + @angle:cd-na-cy @atom:cd @atom:na @atom:cy + @angle:br-c3-c2 @atom:br @atom:c3 @atom:c2 + @angle:ce-ce-cg @atom:ce @atom:ce @atom:cg + @angle:cl-cd-nd @atom:cl @atom:cd @atom:nd + @angle:n-ca-na @atom:n @atom:ca @atom:na + @angle:cx-cd-nd @atom:cx @atom:cd @atom:nd + @angle:cl-p5-os @atom:cl @atom:p5 @atom:os + @angle:cx-ss-cy @atom:cx @atom:ss @atom:cy + @angle:cc-cg-ch @atom:cc @atom:cg @atom:ch + @angle:cc-sy-oh @atom:cc @atom:sy @atom:oh + @angle:cq-ca-os @atom:cq @atom:ca @atom:os + @angle:ca-cd-ca @atom:ca @atom:cd @atom:ca + @angle:f-py-nf @atom:f @atom:py @atom:nf + @angle:ca-nh-cf @atom:ca @atom:nh @atom:cf + @angle:cf-cx-cx @atom:cf @atom:cx @atom:cx + @angle:py-nf-py @atom:py @atom:nf @atom:py + @angle:c-cc-ss @atom:c @atom:cc @atom:ss + @angle:cc-na-cx @atom:cc @atom:na @atom:cx + @angle:c2-cf-cx @atom:c2 @atom:cf @atom:cx + @angle:ce-cd-os @atom:ce @atom:cd @atom:os + @angle:cd-cc-cx @atom:cd @atom:cc @atom:cx + @angle:cf-n1-n1 @atom:cf @atom:n1 @atom:n1 + @angle:cf-n-hn @atom:cf @atom:n @atom:hn + @angle:ce-ce-nf @atom:ce @atom:ce @atom:nf + @angle:cf-no-o @atom:cf @atom:no @atom:o + @angle:h4-cf-nh @atom:h4 @atom:cf @atom:nh + @angle:nf-c-s @atom:nf @atom:c @atom:s + @angle:na-cd-sh @atom:na @atom:cd @atom:sh + @angle:cc-cy-hc @atom:cc @atom:cy @atom:hc + @angle:cf-cc-na @atom:cf @atom:cc @atom:na + @angle:c-cf-h4 @atom:c @atom:cf @atom:h4 + @angle:ce-cd-n @atom:ce @atom:cd @atom:n + @angle:cf-c3-h2 @atom:cf @atom:c3 @atom:h2 + @angle:na-cc-na @atom:na @atom:cc @atom:na + @angle:ch-ca-nb @atom:ch @atom:ca @atom:nb + @angle:cf-c2-f @atom:cf @atom:c2 @atom:f + @angle:cg-cc-nc @atom:cg @atom:cc @atom:nc + @angle:h5-cd-n2 @atom:h5 @atom:cd @atom:n2 + @angle:cd-c3-cf @atom:cd @atom:c3 @atom:cf + @angle:nf-cc-ss @atom:nf @atom:cc @atom:ss + @angle:na-cc-nf @atom:na @atom:cc @atom:nf + @angle:nf-cf-ne @atom:nf @atom:cf @atom:ne + @angle:n-cd-os @atom:n @atom:cd @atom:os + @angle:ce-cf-os @atom:ce @atom:cf @atom:os + @angle:br-cf-c2 @atom:br @atom:cf @atom:c2 + @angle:cq-nb-na @atom:cq @atom:nb @atom:na + @angle:cc-ce-nf @atom:cc @atom:ce @atom:nf + @angle:cf-s4-ss @atom:cf @atom:s4 @atom:ss + @angle:br-cd-ss @atom:br @atom:cd @atom:ss + @angle:c-cf-ss @atom:c @atom:cf @atom:ss + @angle:c2-cd-ss @atom:c2 @atom:cd @atom:ss + @angle:n2-s4-nf @atom:n2 @atom:s4 @atom:nf + @angle:nd-c-s @atom:nd @atom:c @atom:s + @angle:c2-cf-ss @atom:c2 @atom:cf @atom:ss + @angle:cd-cd-ne @atom:cd @atom:cd @atom:ne + @angle:ca-nc-cc @atom:ca @atom:nc @atom:cc + @angle:cd-n2-oh @atom:cd @atom:n2 @atom:oh + @angle:ca-cf-n @atom:ca @atom:cf @atom:n + @angle:h4-cf-sx @atom:h4 @atom:cf @atom:sx + @angle:c3-cf-nf @atom:c3 @atom:cf @atom:nf + @angle:c1-n1-cf @atom:c1 @atom:n1 @atom:cf + @angle:c3-n2-cc @atom:c3 @atom:n2 @atom:cc + @angle:ca-cf-ch @atom:ca @atom:cf @atom:ch + @angle:c2-cd-na @atom:c2 @atom:cd @atom:na + @angle:n2-ce-ne @atom:n2 @atom:ce @atom:ne + @angle:nh-cf-nh @atom:nh @atom:cf @atom:nh + @angle:cc-c-nf @atom:cc @atom:c @atom:nf + @angle:cf-cx-os @atom:cf @atom:cx @atom:os + @angle:nb-ca-nf @atom:nb @atom:ca @atom:nf + @angle:br-ca-cq @atom:br @atom:ca @atom:cq + @angle:cd-cf-cd @atom:cd @atom:cf @atom:cd + @angle:cf-ce-sy @atom:cf @atom:ce @atom:sy + @angle:cc-cc-no @atom:cc @atom:cc @atom:no + @angle:cf-c3-f @atom:cf @atom:c3 @atom:f + @angle:cx-cd-na @atom:cx @atom:cd @atom:na + @angle:c3-ce-cd @atom:c3 @atom:ce @atom:cd + @angle:cf-cf-s4 @atom:cf @atom:cf @atom:s4 + @angle:c-c-cf @atom:c @atom:c @atom:cf + @angle:cf-cy-h1 @atom:cf @atom:cy @atom:h1 + @angle:ch-cf-ss @atom:ch @atom:cf @atom:ss + @angle:cf-cv-ss @atom:cf @atom:cv @atom:ss + @angle:c-cx-cf @atom:c @atom:cx @atom:cf + @angle:c3-ss-ce @atom:c3 @atom:ss @atom:ce + @angle:cf-cy-hc @atom:cf @atom:cy @atom:hc + @angle:br-cd-nd @atom:br @atom:cd @atom:nd + @angle:ca-nf-cc @atom:ca @atom:nf @atom:cc + @angle:cd-cc-o @atom:cd @atom:cc @atom:o + @angle:cd-na-sy @atom:cd @atom:na @atom:sy + @angle:ca-c-nd @atom:ca @atom:c @atom:nd + @angle:cc-nf-sy @atom:cc @atom:nf @atom:sy + @angle:nd-ss-ss @atom:nd @atom:ss @atom:ss + @angle:c3-s6-nf @atom:c3 @atom:s6 @atom:nf + @angle:n-nd-nc @atom:n @atom:nd @atom:nc + @angle:nf-c-os @atom:nf @atom:c @atom:os + @angle:br-cf-cf @atom:br @atom:cf @atom:cf + @angle:cd-c2-oh @atom:cd @atom:c2 @atom:oh + @angle:nd-cd-os @atom:nd @atom:cd @atom:os + @angle:br-cf-ce @atom:br @atom:cf @atom:ce + @angle:h5-cf-nf @atom:h5 @atom:cf @atom:nf + @angle:br-cd-ca @atom:br @atom:cd @atom:ca + @angle:cd-c3-s4 @atom:cd @atom:c3 @atom:s4 + @angle:cf-ce-sx @atom:cf @atom:ce @atom:sx + @angle:cd-cd-i @atom:cd @atom:cd @atom:i + @angle:c-ch-cg @atom:c @atom:ch @atom:cg + @angle:cf-c3-hx @atom:cf @atom:c3 @atom:hx + @angle:cf-cf-ch @atom:cf @atom:cf @atom:ch + @angle:cl-cc-nc @atom:cl @atom:cc @atom:nc + @angle:cx-cc-nc @atom:cx @atom:cc @atom:nc + @angle:cd-ch-cg @atom:cd @atom:ch @atom:cg + @angle:cd-sy-oh @atom:cd @atom:sy @atom:oh + } # (end of Angles By Type) + + write_once("In Settings") { + dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X + dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 + dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 + dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value + dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) + dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X + dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X + dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 + dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X + dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated + dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond + dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 + dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 + dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 + dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 + dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 + dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 + dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 + dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 + dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 + dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds + dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 + dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 + dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 + dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 + dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 + dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 + dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. + dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 + dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 + dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 + dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond + dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond + dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated + dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! + dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! + dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 + dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 + dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! + dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! + dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X + dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X + dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 + dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 + dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 + dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 + dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 + dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 + dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 + dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 + dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 + dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X + dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 + dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 + dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 + dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 + dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X + dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X + dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 + dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X + dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X + dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 + dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X + dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 + dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X + dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 + dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 + dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X + dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 + dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X + dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 + dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 + dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 + dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 + dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 + dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 + dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 + dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 + dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 + dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 + dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 + dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 + dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 + dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 + dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 + dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 + dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 + dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond + dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol + dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol + dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X + dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 + dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 + dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 + dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 + dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 + dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond + dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 + dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 + dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 + dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 + dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 + dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 + dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 + dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 + dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 + dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 + dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 + dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 + dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 + dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 + dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 + dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 + dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 + dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 + dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 + dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 + dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 + dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 + dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 + dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 + dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 + dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 + dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 + dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 + dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 + dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 + dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 + dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 + dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 + dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 + dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 + dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 + dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 + dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 + dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 + dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 + dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 + dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 + dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 + dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 + dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 + dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 + dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 + dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 + dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 + dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 + dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 + dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 + dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 + dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 + dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 + dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 + dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 + dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 + dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 + dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 + dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 + dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 + dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 + dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 + dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 + dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 + dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 + dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 + dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 + dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 + dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 + dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 + dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 + dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 + dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 + dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 + dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 + dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 + dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 + dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 + dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 + dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 + dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 + dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 + dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 + dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 + dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 + dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 + dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 + dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 + dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 + dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 + dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond + dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. + dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 + dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 + dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 + dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 + dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 + dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 + dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 + dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 + dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 + dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 + dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 + dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 + dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 + dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 + dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 + dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 + dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 + dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 + dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 + dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 + dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 + dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 + dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 + dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 + dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 + dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 + dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 + dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 + dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 + dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 + dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 + dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 + dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 + dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 + dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 + dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 + dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 + dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 + dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 + dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 + dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 + dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! + dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 + dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW + dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW + dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 + dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 TorType=1 + dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # TorType=1 + dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 TorType=1 + dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK TorType=1 + dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 + dihedral_coeff @dihedral:c3-n4-c3-ca fourier 2 0.156 3 0.0 0.7 2 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:oh-c3-c3-n4 fourier 2 0.144 3 0.0 1.3 2 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c3-n4-c3 fourier 1 0.156 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c-os-p5 fourier 2 2.7 2 180.0 2.0 1 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c-os-p5-o fourier 3 0.8 2 0.0 1.1 1 0.0 0.5 3 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-c3-os-p5 fourier 2 0.383 3 0.0 3.95 1 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:c3-os-p5-o fourier 2 0.8 2 0.0 0.55 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:ca-ca-os-p5 fourier 1 1.75 2 180.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:ca-os-p5-o fourier 2 0.8 2 180.0 0.1 3 0.0 # Junmei, 2015 TorType=1 + dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.5 3 0.0 1.82 1 0.0 # m9 GA AUE=0.9626 RMSE=1.1958 TorType=2 + dihedral_coeff @dihedral:c-n-c2-c2 fourier 2 1.57 2 180.0 1.53 1 180.0 # c25 GA AUE=0.3367 RMSE=0.3900 TorType=2 + dihedral_coeff @dihedral:c3-ss-c2-c2 fourier 2 1.28 2 180.0 1.2 3 180.0 # c39 GA AUE=0.3908 RMSE=0.4760 TorType=2 + dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 5.29 2 180.0 0.4 1 180.0 # c22 GA AUE=2.0091 RMSE=3.0745 TorType=2 + dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.13 3 0.0 0.29 2 180.0 0.11 1 0.0 # c42 GA AUE=0.2975 RMSE=0.3306 TorType=2 + dihedral_coeff @dihedral:n-c-c3-c3 fourier 2 0.0 4 180.0 0.71 2 180.0 # p20 GA AUE=0.5445 RMSE=0.7015 TorType=2 + dihedral_coeff @dihedral:c3-os-c3-c3 fourier 2 0.24 3 0.0 0.16 2 0.0 # p29 GA AUE=0.4256 RMSE=0.5201 TorType=2 + dihedral_coeff @dihedral:ca-nh-n3-c3 fourier 1 1.12 2 0.0 # c115 SS AUE=2.2848 RMSE=2.9445 TorType=2 + dihedral_coeff @dihedral:hs-sh-ss-c3 fourier 2 1.6 3 0.0 2.81 2 0.0 # c223 GA AUE=0.7163 RMSE=0.8348 TorType=2 + dihedral_coeff @dihedral:ho-oh-nh-ca fourier 2 1.43 1 0.0 0.5 2 0.0 # c156 GA AUE=0.4441 RMSE=0.5406 TorType=2 + dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.5 3 0.0 0.93 1 0.0 # m8 GA AUE=0.9322 RMSE=1.0556 TorType=2 + dihedral_coeff @dihedral:c-n-c3-c3 fourier 3 0.1 4 180.0 0.17 3 0.0 1.02 1 180.0 # p19 GA AUE=0.2882 RMSE=0.4031 TorType=2 + dihedral_coeff @dihedral:c2-p2-n-c fourier 2 1.48 2 180.0 2.15 1 180.0 # c88 GA AUE=0.5049 RMSE=0.6214 TorType=2 + dihedral_coeff @dihedral:f-c3-c3-f fourier 2 1.0 3 0.0 0.64 1 180.0 # m7 GA AUE=1.3130 RMSE=1.6963 TorType=2 + dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.36 3 180.0 1.47 1 0.0 # c23 GA AUE=0.0738 RMSE=0.0893 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.21 3 0.0 0.08 1 0.0 # m5 GA AUE=0.2036 RMSE=0.2389 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.08 3 0.0 # m2 SS AUE=0.2468 RMSE=0.2989 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.22 3 0.0 0.25 1 180.0 # m4 GA AUE=0.1732 RMSE=0.2055 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.22 3 0.0 1.97 1 180.0 # m3 GA AUE=0.0868 RMSE=0.1021 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.12 3 0.0 # m1 SS AUE=0.2420 RMSE=0.2944 TorType=2 + dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.18 3 0.0 0.51 1 0.0 # m11 GA AUE=0.1021 RMSE=0.1307 TorType=2 + dihedral_coeff @dihedral:n-c-c3-n fourier 2 0.1 1 180.0 2.12 2 180.0 # p17 GA AUE=0.9129 RMSE=1.0401 TorType=2 + dihedral_coeff @dihedral:oh-c3-c3-os fourier 3 1.01 3 0.0 0.0 2 0.0 0.02 1 180.0 # suger5ring,suger6ring GA AUE=0.6597 RMSE=0.8978 TorType=2 + dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.0 3 0.0 2.61 2 0.0 # c191 GA AUE=0.2324 RMSE=0.3542 TorType=2 + dihedral_coeff @dihedral:c3-n-c-c3 fourier 2 0.26 2 180.0 0.5 1 0.0 # c5 GA AUE=0.9706 RMSE=1.2796 TorType=2 + dihedral_coeff @dihedral:c3-os-c-c3 fourier 3 1.58 1 180.0 3.18 2 180.0 0.73 3 0.0 # c13 GA AUE=0.2469 RMSE=0.2990 TorType=2 + dihedral_coeff @dihedral:hs-sh-c-c3 fourier 2 1.08 2 180.0 1.92 1 180.0 # c18 GA AUE=0.2126 RMSE=0.3029 TorType=2 + dihedral_coeff @dihedral:os-c3-os-c3 fourier 3 0.0 3 180.0 1.24 2 0.0 0.97 1 180.0 # cococ,lactose2,t12 GA AUE=0.8913 RMSE=1.4261 TorType=2 + dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.15 2 0.0 0.89 3 0.0 # c226,p2 GA AUE=0.4785 RMSE=0.5249 TorType=2 + dihedral_coeff @dihedral:o-c-c3-hc fourier 2 0.83 1 0.0 0.04 3 180.0 # CH3COO,CH3COOH GA AUE=0.0144 RMSE=0.0193 TorType=2 + dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 1 0.0 3 0.0 # m19 SS AUE=0.1539 RMSE=0.2110 TorType=2 + dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.9 3 0.0 1.13 2 0.0 # p5,ch2oh2 GA AUE=0.9894 RMSE=1.1930 TorType=2 + dihedral_coeff @dihedral:os-c3-c3-os fourier 3 0.0 3 0.0 0.0 2 180.0 0.17 1 180.0 # p28,suger5ring,suger6ring,coccoc GA AUE=1.1750 RMSE=1.6708 TorType=2 + dihedral_coeff @dihedral:c1-c1-c3-c1 fourier 1 0.0 2 0.0 # t5 SS AUE=0.0048 RMSE=0.0058 TorType=3 + dihedral_coeff @dihedral:c2-c2-c3-c2 fourier 1 0.112 2 0.0 # t4 SS AUE=0.5917 RMSE=0.7276 TorType=3 + dihedral_coeff @dihedral:c2-ce-ca-ca fourier 1 0.505 2 180.0 # add6f SS AUE=0.2273 RMSE=0.3302 TorType=3 + dihedral_coeff @dihedral:c2-ce-ce-c3 fourier 1 0.5 2 180.0 # set1_2 SS AUE=0.6541 RMSE=0.8643 TorType=3 + dihedral_coeff @dihedral:c2-cf-cd-cc fourier 1 0.5 2 180.0 # add6d SS AUE=0.3708 RMSE=0.4956 TorType=3 + dihedral_coeff @dihedral:c2-n2-c3-n2 fourier 2 1.57 2 180.0 2.73 1 180.0 # t14 GA AUE=1.3428 RMSE=1.6221 TorType=3 + dihedral_coeff @dihedral:c2-n2-na-cd fourier 1 1.575 2 180.0 # c99 SS AUE=0.2455 RMSE=0.3271 TorType=3 + dihedral_coeff @dihedral:c2-n2-n-c fourier 1 2.79 1 180.0 # c80 SS AUE=2.1704 RMSE=2.7351 TorType=3 + dihedral_coeff @dihedral:c2-n2-nh-c2 fourier 1 1.2 2 0.0 # set3_6 SS AUE=1.7161 RMSE=2.4147 TorType=3 + dihedral_coeff @dihedral:c2-ne-ca-ca fourier 1 0.495 3 0.0 # c63 SS AUE=1.1301 RMSE=1.4142 TorType=3 + dihedral_coeff @dihedral:c2-ne-ce-c2 fourier 1 0.17 2 180.0 # c26 SS AUE=0.7462 RMSE=0.9083 TorType=3 + dihedral_coeff @dihedral:c2-ne-ce-c3 fourier 1 0.82 2 0.0 # set1_6 SS AUE=0.2966 RMSE=0.4200 TorType=3 + dihedral_coeff @dihedral:c2-nh-c2-c2 fourier 1 0.98 2 180.0 # set3_2 SS AUE=0.5762 RMSE=0.7682 TorType=3 + dihedral_coeff @dihedral:c2-nh-c2-c3 fourier 1 3.14 2 180.0 # set3_26 SS AUE=0.5612 RMSE=0.7360 TorType=3 + dihedral_coeff @dihedral:c2-nh-c3-h1 fourier 1 0.4 3 0.0 # set3_3 SS AUE=0.2455 RMSE=0.3092 TorType=3 + dihedral_coeff @dihedral:c2-nh-ca-ca fourier 1 0.55 2 180.0 # set3_4 SS AUE=0.8992 RMSE=1.3720 TorType=3 + dihedral_coeff @dihedral:c2-nh-nh-c2 fourier 1 2.93 3 0.0 # set3_24 SS AUE=2.3906 RMSE=3.0117 TorType=3 + dihedral_coeff @dihedral:c2-p2-c3-p2 fourier 1 2.07 1 180.0 # t18 SS AUE=0.4761 RMSE=0.6635 TorType=3 + dihedral_coeff @dihedral:c2-p2-n4-hn fourier 1 0.0 3 180.0 # c133 SS AUE=0.2623 RMSE=0.3265 TorType=3 + dihedral_coeff @dihedral:c2-p2-na-cc fourier 1 1.83 2 180.0 # c146 SS AUE=0.3236 RMSE=0.3673 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-c2 fourier 1 1.33 2 180.0 # set3_14 SS AUE=0.4660 RMSE=0.7730 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-c3 fourier 1 2.4 2 180.0 # c119 SS AUE=1.0662 RMSE=1.4725 TorType=3 + dihedral_coeff @dihedral:c2-p2-nh-ca fourier 1 1.88 1 180.0 # c158 SS AUE=1.5854 RMSE=1.8810 TorType=3 + dihedral_coeff @dihedral:c2-pe-ca-ca fourier 1 1.065 2 180.0 # c71 SS AUE=0.2838 RMSE=0.3291 TorType=3 + dihedral_coeff @dihedral:c2-pe-ce-c2 fourier 1 0.825 2 180.0 # c34 SS AUE=0.3082 RMSE=0.3467 TorType=3 + dihedral_coeff @dihedral:c2-pe-ce-c3 fourier 1 3.64 1 180.0 # set1_14 SS AUE=0.2869 RMSE=0.3329 TorType=3 + dihedral_coeff @dihedral:c2-pe-ne-c2 fourier 1 0.29 1 0.0 # c104 SS AUE=0.4118 RMSE=0.5379 TorType=3 + dihedral_coeff @dihedral:c2-pe-pe-c2 fourier 1 0.68 2 180.0 # c196 SS AUE=0.2486 RMSE=0.3241 TorType=3 + dihedral_coeff @dihedral:c3-c2-nh-ca fourier 2 1.16 2 180.0 1.88 1 0.0 # set1_10 GA AUE=0.3625 RMSE=0.5970 TorType=3 + dihedral_coeff @dihedral:c3-c3-c3-hc fourier 1 0.08 3 0.0 # t2 SS AUE=0.2507 RMSE=0.3027 TorType=3 + dihedral_coeff @dihedral:c3-c3-cc-ca fourier 1 0.082 3 0.0 # p3 SS AUE=0.4586 RMSE=0.5633 TorType=3 + dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.65 4 180.0 0.03 3 180.0 2.26 1 0.0 # sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3 + dihedral_coeff @dihedral:c3-c-c3-c3 fourier 1 0.332 2 180.0 # p10 SS AUE=0.3226 RMSE=0.4401 TorType=3 + dihedral_coeff @dihedral:c3-c-ce-c3 fourier 1 4.11 2 0.0 # set3_25 SS AUE=0.6933 RMSE=1.1187 TorType=3 + dihedral_coeff @dihedral:c3-ce-ce-c3 fourier 1 0.5 2 180.0 # set3_22 SS AUE=1.0809 RMSE=1.3455 TorType=3 + dihedral_coeff @dihedral:c3-n2-c2-c3 fourier 1 10.37 2 180.0 # c7 SS AUE=1.1629 RMSE=1.3902 TorType=3 + dihedral_coeff @dihedral:c3-n3-n3-c3 fourier 1 2.31 2 0.0 # c112 SS AUE=0.8815 RMSE=1.0390 TorType=3 + dihedral_coeff @dihedral:c3-n3-nh-c2 fourier 1 1.355 2 0.0 # set3_7 SS AUE=1.4104 RMSE=1.6750 TorType=3 + dihedral_coeff @dihedral:c3-n4-ca-ca fourier 1 1.495 2 0.0 # c65 SS AUE=0.2872 RMSE=0.3575 TorType=3 + dihedral_coeff @dihedral:c3-n4-n4-c3 fourier 1 0.244 3 0.0 # c127 SS AUE=0.6207 RMSE=0.7993 TorType=3 + dihedral_coeff @dihedral:c3-nh-c2-c2 fourier 2 0.95 2 180.0 1.12 3 180.0 # c27 GA AUE=0.7690 RMSE=1.0440 TorType=3 + dihedral_coeff @dihedral:c3-nh-c2-c3 fourier 1 2.495 2 180.0 # set1_7 SS AUE=0.8853 RMSE=1.2321 TorType=3 + dihedral_coeff @dihedral:c3-os-c2-c2 fourier 2 2.52 2 180.0 2.0 1 180.0 # c33 GA AUE=0.9155 RMSE=1.0796 TorType=3 + dihedral_coeff @dihedral:c3-os-c2-c3 fourier 1 4.79 2 180.0 # set1_13 SS AUE=0.9973 RMSE=1.5097 TorType=3 + dihedral_coeff @dihedral:c3-os-c3-h1 fourier 1 0.337 3 0.0 # c52 SS AUE=0.2706 RMSE=0.3300 TorType=3 + dihedral_coeff @dihedral:c3-os-ca-ca fourier 1 1.61 2 180.0 # c70 SS AUE=0.3151 RMSE=0.3580 TorType=3 + dihedral_coeff @dihedral:c3-os-n2-c2 fourier 2 2.2 2 180.0 0.9 3 180.0 # c103 SS AUE=1.2430 RMSE=1.4817 TorType=3 + dihedral_coeff @dihedral:c3-os-n3-c3 fourier 1 0.84 2 0.0 # c118 SS AUE=0.7374 RMSE=0.9683 TorType=3 + dihedral_coeff @dihedral:c3-os-n4-c3 fourier 1 0.62 3 180.0 # c132 SS AUE=0.8090 RMSE=0.9444 TorType=3 + dihedral_coeff @dihedral:c3-os-na-cc fourier 1 0.19 2 0.0 # c145 SS AUE=0.2720 RMSE=0.3305 TorType=3 + dihedral_coeff @dihedral:c3-os-n-c fourier 1 0.42 2 0.0 # c87 SS AUE=0.3019 RMSE=0.3567 TorType=3 + dihedral_coeff @dihedral:c3-os-nh-c2 fourier 1 1.15 1 0.0 # set3_13 SS AUE=0.9655 RMSE=1.1845 TorType=3 + dihedral_coeff @dihedral:c3-os-nh-ca fourier 1 0.5 1 0.0 # c157 SS AUE=0.8647 RMSE=1.0585 TorType=3 + dihedral_coeff @dihedral:c3-os-no-o fourier 1 2.515 2 180.0 # c168 SS AUE=0.3706 RMSE=0.4248 TorType=3 + dihedral_coeff @dihedral:c3-os-oh-ho fourier 1 1.01 2 0.0 # c178 SS AUE=0.2810 RMSE=0.3796 TorType=3 + dihedral_coeff @dihedral:c3-os-os-c3 fourier 1 0.38 1 0.0 # c187 SS AUE=0.4838 RMSE=0.6593 TorType=3 + dihedral_coeff @dihedral:c3-os-p2-c2 fourier 2 2.94 2 180.0 1.85 1 180.0 # c188 GA AUE=0.3661 RMSE=0.4565 TorType=3 + dihedral_coeff @dihedral:c3-p3-c2-c2 fourier 1 0.297 2 0.0 # c35 SS AUE=1.0902 RMSE=1.4763 TorType=3 + dihedral_coeff @dihedral:c3-p3-c2-c3 fourier 1 0.95 2 180.0 # set1_15 SS AUE=0.4182 RMSE=0.4905 TorType=3 + dihedral_coeff @dihedral:c3-p3-ca-ca fourier 1 0.177 2 180.0 # c72 SS AUE=0.2797 RMSE=0.3319 TorType=3 + dihedral_coeff @dihedral:c3-p3-n2-c2 fourier 1 5.0 2 180.0 # c105 SS AUE=0.8649 RMSE=1.0889 TorType=3 + dihedral_coeff @dihedral:c3-p3-n3-c3 fourier 1 2.85 2 0.0 # c120 SS AUE=0.8776 RMSE=1.2067 TorType=3 + dihedral_coeff @dihedral:c3-p3-n4-c3 fourier 1 0.067 3 0.0 # c134 SS AUE=0.1760 RMSE=0.2433 TorType=3 + dihedral_coeff @dihedral:c3-p3-na-cc fourier 1 1.025 2 0.0 # c147 SS AUE=0.2741 RMSE=0.3331 TorType=3 + dihedral_coeff @dihedral:c3-p3-n-c fourier 1 1.83 2 0.0 # c89 SS AUE=0.9690 RMSE=1.3708 TorType=3 + dihedral_coeff @dihedral:c3-p3-nh-c2 fourier 1 1.85 2 0.0 # set3_15 SS AUE=0.8611 RMSE=0.9832 TorType=3 + dihedral_coeff @dihedral:c3-p3-no-o fourier 1 1.4 2 180.0 # c170 SS AUE=0.5082 RMSE=0.5728 TorType=3 + dihedral_coeff @dihedral:c3-p3-oh-ho fourier 1 0.24 3 180.0 # c180 SS AUE=0.9983 RMSE=1.2838 TorType=3 + dihedral_coeff @dihedral:c3-p3-p2-c2 fourier 1 0.2 1 0.0 # c197 SS AUE=0.5014 RMSE=0.7016 TorType=3 + dihedral_coeff @dihedral:c3-p3-p3-c3 fourier 1 0.375 3 0.0 # c204 SS AUE=0.8032 RMSE=0.9405 TorType=3 + dihedral_coeff @dihedral:c3-p4-n3-c3 fourier 1 1.778 2 180.0 # c121 SS AUE=1.1246 RMSE=1.4091 TorType=3 + dihedral_coeff @dihedral:c3-p4-n4-hn fourier 1 0.005 3 0.0 # c135 SS AUE=0.2627 RMSE=0.3254 TorType=3 + dihedral_coeff @dihedral:c3-p4-na-cc fourier 2 1.0 3 0.0 0.64 2 180.0 # c148 GA AUE=0.9954 RMSE=1.1119 TorType=3 + dihedral_coeff @dihedral:c3-p4-nh-c2 fourier 1 0.9 1 0.0 # set3_16 SS AUE=1.0315 RMSE=1.1976 TorType=3 + dihedral_coeff @dihedral:c3-p4-nh-ca fourier 2 0.0 3 180.0 0.84 2 180.0 # c160 GA AUE=1.0676 RMSE=1.4622 TorType=3 + dihedral_coeff @dihedral:c3-p4-os-c3 fourier 1 0.6 2 180.0 # c190 SS AUE=0.5663 RMSE=0.6640 TorType=3 + dihedral_coeff @dihedral:c3-p4-p3-c3 fourier 1 1.4 1 0.0 # c205 SS AUE=0.7593 RMSE=0.9141 TorType=3 + dihedral_coeff @dihedral:c3-px-ca-ca fourier 1 0.432 2 180.0 # c73 SS AUE=0.4755 RMSE=0.6108 TorType=3 + dihedral_coeff @dihedral:c3-px-c-c3 fourier 2 0.0 2 0.0 0.58 1 180.0 # c16 GA AUE=1.0361 RMSE=1.3175 TorType=3 + dihedral_coeff @dihedral:c3-px-ce-c2 fourier 1 1.13 2 0.0 # c36 SS AUE=1.2444 RMSE=1.6024 TorType=3 + dihedral_coeff @dihedral:c3-px-ce-c3 fourier 1 0.81 2 180.0 # set1_16 SS AUE=0.9969 RMSE=1.2788 TorType=3 + dihedral_coeff @dihedral:c3-px-ne-c2 fourier 2 0.61 3 0.0 1.44 1 0.0 # c106 GA AUE=1.6606 RMSE=2.1207 TorType=3 + dihedral_coeff @dihedral:c3-px-pe-c2 fourier 1 1.565 2 0.0 # c198 SS AUE=1.0967 RMSE=1.2917 TorType=3 + dihedral_coeff @dihedral:c3-s4-c3-h1 fourier 1 0.117 3 0.0 # c59 SS AUE=0.2210 RMSE=0.2792 TorType=3 + dihedral_coeff @dihedral:c3-s4-n3-c3 fourier 1 3.1 2 0.0 # c125 SS AUE=1.3654 RMSE=1.8896 TorType=3 + dihedral_coeff @dihedral:c3-s4-n4-c3 fourier 1 0.2 3 0.0 # c139 SS AUE=0.7713 RMSE=0.9400 TorType=3 + dihedral_coeff @dihedral:c3-s4-na-cc fourier 1 0.55 2 0.0 # c152 SS AUE=0.5159 RMSE=0.7408 TorType=3 + dihedral_coeff @dihedral:c3-s4-nh-c2 fourier 3 0.235 2 180.0 0.5 3 0.0 1.302 1 0.0 # set3_20 GA AUE=1.5742 RMSE=1.9736 TorType=3 + dihedral_coeff @dihedral:c3-s4-no-o fourier 1 1.13 2 180.0 # c175 SS AUE=0.7753 RMSE=0.8760 TorType=3 + dihedral_coeff @dihedral:c3-s4-oh-ho fourier 1 0.0 1 180.0 # c185 SS AUE=1.7272 RMSE=2.1061 TorType=3 + dihedral_coeff @dihedral:c3-s4-os-c3 fourier 1 1.31 1 180.0 # c194 SS AUE=0.9618 RMSE=1.1506 TorType=3 + dihedral_coeff @dihedral:c3-s4-p3-c3 fourier 1 2.22 2 0.0 # c209 SS AUE=1.9189 RMSE=2.5861 TorType=3 + dihedral_coeff @dihedral:c3-s4-sh-hs fourier 2 0.0 3 0.0 0.56 2 180.0 # c224 GA AUE=1.1511 RMSE=1.3863 TorType=3 + dihedral_coeff @dihedral:c3-s4-ss-c3 fourier 1 0.05 3 0.0 # c227 SS AUE=0.7707 RMSE=0.9378 TorType=3 + dihedral_coeff @dihedral:c3-s6-c3-h1 fourier 1 0.089 3 0.0 # c60 SS AUE=0.0648 RMSE=0.0808 TorType=3 + dihedral_coeff @dihedral:c3-s6-n3-c3 fourier 1 3.61 2 0.0 # c126 SS AUE=1.8933 RMSE=2.6424 TorType=3 + dihedral_coeff @dihedral:c3-s6-n4-c3 fourier 1 1.47 1 0.0 # c140 SS AUE=0.2994 RMSE=0.3260 TorType=3 + dihedral_coeff @dihedral:c3-s6-na-cc fourier 1 3.938 2 180.0 # c153 SS AUE=0.8118 RMSE=1.0393 TorType=3 + dihedral_coeff @dihedral:c3-s6-n-c fourier 1 0.768 2 180.0 # c95 SS AUE=0.4645 RMSE=0.6488 TorType=3 + dihedral_coeff @dihedral:c3-s6-nh-c2 fourier 1 0.667 2 0.0 # set3_21 SS AUE=1.6191 RMSE=2.2150 TorType=3 + dihedral_coeff @dihedral:c3-s6-no-o fourier 1 0.348 2 0.0 # c176 SS AUE=0.2701 RMSE=0.3306 TorType=3 + dihedral_coeff @dihedral:c3-s6-oh-ho fourier 1 11.69 1 180.0 # c186 SS AUE=0.6401 RMSE=0.8081 TorType=3 + dihedral_coeff @dihedral:c3-s6-os-c3 fourier 1 0.533 2 180.0 # c195 SS AUE=0.9691 RMSE=1.1571 TorType=3 + dihedral_coeff @dihedral:c3-s6-p3-c3 fourier 1 0.183 3 0.0 # c210 SS AUE=0.5556 RMSE=0.6476 TorType=3 + dihedral_coeff @dihedral:c3-s6-sh-hs fourier 1 4.317 2 180.0 # c225 SS AUE=1.0170 RMSE=1.0970 TorType=3 + dihedral_coeff @dihedral:c3-s6-ss-c3 fourier 1 2.4 2 180.0 # c228 SS AUE=0.8201 RMSE=1.0146 TorType=3 + dihedral_coeff @dihedral:c3-ss-c2-c3 fourier 1 2.025 2 180.0 # set1_19 SS AUE=0.5269 RMSE=0.6098 TorType=3 + dihedral_coeff @dihedral:c3-ss-c3-c3 fourier 1 0.167 3 0.0 # p9 SS AUE=0.4614 RMSE=0.5750 TorType=3 + dihedral_coeff @dihedral:c3-ss-c3-h1 fourier 1 0.22 3 0.0 # c58 SS AUE=0.2551 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:c3-ss-ca-ca fourier 1 0.75 2 180.0 # c76 SS AUE=0.2509 RMSE=0.3297 TorType=3 + dihedral_coeff @dihedral:c3-ss-n2-c2 fourier 2 1.35 2 180.0 1.38 1 180.0 # c109 GA AUE=0.6324 RMSE=0.7825 TorType=3 + dihedral_coeff @dihedral:c3-ss-n3-c3 fourier 1 2.68 2 0.0 # c124 SS AUE=1.0072 RMSE=1.2488 TorType=3 + dihedral_coeff @dihedral:c3-ss-n4-c3 fourier 1 0.39 3 0.0 # c138 SS AUE=0.3868 RMSE=0.4909 TorType=3 + dihedral_coeff @dihedral:c3-ss-n-c fourier 1 0.5 2 0.0 # c93 SS AUE=0.5560 RMSE=0.7560 TorType=3 + dihedral_coeff @dihedral:c3-ss-nh-c2 fourier 1 1.1 2 0.0 # set3_19 SS AUE=0.9372 RMSE=1.1240 TorType=3 + dihedral_coeff @dihedral:c3-ss-no-o fourier 1 2.295 2 180.0 # c174 SS AUE=0.3406 RMSE=0.3839 TorType=3 + dihedral_coeff @dihedral:c3-ss-oh-ho fourier 1 2.13 2 0.0 # c184 SS AUE=0.2806 RMSE=0.3277 TorType=3 + dihedral_coeff @dihedral:c3-ss-os-c3 fourier 1 1.74 2 0.0 # c193 SS AUE=0.5504 RMSE=0.6616 TorType=3 + dihedral_coeff @dihedral:c3-ss-p2-c2 fourier 1 2.97 2 180.0 # c201 SS AUE=0.8463 RMSE=1.2678 TorType=3 + dihedral_coeff @dihedral:c3-ss-p3-c3 fourier 1 3.75 2 0.0 # c208 SS AUE=0.5096 RMSE=0.5972 TorType=3 + dihedral_coeff @dihedral:c3-ss-p4-c3 fourier 1 0.57 2 180.0 # c214 SS AUE=0.7214 RMSE=0.9325 TorType=3 + dihedral_coeff @dihedral:c3-sx-ca-ca fourier 1 0.64 2 0.0 # c77 SS AUE=0.6566 RMSE=0.8245 TorType=3 + dihedral_coeff @dihedral:c3-sx-ce-c2 fourier 2 1.46 2 0.0 1.5 3 180.0 # c40 GA AUE=1.8189 RMSE=2.2140 TorType=3 + dihedral_coeff @dihedral:c3-sx-ce-c3 fourier 3 1.5 3 0.0 4.16 2 0.0 3.1 1 180.0 # set1_20 GA AUE=2.1436 RMSE=3.2053 TorType=3 + dihedral_coeff @dihedral:c3-sx-ne-c2 fourier 2 1.0 3 180.0 1.9 1 180.0 # c110 GA AUE=1.5150 RMSE=1.7663 TorType=3 + dihedral_coeff @dihedral:c3-sx-pe-c2 fourier 1 4.19 2 0.0 # c202 SS AUE=2.6033 RMSE=3.2866 TorType=3 + dihedral_coeff @dihedral:c3-sx-px-c3 fourier 1 2.67 1 0.0 # c215 SS AUE=0.8306 RMSE=1.0179 TorType=3 + dihedral_coeff @dihedral:c3-sx-sx-c3 fourier 1 2.92 1 0.0 # c229 SS AUE=2.7179 RMSE=3.6787 TorType=3 + dihedral_coeff @dihedral:c3-sx-sy-c3 fourier 1 4.94 2 180.0 # c230 SS AUE=1.7022 RMSE=1.9951 TorType=3 + dihedral_coeff @dihedral:c3-sy-ca-ca fourier 1 1.22 2 180.0 # c78 SS AUE=0.2941 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:c3-sy-ce-c2 fourier 1 0.935 2 180.0 # c41 SS AUE=0.9708 RMSE=1.2822 TorType=3 + dihedral_coeff @dihedral:c3-sy-ce-c3 fourier 3 0.64 3 0.0 0.333 2 180.0 1.04 1 180.0 # set1_21 GA AUE=0.6383 RMSE=0.7388 TorType=3 + dihedral_coeff @dihedral:c3-sy-ne-c2 fourier 2 0.34 3 180.0 7.467 1 180.0 # c111 GA AUE=0.2248 RMSE=0.3231 TorType=3 + dihedral_coeff @dihedral:c3-sy-pe-c2 fourier 1 0.237 3 180.0 # c203 SS AUE=0.3743 RMSE=0.4294 TorType=3 + dihedral_coeff @dihedral:c3-sy-px-c3 fourier 1 0.062 3 0.0 # c216 SS AUE=0.6353 RMSE=0.7537 TorType=3 + dihedral_coeff @dihedral:c3-sy-sy-c3 fourier 1 0.378 2 0.0 # c231 SS AUE=1.1799 RMSE=1.3634 TorType=3 + dihedral_coeff @dihedral:ca-c3-c3-c fourier 1 0.1 3 0.0 # p22 SS AUE=0.8008 RMSE=1.0051 TorType=3 + dihedral_coeff @dihedral:ca-c3-c3-n fourier 1 0.21 3 0.0 # p16 SS AUE=0.6330 RMSE=0.8053 TorType=3 + dihedral_coeff @dihedral:ca-ca-c3-ca fourier 1 0.0 2 180.0 # t1 SS AUE=0.1988 RMSE=0.2606 TorType=3 + dihedral_coeff @dihedral:ca-ca-ce-c2 fourier 1 0.618 2 180.0 # c24 SS AUE=0.2364 RMSE=0.3330 TorType=3 + dihedral_coeff @dihedral:ca-ca-ce-c3 fourier 1 0.54 2 180.0 # set1_4 SS AUE=0.2602 RMSE=0.3333 TorType=3 + dihedral_coeff @dihedral:ca-ca-os-c fourier 1 0.65 2 180.0 # t35b SS AUE=0.2491 RMSE=0.3333 TorType=3 + dihedral_coeff @dihedral:ca-cf-ce-ca fourier 1 8.51 2 180.0 # add6b SS AUE=4.0000 RMSE=5.4296 TorType=3 + dihedral_coeff @dihedral:ca-c-os-c3 fourier 1 2.685 2 180.0 # t36b SS AUE=1.2217 RMSE=1.4489 TorType=3 + dihedral_coeff @dihedral:ca-cp-cp-ca fourier 1 0.795 2 180.0 # c61 SS AUE=0.2914 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:ca-nh-c2-c2 fourier 1 1.92 1 180.0 # c30 SS AUE=0.8599 RMSE=1.1406 TorType=3 + dihedral_coeff @dihedral:ca-nh-n2-c2 fourier 3 1.37 3 180.0 2.0 2 0.0 0.0 1 180.0 # c100 GA AUE=2.0208 RMSE=2.4869 TorType=3 + dihedral_coeff @dihedral:ca-nh-n4-c3 fourier 1 0.1 3 0.0 # c129 SS AUE=1.1901 RMSE=1.4071 TorType=3 + dihedral_coeff @dihedral:ca-nh-na-cd fourier 1 0.7 2 0.0 # c142 SS AUE=0.5118 RMSE=0.8838 TorType=3 + dihedral_coeff @dihedral:ca-nh-n-c fourier 1 0.605 2 0.0 # c84 SS AUE=1.2184 RMSE=1.3197 TorType=3 + dihedral_coeff @dihedral:ca-nh-nh-c2 fourier 1 1.49 3 0.0 # set3_10 SS AUE=2.7548 RMSE=3.5233 TorType=3 + dihedral_coeff @dihedral:ca-nh-nh-ca fourier 1 4.59 1 0.0 # c154 SS AUE=3.6427 RMSE=5.6136 TorType=3 + dihedral_coeff @dihedral:ca-nh-no-o fourier 1 0.62 2 180.0 # c155 SS AUE=1.3263 RMSE=1.9039 TorType=3 + dihedral_coeff @dihedral:ca-nh-p3-c3 fourier 2 1.94 2 180.0 0.54 3 0.0 # c159 GA AUE=0.8724 RMSE=1.1678 TorType=3 + dihedral_coeff @dihedral:ca-nh-p5-os fourier 1 0.467 2 0.0 # c161 SS AUE=0.8323 RMSE=0.9798 TorType=3 + dihedral_coeff @dihedral:ca-nh-s4-c3 fourier 2 1.245 2 0.0 0.225 3 0.0 # c164 GA AUE=1.5450 RMSE=1.8592 TorType=3 + dihedral_coeff @dihedral:ca-nh-s6-c3 fourier 1 1.93 3 0.0 # c165 SS AUE=0.7711 RMSE=0.9257 TorType=3 + dihedral_coeff @dihedral:ca-nh-ss-c3 fourier 2 1.29 2 180.0 1.19 1 180.0 # c163 GA AUE=0.9564 RMSE=1.5597 TorType=3 + dihedral_coeff @dihedral:ca-nh-sy-ca fourier 2 0.1 2 180.0 0.99 3 0.0 # add6a SS AUE=0.6854 RMSE=0.9512 TorType=3 + dihedral_coeff @dihedral:ca-os-c-o fourier 1 1.275 2 180.0 # t35a SS AUE=1.2481 RMSE=1.5211 TorType=3 + dihedral_coeff @dihedral:c-c3-c3-n fourier 1 0.21 3 0.0 # p26 SS AUE=1.0437 RMSE=1.3000 TorType=3 + dihedral_coeff @dihedral:c-c3-n-c fourier 2 0.39 2 180.0 0.64 1 0.0 # p18 GA AUE=0.4030 RMSE=0.5768 TorType=3 + dihedral_coeff @dihedral:cc-na-c2-c2 fourier 1 0.728 2 180.0 # c29 SS AUE=0.2592 RMSE=0.3329 TorType=3 + dihedral_coeff @dihedral:cc-na-c2-c3 fourier 1 1.125 2 180.0 # set1_9 SS AUE=0.3784 RMSE=0.4839 TorType=3 + dihedral_coeff @dihedral:cc-na-ca-ca fourier 1 0.603 2 180.0 # c66 SS AUE=0.2705 RMSE=0.3328 TorType=3 + dihedral_coeff @dihedral:cc-na-na-cd fourier 1 0.4 2 0.0 # c141 SS AUE=0.5320 RMSE=0.6402 TorType=3 + dihedral_coeff @dihedral:cc-na-nh-c2 fourier 1 0.7 2 0.0 # set3_9 SS AUE=0.7727 RMSE=0.9375 TorType=3 + dihedral_coeff @dihedral:cc-n-c-c3 fourier 1 0.5 2 180.0 # set2_9 SS AUE=0.2224 RMSE=0.3240 TorType=3 + dihedral_coeff @dihedral:cd-cc-c3-c3 fourier 1 0.157 3 180.0 # p1 SS AUE=0.2727 RMSE=0.3320 TorType=3 + dihedral_coeff @dihedral:cd-na-c3-na fourier 1 0.023 2 0.0 # t16 SS AUE=0.2606 RMSE=0.3332 TorType=3 + dihedral_coeff @dihedral:c-n-c2-c3 fourier 1 1.51 1 180.0 # set1_5 SS AUE=0.6699 RMSE=0.8754 TorType=3 + dihedral_coeff @dihedral:c-n-c3-n fourier 1 2.08 2 0.0 # t17 SS AUE=0.8425 RMSE=1.0798 TorType=3 + dihedral_coeff @dihedral:c-n-ca-ca fourier 1 0.95 2 180.0 # c62 SS AUE=0.8788 RMSE=0.9694 TorType=3 + dihedral_coeff @dihedral:c-n-n-c fourier 2 3.0 2 180.0 2.49 1 0.0 # c79 GA AUE=1.1290 RMSE=1.3734 TorType=3 + dihedral_coeff @dihedral:c-n-nh-c2 fourier 1 0.6 2 0.0 # set3_5 SS AUE=0.7968 RMSE=0.8909 TorType=3 + dihedral_coeff @dihedral:c-os-c-c3 fourier 1 1.98 1 180.0 # set3_29 SS AUE=0.2568 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:cz-nh-c3-c3 fourier 1 0.248 2 180.0 # p11 SS AUE=0.2819 RMSE=0.3532 TorType=3 + dihedral_coeff @dihedral:h1-c3-n2-c2 fourier 1 0.165 3 180.0 # c45 SS AUE=0.6984 RMSE=0.9045 TorType=3 + dihedral_coeff @dihedral:h1-c3-n3-c3 fourier 1 0.225 3 0.0 # c46 SS AUE=0.2936 RMSE=0.3481 TorType=3 + dihedral_coeff @dihedral:h1-c3-na-cc fourier 1 0.0 2 180.0 # c48 SS AUE=0.0685 RMSE=0.0813 TorType=3 + dihedral_coeff @dihedral:h1-c3-n-c fourier 1 0.0 2 180.0 # c44 SS AUE=0.1670 RMSE=0.1874 TorType=3 + dihedral_coeff @dihedral:h1-c3-nh-ca fourier 1 0.332 2 0.0 # c49 SS AUE=1.0901 RMSE=1.3252 TorType=3 + dihedral_coeff @dihedral:h1-c3-no-o fourier 1 0.0 2 180.0 # c50 SS AUE=0.0210 RMSE=0.0225 TorType=3 + dihedral_coeff @dihedral:h1-c3-os-p5 fourier 1 0.217 3 0.0 # c56 SS AUE=0.3987 RMSE=0.4985 TorType=3 + dihedral_coeff @dihedral:hc-c3-c2-c3 fourier 1 0.31 2 0.0 # set1_3 SS AUE=0.6796 RMSE=0.8466 TorType=3 + dihedral_coeff @dihedral:hc-c3-c3-i fourier 1 0.21 3 0.0 # m6 SS AUE=0.3234 RMSE=0.3857 TorType=3 + dihedral_coeff @dihedral:hc-c3-c3-n3 fourier 1 0.1 3 0.0 # m12 SS AUE=0.1396 RMSE=0.1646 TorType=3 + dihedral_coeff @dihedral:hc-c3-ca-ca fourier 1 0.0 2 180.0 # c43 SS AUE=0.0203 RMSE=0.0347 TorType=3 + dihedral_coeff @dihedral:hc-c3-p2-c2 fourier 1 0.933 2 180.0 # c53 SS AUE=0.3657 RMSE=0.4529 TorType=3 + dihedral_coeff @dihedral:hc-c3-p3-c3 fourier 1 0.145 3 0.0 # c54 SS AUE=0.2605 RMSE=0.3289 TorType=3 + dihedral_coeff @dihedral:hc-c3-p4-c3 fourier 1 0.05 3 0.0 # c55 SS AUE=0.1589 RMSE=0.2005 TorType=3 + dihedral_coeff @dihedral:hn-n3-c3-c3 fourier 1 0.217 3 0.0 # m20 SS AUE=0.7039 RMSE=0.8271 TorType=3 + dihedral_coeff @dihedral:hn-n4-c2-c2 fourier 1 0.082 3 180.0 # c28 SS AUE=0.6341 RMSE=0.7948 TorType=3 + dihedral_coeff @dihedral:hn-n4-c2-c3 fourier 1 0.087 3 0.0 # set1_8 SS AUE=0.2828 RMSE=0.3296 TorType=3 + dihedral_coeff @dihedral:hn-n4-c3-hx fourier 1 0.109 3 0.0 # c47 SS AUE=0.2716 RMSE=0.3296 TorType=3 + dihedral_coeff @dihedral:hn-n4-n2-c2 fourier 1 8.663 2 180.0 # c98 SS AUE=0.3876 RMSE=0.4783 TorType=3 + dihedral_coeff @dihedral:hn-n4-n3-c3 fourier 1 0.188 3 0.0 # c113 SS AUE=0.3464 RMSE=0.4155 TorType=3 + dihedral_coeff @dihedral:hn-n4-na-cd fourier 1 0.15 3 0.0 # c128 SS AUE=0.1276 RMSE=0.1509 TorType=3 + dihedral_coeff @dihedral:hn-n4-n-c fourier 1 1.445 2 0.0 # c82 SS AUE=0.4066 RMSE=0.5885 TorType=3 + dihedral_coeff @dihedral:hn-n4-nh-c2 fourier 1 0.213 3 0.0 # set3_8 SS AUE=0.2620 RMSE=0.3316 TorType=3 + dihedral_coeff @dihedral:hn-nh-na-cd fourier 1 0.802 2 0.0 # c114 SS AUE=0.2869 RMSE=0.3676 TorType=3 + dihedral_coeff @dihedral:ho-oh-c2-c2 fourier 1 1.12 2 180.0 # c32 SS AUE=0.2661 RMSE=0.3303 TorType=3 + dihedral_coeff @dihedral:ho-oh-c2-c3 fourier 1 1.51 1 180.0 # set1_12 SS AUE=1.5331 RMSE=1.7625 TorType=3 + dihedral_coeff @dihedral:ho-oh-c3-h1 fourier 1 0.113 3 0.0 # c51 SS AUE=0.2631 RMSE=0.3230 TorType=3 + dihedral_coeff @dihedral:ho-oh-ca-ca fourier 1 0.835 2 180.0 # c69 SS AUE=0.2718 RMSE=0.3256 TorType=3 + dihedral_coeff @dihedral:ho-oh-n2-c2 fourier 1 2.37 2 180.0 # c102 SS AUE=0.3163 RMSE=0.3944 TorType=3 + dihedral_coeff @dihedral:ho-oh-n3-c3 fourier 1 1.23 2 0.0 # c117 SS AUE=0.7804 RMSE=0.9479 TorType=3 + dihedral_coeff @dihedral:ho-oh-n4-c3 fourier 1 0.34 3 0.0 # c131 SS AUE=0.4375 RMSE=0.5350 TorType=3 + dihedral_coeff @dihedral:ho-oh-na-cc fourier 1 0.44 2 0.0 # c144 SS AUE=0.2865 RMSE=0.3255 TorType=3 + dihedral_coeff @dihedral:ho-oh-nh-c2 fourier 1 0.85 2 0.0 # set3_12 SS AUE=0.6311 RMSE=0.7217 TorType=3 + dihedral_coeff @dihedral:ho-oh-no-o fourier 1 1.36 2 180.0 # c167 SS AUE=0.2872 RMSE=0.3226 TorType=3 + dihedral_coeff @dihedral:ho-oh-oh-ho fourier 1 1.21 2 0.0 # c177 SS AUE=0.6716 RMSE=0.7402 TorType=3 + dihedral_coeff @dihedral:ho-oh-p2-c2 fourier 1 1.41 2 180.0 # c179 SS AUE=0.6083 RMSE=0.8611 TorType=3 + dihedral_coeff @dihedral:ho-oh-p4-c3 fourier 1 0.83 1 180.0 # c181 SS AUE=0.8966 RMSE=1.0772 TorType=3 + dihedral_coeff @dihedral:ho-oh-p5-o fourier 1 0.367 3 0.0 # c182 SS AUE=0.8891 RMSE=1.0397 TorType=3 + dihedral_coeff @dihedral:hs-sh-c2-c2 fourier 1 0.64 2 180.0 # c38 SS AUE=0.5356 RMSE=0.6146 TorType=3 + dihedral_coeff @dihedral:hs-sh-c2-c3 fourier 1 1.46 1 180.0 # set1_18 SS AUE=1.6292 RMSE=1.8635 TorType=3 + dihedral_coeff @dihedral:hs-sh-c3-h1 fourier 1 0.143 3 0.0 # c57 SS AUE=0.2676 RMSE=0.3251 TorType=3 + dihedral_coeff @dihedral:hs-sh-ca-ca fourier 1 0.105 2 180.0 # c75 SS AUE=0.2588 RMSE=0.3299 TorType=3 + dihedral_coeff @dihedral:hs-sh-n2-c2 fourier 1 1.91 2 180.0 # c108 SS AUE=0.5066 RMSE=0.9568 TorType=3 + dihedral_coeff @dihedral:hs-sh-n3-c3 fourier 1 3.34 2 0.0 # c123 SS AUE=1.0521 RMSE=1.3809 TorType=3 + dihedral_coeff @dihedral:hs-sh-n4-c3 fourier 1 0.5 3 0.0 # c137 SS AUE=1.0514 RMSE=1.3202 TorType=3 + dihedral_coeff @dihedral:hs-sh-na-cc fourier 1 1.255 2 0.0 # c150 SS AUE=0.2920 RMSE=0.3622 TorType=3 + dihedral_coeff @dihedral:hs-sh-nh-c2 fourier 1 0.795 2 0.0 # set3_18 SS AUE=1.0130 RMSE=1.2554 TorType=3 + dihedral_coeff @dihedral:hs-sh-no-o fourier 1 1.3 2 180.0 # c173 SS AUE=0.2229 RMSE=0.2551 TorType=3 + dihedral_coeff @dihedral:hs-sh-oh-ho fourier 1 2.01 2 0.0 # c183 SS AUE=0.2853 RMSE=0.3308 TorType=3 + dihedral_coeff @dihedral:hs-sh-os-c3 fourier 1 1.85 2 0.0 # c192 SS AUE=0.4441 RMSE=0.5536 TorType=3 + dihedral_coeff @dihedral:hs-sh-p2-c2 fourier 1 0.89 2 180.0 # c200 SS AUE=0.2562 RMSE=0.3521 TorType=3 + dihedral_coeff @dihedral:hs-sh-p3-c3 fourier 1 3.6 2 0.0 # c207 SS AUE=0.5012 RMSE=0.6062 TorType=3 + dihedral_coeff @dihedral:hs-sh-p4-c3 fourier 1 0.585 1 180.0 # c213 SS AUE=1.2130 RMSE=1.4705 TorType=3 + dihedral_coeff @dihedral:hs-sh-p5-os fourier 2 2.89 2 0.0 1.29 1 0.0 # c218 GA AUE=0.8635 RMSE=1.2959 TorType=3 + dihedral_coeff @dihedral:hs-sh-sh-hs fourier 1 2.64 2 0.0 # c222 SS AUE=0.2962 RMSE=0.3759 TorType=3 + dihedral_coeff @dihedral:n2-c2-c3-c2 fourier 1 0.558 2 180.0 # t9 SS AUE=0.7685 RMSE=0.9760 TorType=3 + dihedral_coeff @dihedral:n3-c3-c3-c3 fourier 1 0.21 3 0.0 # p8 SS AUE=0.4096 RMSE=0.5005 TorType=3 + dihedral_coeff @dihedral:n3-c3-c3-ca fourier 1 0.1 3 0.0 # m16 SS AUE=0.8325 RMSE=1.0411 TorType=3 + dihedral_coeff @dihedral:n3-c3-n3-hn fourier 1 1.75 2 0.0 # t13 SS AUE=0.6939 RMSE=0.8306 TorType=3 + dihedral_coeff @dihedral:n4-c3-c3-c3 fourier 1 0.21 3 0.0 # p12 SS AUE=0.5399 RMSE=0.6216 TorType=3 + dihedral_coeff @dihedral:n4-c3-n4-hn fourier 1 0.1 3 0.0 # t26 SS AUE=0.0245 RMSE=0.0373 TorType=3 + dihedral_coeff @dihedral:n-c3-c3-c3 fourier 1 0.1 3 0.0 # p23 SS AUE=0.2641 RMSE=0.3317 TorType=3 + dihedral_coeff @dihedral:nh-c3-c3-c3 fourier 1 0.21 3 0.0 # p13 SS AUE=0.8361 RMSE=0.9491 TorType=3 + dihedral_coeff @dihedral:o-c-c3-c3 fourier 1 0.27 2 180.0 # p14 SS AUE=0.2361 RMSE=0.3321 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-c3 fourier 1 0.21 3 0.0 # p7 SS AUE=0.6517 RMSE=0.7713 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-c fourier 1 0.21 3 0.0 # p25 SS AUE=0.3653 RMSE=0.6406 TorType=3 + dihedral_coeff @dihedral:oh-c3-c3-n fourier 1 0.101 3 0.0 # p24 SS AUE=0.9998 RMSE=1.2475 TorType=3 + dihedral_coeff @dihedral:oh-c3-oh-ho fourier 1 1.57 2 0.0 # t11 SS AUE=0.6180 RMSE=0.8544 TorType=3 + dihedral_coeff @dihedral:o-no-c2-c2 fourier 1 0.398 2 180.0 # c31 SS AUE=0.2143 RMSE=0.3292 TorType=3 + dihedral_coeff @dihedral:o-no-c2-c3 fourier 1 0.66 2 180.0 # set1_11 SS AUE=0.2915 RMSE=0.3323 TorType=3 + dihedral_coeff @dihedral:o-no-c3-no fourier 1 5.02 2 180.0 # t15 SS AUE=0.7609 RMSE=0.9238 TorType=3 + dihedral_coeff @dihedral:o-no-ca-ca fourier 1 0.7 2 180.0 # c68 SS AUE=0.2638 RMSE=0.3293 TorType=3 + dihedral_coeff @dihedral:o-no-cd-cc fourier 1 1.075 2 180.0 # add6e SS AUE=0.2138 RMSE=0.3290 TorType=3 + dihedral_coeff @dihedral:o-no-n2-c2 fourier 1 1.03 2 180.0 # c101 SS AUE=0.3306 RMSE=0.4189 TorType=3 + dihedral_coeff @dihedral:o-no-n3-c3 fourier 1 2.17 2 180.0 # c116 SS AUE=2.5004 RMSE=3.2115 TorType=3 + dihedral_coeff @dihedral:o-no-n4-c3 fourier 1 1.25 2 180.0 # c130 SS AUE=0.1901 RMSE=0.4144 TorType=3 + dihedral_coeff @dihedral:o-no-na-cc fourier 1 1.09 2 180.0 # c143 SS AUE=0.5033 RMSE=0.6912 TorType=3 + dihedral_coeff @dihedral:o-no-nh-c2 fourier 1 0.0 2 180.0 # set3_11 SS AUE=2.0620 RMSE=2.8356 TorType=3 + dihedral_coeff @dihedral:o-no-no-o fourier 2 0.15 4 180.0 1.45 2 180.0 # c166 GA AUE=0.3903 RMSE=0.4419 TorType=3 + dihedral_coeff @dihedral:o-no-p2-c2 fourier 1 0.99 2 180.0 # c169 SS AUE=0.2765 RMSE=0.3321 TorType=3 + dihedral_coeff @dihedral:o-no-p4-c3 fourier 1 0.502 2 180.0 # c171 SS AUE=0.3449 RMSE=0.3960 TorType=3 + dihedral_coeff @dihedral:o-py-ne-c2 fourier 2 0.9 3 180.0 2.46 1 0.0 # c107 GA AUE=0.4990 RMSE=0.6000 TorType=3 + dihedral_coeff @dihedral:o-s4-c3-s4 fourier 1 1.34 1 180.0 # t25 SS AUE=1.1411 RMSE=1.4982 TorType=3 + dihedral_coeff @dihedral:o-s6-c3-s6 fourier 1 0.092 3 0.0 # t24 SS AUE=0.4257 RMSE=0.4949 TorType=3 + dihedral_coeff @dihedral:os-c-c3-c fourier 2 2.0 2 180.0 1.85 1 180.0 # t42 GA AUE=0.4321 RMSE=0.5299 TorType=3 + dihedral_coeff @dihedral:os-p3-os-c3 fourier 1 2.04 2 0.0 # c189 SS AUE=1.0926 RMSE=1.3514 TorType=3 + dihedral_coeff @dihedral:os-p5-n3-c3 fourier 1 5.0 2 180.0 # c122 SS AUE=2.8241 RMSE=3.6042 TorType=3 + dihedral_coeff @dihedral:os-p5-n4-c3 fourier 1 0.143 3 0.0 # c136 SS AUE=0.4630 RMSE=0.6433 TorType=3 + dihedral_coeff @dihedral:os-p5-na-cc fourier 1 2.18 2 180.0 # c149 SS AUE=0.6556 RMSE=0.9113 TorType=3 + dihedral_coeff @dihedral:os-p5-nh-c2 fourier 1 0.5 2 0.0 # set3_17 SS AUE=0.9578 RMSE=1.1771 TorType=3 + dihedral_coeff @dihedral:os-p5-no-o fourier 2 2.733 2 0.0 0.317 3 0.0 # c172 GA AUE=0.6484 RMSE=0.8206 TorType=3 + dihedral_coeff @dihedral:os-p5-p3-c3 fourier 1 2.005 2 180.0 # c206 SS AUE=1.1482 RMSE=1.4324 TorType=3 + dihedral_coeff @dihedral:os-p5-ss-c3 fourier 1 4.467 2 180.0 # c219 SS AUE=0.9050 RMSE=1.1227 TorType=3 + dihedral_coeff @dihedral:os-py-ca-ca fourier 1 1.8 2 180.0 # c74 SS AUE=0.8528 RMSE=1.0796 TorType=3 + dihedral_coeff @dihedral:os-py-ce-c2 fourier 1 1.767 2 180.0 # c37 SS AUE=0.8275 RMSE=1.0644 TorType=3 + dihedral_coeff @dihedral:os-py-ce-c3 fourier 1 4.2 2 180.0 # set1_17 SS AUE=0.9222 RMSE=1.1571 TorType=3 + dihedral_coeff @dihedral:os-py-pe-c2 fourier 1 2.567 1 0.0 # c199 SS AUE=0.6931 RMSE=0.8807 TorType=3 + dihedral_coeff @dihedral:os-py-py-c3 fourier 1 0.386 2 0.0 # c212 SS AUE=0.6618 RMSE=0.8385 TorType=3 + dihedral_coeff @dihedral:os-py-py-os fourier 1 0.387 2 0.0 # c217 SS AUE=0.6636 RMSE=1.0913 TorType=3 + dihedral_coeff @dihedral:os-py-sx-c3 fourier 1 0.348 3 0.0 # c220 SS AUE=0.6436 RMSE=0.8137 TorType=3 + dihedral_coeff @dihedral:os-py-sy-c3 fourier 2 2.86 2 0.0 0.38 1 0.0 # c221 GA AUE=1.1694 RMSE=1.4143 TorType=3 + dihedral_coeff @dihedral:p3-c3-p3-hp fourier 1 0.215 3 0.0 # t19 SS AUE=1.0811 RMSE=1.2418 TorType=3 + dihedral_coeff @dihedral:s-c-c3-c fourier 1 0.332 2 180.0 # t10 SS AUE=0.9021 RMSE=1.2368 TorType=3 + dihedral_coeff @dihedral:sh-c3-c3-n fourier 1 0.21 3 0.0 # p4 SS AUE=1.1296 RMSE=1.3941 TorType=3 + dihedral_coeff @dihedral:sh-c3-sh-hs fourier 1 0.083 3 0.0 # t22 SS AUE=0.4554 RMSE=0.5406 TorType=3 + dihedral_coeff @dihedral:ss-c3-ss-c3 fourier 1 0.497 3 0.0 # t23 SS AUE=0.5714 RMSE=0.8553 TorType=3 + dihedral_coeff @dihedral:c3-c3-ca-ca fourier 1 0.245 2 180.0 # m15,m17 SS AUE=0.2499 RMSE=0.3414 TorType=3 + dihedral_coeff @dihedral:c3-c3-c-o fourier 3 0.03 2 180.0 0.55 3 180.0 0.74 1 0.0 # sialic1,t37,t41 GA AUE=0.7374 RMSE=0.9897 TorType=3 + dihedral_coeff @dihedral:c3-c3-os-c3 fourier 3 0.91 3 0.0 1.0 2 0.0 0.0 1 0.0 # lactose1,ccoc GA AUE=1.5236 RMSE=2.4206 TorType=3 + dihedral_coeff @dihedral:ca-ca-c-o fourier 1 0.5225 2 180.0 # phcooh,t36a SS AUE=0.2702 RMSE=0.3317 TorType=3 + dihedral_coeff @dihedral:o-c-c3-c fourier 2 1.36 1 0.0 0.18 3 180.0 # t6,t7,t8 GA AUE=0.3790 RMSE=0.4991 TorType=3 + dihedral_coeff @dihedral:os-c3-c-o fourier 3 0.63 2 180.0 1.0 3 180.0 0.08 1 0.0 # iduronic2,t39,t40 GA AUE=1.0545 RMSE=1.4852 TorType=3 + dihedral_coeff @dihedral:c2-ce-cs-c3 fourier 1 2.18 2 0.0 # set2_2 SS AUE=0.8412 RMSE=1.0280 TorType=3 + dihedral_coeff @dihedral:c2-ce-c-c3 fourier 1 2.97 2 0.0 # c2 SS AUE=0.5377 RMSE=0.6518 TorType=3 + dihedral_coeff @dihedral:c2-ce-ce-c2 fourier 1 0.5 2 180.0 # c232,t3 SS AUE=0.7154 RMSE=0.9564 TorType=3 + dihedral_coeff @dihedral:c2-n-c-c3 fourier 1 0.77 1 180.0 # set3_1 SS AUE=1.1124 RMSE=1.4578 TorType=3 + dihedral_coeff @dihedral:c2-n-cs-c3 fourier 1 2.833 2 180.0 # set3_27 SS AUE=0.3805 RMSE=0.4661 TorType=3 + dihedral_coeff @dihedral:c2-ne-c-c3 fourier 1 2.08 1 180.0 # c6 SS AUE=0.4876 RMSE=0.8222 TorType=3 + dihedral_coeff @dihedral:c2-ne-cs-c3 fourier 1 4.67 1 180.0 # set2_6 SS AUE=1.2531 RMSE=1.5945 TorType=3 + dihedral_coeff @dihedral:c2-pe-c-c3 fourier 1 1.75 1 180.0 # c14 SS AUE=1.0447 RMSE=1.2490 TorType=3 + dihedral_coeff @dihedral:c2-pe-cs-c3 fourier 1 2.96 1 180.0 # set2_14 SS AUE=0.8598 RMSE=1.0604 TorType=3 + dihedral_coeff @dihedral:c3-cs-cs-c3 fourier 1 0.455 2 180.0 # set3_23 SS AUE=0.7278 RMSE=1.0389 TorType=3 + dihedral_coeff @dihedral:c3-c-c-c3 fourier 1 0.512 2 180.0 # c1 SS AUE=0.2443 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:c3-c-cs-c3 fourier 1 0.8 2 180.0 # set2_1 SS AUE=1.0068 RMSE=1.3922 TorType=3 + dihedral_coeff @dihedral:c3-c-n-ca fourier 2 0.75 2 180.0 0.5 3 0.0 # c10 GA AUE=1.0418 RMSE=1.1578 TorType=3 + dihedral_coeff @dihedral:c3-cs-n-ca fourier 1 3.913 2 180.0 # set2_10 SS AUE=1.3234 RMSE=1.7703 TorType=3 + dihedral_coeff @dihedral:c3-n7-c3-c3 fourier 2 0.02 3 180.0 0.05 2 0.0 # m13 GA AUE=0.3404 RMSE=0.4405 TorType=3 + dihedral_coeff @dihedral:c3-n3-c3-c3 fourier 2 0.58 3 0.0 0.28 2 180.0 # m14 GA AUE=0.4298 RMSE=0.5205 TorType=3 + dihedral_coeff @dihedral:c3-n-cs-c3 fourier 2 2.0 2 180.0 2.31 1 0.0 # set2_7 GA AUE=0.7571 RMSE=0.9582 TorType=3 + dihedral_coeff @dihedral:c3-nu-ca-ca fourier 1 0.55 2 180.0 # c67 SS AUE=0.5825 RMSE=0.8345 TorType=3 + dihedral_coeff @dihedral:c3-nh-ca-ca fourier 1 0.733 2 180.0 # c64 SS AUE=0.6264 RMSE=0.7797 TorType=3 + dihedral_coeff @dihedral:c3-os-cs-c3 fourier 3 0.12 1 0.0 3.47 2 180.0 0.73 3 0.0 # set2_13 GA AUE=0.2180 RMSE=0.2948 TorType=3 + dihedral_coeff @dihedral:c3-p3-c-c3 fourier 1 1.538 2 180.0 # c15 SS AUE=0.3737 RMSE=0.4391 TorType=3 + dihedral_coeff @dihedral:c3-p3-cs-c3 fourier 1 2.05 2 180.0 # set2_15 SS AUE=0.4669 RMSE=0.6407 TorType=3 + dihedral_coeff @dihedral:c3-ss-c-c3 fourier 1 2.1 2 180.0 # c19 SS AUE=0.9147 RMSE=1.1012 TorType=3 + dihedral_coeff @dihedral:c3-ss-cs-c3 fourier 1 3.585 2 180.0 # set2_19 SS AUE=0.3546 RMSE=0.4561 TorType=3 + dihedral_coeff @dihedral:c3-sx-c-c3 fourier 2 0.95 2 0.0 1.46 1 180.0 # c20 GA AUE=1.4077 RMSE=1.8160 TorType=3 + dihedral_coeff @dihedral:c3-sx-cs-c3 fourier 2 0.0 2 180.0 0.82 1 180.0 # set2_20 GA AUE=1.3014 RMSE=1.5331 TorType=3 + dihedral_coeff @dihedral:c3-sy-cs-c3 fourier 1 0.167 2 0.0 # set2_21 SS AUE=0.4320 RMSE=0.5527 TorType=3 + dihedral_coeff @dihedral:c3-sy-c-c3 fourier 1 0.833 2 0.0 # c21 SS AUE=1.1437 RMSE=1.4496 TorType=3 + dihedral_coeff @dihedral:ca-ca-c-c3 fourier 1 0.552 2 180.0 # c4 SS AUE=0.2254 RMSE=0.3313 TorType=3 + dihedral_coeff @dihedral:ca-ca-cs-c3 fourier 1 0.63 2 180.0 # set2_4 SS AUE=0.2690 RMSE=0.3277 TorType=3 + dihedral_coeff @dihedral:c-c3-c3-c3 fourier 1 0.1 3 0.0 # p15,p21 SS AUE=0.6594 RMSE=0.8092 TorType=3 + dihedral_coeff @dihedral:c-n-cs-c3 fourier 1 0.57 2 0.0 # set2_5 SS AUE=1.0844 RMSE=1.5574 TorType=3 + dihedral_coeff @dihedral:c-n-c-c3 fourier 2 0.0 2 180.0 1.72 1 180.0 # set3_28 GA AUE=1.6503 RMSE=2.2241 TorType=3 + dihedral_coeff @dihedral:hc-c3-c-c3 fourier 1 0.0 2 0.0 # c3 SS AUE=0.0845 RMSE=0.1001 TorType=3 + dihedral_coeff @dihedral:hc-c3-cs-c3 fourier 1 0.665 2 0.0 # set2_3 SS AUE=0.5619 RMSE=0.7242 TorType=3 + dihedral_coeff @dihedral:hn-n4-c-c3 fourier 2 1.025 2 180.0 0.365 4 180.0 # c8 GA AUE=0.2852 RMSE=0.3192 TorType=3 + dihedral_coeff @dihedral:hn-n4-cs-c3 fourier 2 0.95 2 180.0 0.745 4 0.0 # set2_8 GA AUE=0.7027 RMSE=0.8556 TorType=3 + dihedral_coeff @dihedral:ho-oh-c-c3 fourier 1 1.78 2 180.0 # c12 SS AUE=0.3293 RMSE=0.3814 TorType=3 + dihedral_coeff @dihedral:ho-oh-cs-c3 fourier 1 2.92 2 180.0 # set2_12 SS AUE=0.3286 RMSE=0.4081 TorType=3 + dihedral_coeff @dihedral:hs-sh-cs-c3 fourier 2 2.69 2 180.0 1.39 1 180.0 # set2_18 GA AUE=0.2516 RMSE=0.2978 TorType=3 + dihedral_coeff @dihedral:o-n-c-c3 fourier 1 0.37 2 180.0 # c11 SS AUE=0.3392 RMSE=0.4173 TorType=3 + dihedral_coeff @dihedral:o-n-cs-c3 fourier 1 0.52 2 0.0 # set2_11 SS AUE=0.2859 RMSE=0.3263 TorType=3 + dihedral_coeff @dihedral:o-p5-c3-p5 fourier 2 2.59 2 180.0 3.17 1 0.0 # t20 GA AUE=1.4330 RMSE=1.6847 TorType=3 + dihedral_coeff @dihedral:os-py-c-c3 fourier 1 2.37 2 0.0 # c17 SS AUE=1.1966 RMSE=1.4736 TorType=3 + dihedral_coeff @dihedral:os-py-cs-c3 fourier 1 0.5 2 0.0 # set2_17 SS AUE=0.8458 RMSE=1.0943 TorType=3 + } # (end of dihedral_coeffs) + + write_once("Data Dihedrals By Type") { + @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* + @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* + @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* + @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* + @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* + @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* + @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* + @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* + @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* + @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* + @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* + @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* + @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* + @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* + @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* + @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* + @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* + @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* + @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* + @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* + @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* + @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* + @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* + @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* + @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* + @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* + @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* + @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* + @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* + @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* + @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* + @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* + @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* + @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* + @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* + @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* + @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* + @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* + @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* + @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* + @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* + @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* + @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* + @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* + @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* + @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* + @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* + @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* + @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* + @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:* + @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:* + @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:* + @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:* + @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:* + @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:* + @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:* + @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:* + @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:* + @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:* + @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:* + @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:* + @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:* + @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:* + @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:* + @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:* + @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:* + @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:* + @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:* + @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:* + @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:* + @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:* + @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:* + @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:* + @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:* + @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:* + @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:* + @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:* + @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:* + @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:* + @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:* + @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:* + @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:* + @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:* + @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:* + @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:* + @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:* + @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:* + @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:* + @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:* + @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:* + @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:* + @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:* + @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:* + @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:* + @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:* + @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:* + @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:* + @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:* + @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:* + @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:* + @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:* + @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:* + @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:* + @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:* + @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:* + @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:* + @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:* + @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:* + @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:* + @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:* + @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:* + @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:* + @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:* + @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:* + @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:* + @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:* + @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:* + @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:* + @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:* + @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:* + @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:* + @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:* + @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:* + @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:* + @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:* + @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:* + @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:* + @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:* + @dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:* + @dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:* + @dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:* + @dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:* + @dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:* + @dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:* + @dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:* + @dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:* + @dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:* + @dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:* + @dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:* + @dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:* + @dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:* + @dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:* + @dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:* + @dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:* + @dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:* + @dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:* + @dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:* + @dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:* + @dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:* + @dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:* + @dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:* + @dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:* + @dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:* + @dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:* + @dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:* + @dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:* + @dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:* + @dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:* + @dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:* + @dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:* + @dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:* + @dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:* + @dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:* + @dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:* + @dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:* + @dihedral:X-cx-n-X @atom:* @atom:cx @atom:n @atom:* + @dihedral:X-cy-n-X @atom:* @atom:cy @atom:n @atom:* + @dihedral:X-c3-n2-X @atom:* @atom:c3 @atom:n2 @atom:* + @dihedral:X-c3-ne-X @atom:* @atom:c3 @atom:ne @atom:* + @dihedral:X-c3-nf-X @atom:* @atom:c3 @atom:nf @atom:* + @dihedral:X-c3-n3-X @atom:* @atom:c3 @atom:n3 @atom:* + @dihedral:X-c3-n4-X @atom:* @atom:c3 @atom:n4 @atom:* + @dihedral:X-c3-na-X @atom:* @atom:c3 @atom:na @atom:* + @dihedral:X-c3-nh-X @atom:* @atom:c3 @atom:nh @atom:* + @dihedral:X-c3-no-X @atom:* @atom:c3 @atom:no @atom:* + @dihedral:X-c3-oh-X @atom:* @atom:c3 @atom:oh @atom:* + @dihedral:X-c3-os-X @atom:* @atom:c3 @atom:os @atom:* + @dihedral:X-c3-p2-X @atom:* @atom:c3 @atom:p2 @atom:* + @dihedral:X-c3-pe-X @atom:* @atom:c3 @atom:pe @atom:* + @dihedral:X-c3-pf-X @atom:* @atom:c3 @atom:pf @atom:* + @dihedral:X-c3-p3-X @atom:* @atom:c3 @atom:p3 @atom:* + @dihedral:X-c3-p4-X @atom:* @atom:c3 @atom:p4 @atom:* + @dihedral:X-c3-px-X @atom:* @atom:c3 @atom:px @atom:* + @dihedral:X-c3-p5-X @atom:* @atom:c3 @atom:p5 @atom:* + @dihedral:X-c3-py-X @atom:* @atom:c3 @atom:py @atom:* + @dihedral:X-c3-sh-X @atom:* @atom:c3 @atom:sh @atom:* + @dihedral:X-c3-ss-X @atom:* @atom:c3 @atom:ss @atom:* + @dihedral:X-c3-s4-X @atom:* @atom:c3 @atom:s4 @atom:* + @dihedral:X-c3-sx-X @atom:* @atom:c3 @atom:sx @atom:* + @dihedral:X-c3-s6-X @atom:* @atom:c3 @atom:s6 @atom:* + @dihedral:X-c3-sy-X @atom:* @atom:c3 @atom:sy @atom:* + @dihedral:X-c3-cc-X @atom:* @atom:c3 @atom:cc @atom:* + @dihedral:X-c3-cd-X @atom:* @atom:c3 @atom:cd @atom:* + @dihedral:X-ca-ca-X @atom:* @atom:ca @atom:ca @atom:* + @dihedral:X-ca-cp-X @atom:* @atom:ca @atom:cp @atom:* + @dihedral:X-ca-cq-X @atom:* @atom:ca @atom:cq @atom:* + @dihedral:X-cp-cp-X @atom:* @atom:cp @atom:cp @atom:* + @dihedral:X-cq-cq-X @atom:* @atom:cq @atom:cq @atom:* + @dihedral:X-ca-n-X @atom:* @atom:ca @atom:n @atom:* + @dihedral:X-ca-n2-X @atom:* @atom:ca @atom:n2 @atom:* + @dihedral:X-ca-ne-X @atom:* @atom:ca @atom:ne @atom:* + @dihedral:X-ca-nf-X @atom:* @atom:ca @atom:nf @atom:* + @dihedral:X-ca-n4-X @atom:* @atom:ca @atom:n4 @atom:* + @dihedral:X-ca-na-X @atom:* @atom:ca @atom:na @atom:* + @dihedral:X-ca-nb-X @atom:* @atom:ca @atom:nb @atom:* + @dihedral:X-ca-nc-X @atom:* @atom:ca @atom:nc @atom:* + @dihedral:X-ca-nd-X @atom:* @atom:ca @atom:nd @atom:* + @dihedral:X-ca-nh-X @atom:* @atom:ca @atom:nh @atom:* + @dihedral:X-cc-nh-X @atom:* @atom:cc @atom:nh @atom:* + @dihedral:X-cd-nh-X @atom:* @atom:cd @atom:nh 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@dihedral:c3-sy-ne-c2 @atom:c3 @atom:sy @atom:ne @atom:c2 + @dihedral:c3-sy-ne-c2 @atom:c3 @atom:sy @atom:ne @atom:c2 + @dihedral:c3-sy-pe-c2 @atom:c3 @atom:sy @atom:pe @atom:c2 + @dihedral:c3-sy-px-c3 @atom:c3 @atom:sy @atom:px @atom:c3 + @dihedral:c3-sy-sy-c3 @atom:c3 @atom:sy @atom:sy @atom:c3 + @dihedral:ca-c3-c3-c @atom:ca @atom:c3 @atom:c3 @atom:c + @dihedral:ca-c3-c3-n @atom:ca @atom:c3 @atom:c3 @atom:n + @dihedral:ca-ca-c3-ca @atom:ca @atom:ca @atom:c3 @atom:ca + @dihedral:ca-ca-ce-c2 @atom:ca @atom:ca @atom:ce @atom:c2 + @dihedral:ca-ca-ce-c3 @atom:ca @atom:ca @atom:ce @atom:c3 + @dihedral:ca-ca-os-c @atom:ca @atom:ca @atom:os @atom:c + @dihedral:ca-cf-ce-ca @atom:ca @atom:cf @atom:ce @atom:ca + @dihedral:ca-c-os-c3 @atom:ca @atom:c @atom:os @atom:c3 + @dihedral:ca-cp-cp-ca @atom:ca @atom:cp @atom:cp @atom:ca + @dihedral:ca-nh-c2-c2 @atom:ca @atom:nh @atom:c2 @atom:c2 + @dihedral:ca-nh-n2-c2 @atom:ca @atom:nh @atom:n2 @atom:c2 + @dihedral:ca-nh-n2-c2 @atom:ca @atom:nh @atom:n2 @atom:c2 + @dihedral:ca-nh-n2-c2 @atom:ca @atom:nh @atom:n2 @atom:c2 + @dihedral:ca-nh-n4-c3 @atom:ca @atom:nh @atom:n4 @atom:c3 + @dihedral:ca-nh-na-cd @atom:ca @atom:nh @atom:na @atom:cd + @dihedral:ca-nh-n-c @atom:ca @atom:nh @atom:n @atom:c + @dihedral:ca-nh-nh-c2 @atom:ca @atom:nh @atom:nh @atom:c2 + @dihedral:ca-nh-nh-ca @atom:ca @atom:nh @atom:nh @atom:ca + @dihedral:ca-nh-no-o @atom:ca @atom:nh @atom:no @atom:o + @dihedral:ca-nh-p3-c3 @atom:ca @atom:nh @atom:p3 @atom:c3 + @dihedral:ca-nh-p3-c3 @atom:ca @atom:nh @atom:p3 @atom:c3 + @dihedral:ca-nh-p5-os @atom:ca @atom:nh @atom:p5 @atom:os + @dihedral:ca-nh-s4-c3 @atom:ca @atom:nh @atom:s4 @atom:c3 + @dihedral:ca-nh-s4-c3 @atom:ca @atom:nh @atom:s4 @atom:c3 + @dihedral:ca-nh-s6-c3 @atom:ca @atom:nh @atom:s6 @atom:c3 + @dihedral:ca-nh-ss-c3 @atom:ca @atom:nh @atom:ss @atom:c3 + @dihedral:ca-nh-ss-c3 @atom:ca @atom:nh @atom:ss @atom:c3 + @dihedral:ca-nh-sy-ca @atom:ca @atom:nh @atom:sy @atom:ca + @dihedral:ca-nh-sy-ca @atom:ca @atom:nh @atom:sy @atom:ca + @dihedral:ca-os-c-o @atom:ca @atom:os @atom:c @atom:o + @dihedral:c-c3-c3-n @atom:c @atom:c3 @atom:c3 @atom:n + @dihedral:c-c3-n-c @atom:c @atom:c3 @atom:n @atom:c + @dihedral:c-c3-n-c @atom:c @atom:c3 @atom:n @atom:c + @dihedral:cc-na-c2-c2 @atom:cc @atom:na @atom:c2 @atom:c2 + @dihedral:cc-na-c2-c3 @atom:cc @atom:na @atom:c2 @atom:c3 + @dihedral:cc-na-ca-ca @atom:cc @atom:na @atom:ca @atom:ca + @dihedral:cc-na-na-cd @atom:cc @atom:na @atom:na @atom:cd + @dihedral:cc-na-nh-c2 @atom:cc @atom:na @atom:nh @atom:c2 + @dihedral:cc-n-c-c3 @atom:cc @atom:n @atom:c @atom:c3 + @dihedral:cd-cc-c3-c3 @atom:cd @atom:cc @atom:c3 @atom:c3 + @dihedral:cd-na-c3-na @atom:cd @atom:na @atom:c3 @atom:na + @dihedral:c-n-c2-c3 @atom:c @atom:n @atom:c2 @atom:c3 + @dihedral:c-n-c3-n @atom:c @atom:n @atom:c3 @atom:n + @dihedral:c-n-ca-ca @atom:c @atom:n @atom:ca @atom:ca + @dihedral:c-n-n-c @atom:c @atom:n @atom:n @atom:c + @dihedral:c-n-n-c @atom:c @atom:n @atom:n @atom:c + @dihedral:c-n-nh-c2 @atom:c @atom:n @atom:nh @atom:c2 + @dihedral:c-os-c-c3 @atom:c @atom:os @atom:c @atom:c3 + @dihedral:cz-nh-c3-c3 @atom:cz @atom:nh @atom:c3 @atom:c3 + @dihedral:h1-c3-n2-c2 @atom:h1 @atom:c3 @atom:n2 @atom:c2 + @dihedral:h1-c3-n3-c3 @atom:h1 @atom:c3 @atom:n3 @atom:c3 + @dihedral:h1-c3-na-cc @atom:h1 @atom:c3 @atom:na @atom:cc + @dihedral:h1-c3-n-c @atom:h1 @atom:c3 @atom:n @atom:c + @dihedral:h1-c3-nh-ca @atom:h1 @atom:c3 @atom:nh @atom:ca + @dihedral:h1-c3-no-o @atom:h1 @atom:c3 @atom:no @atom:o + @dihedral:h1-c3-os-p5 @atom:h1 @atom:c3 @atom:os @atom:p5 + @dihedral:hc-c3-c2-c3 @atom:hc @atom:c3 @atom:c2 @atom:c3 + @dihedral:hc-c3-c3-i @atom:hc @atom:c3 @atom:c3 @atom:i + @dihedral:hc-c3-c3-n3 @atom:hc @atom:c3 @atom:c3 @atom:n3 + @dihedral:hc-c3-ca-ca @atom:hc @atom:c3 @atom:ca @atom:ca + @dihedral:hc-c3-p2-c2 @atom:hc @atom:c3 @atom:p2 @atom:c2 + @dihedral:hc-c3-p3-c3 @atom:hc @atom:c3 @atom:p3 @atom:c3 + @dihedral:hc-c3-p4-c3 @atom:hc @atom:c3 @atom:p4 @atom:c3 + @dihedral:hn-n3-c3-c3 @atom:hn @atom:n3 @atom:c3 @atom:c3 + @dihedral:hn-n4-c2-c2 @atom:hn @atom:n4 @atom:c2 @atom:c2 + @dihedral:hn-n4-c2-c3 @atom:hn @atom:n4 @atom:c2 @atom:c3 + @dihedral:hn-n4-c3-hx @atom:hn @atom:n4 @atom:c3 @atom:hx + @dihedral:hn-n4-n2-c2 @atom:hn @atom:n4 @atom:n2 @atom:c2 + @dihedral:hn-n4-n3-c3 @atom:hn @atom:n4 @atom:n3 @atom:c3 + @dihedral:hn-n4-na-cd @atom:hn @atom:n4 @atom:na @atom:cd + @dihedral:hn-n4-n-c @atom:hn @atom:n4 @atom:n @atom:c + @dihedral:hn-n4-nh-c2 @atom:hn @atom:n4 @atom:nh @atom:c2 + @dihedral:hn-nh-na-cd @atom:hn @atom:nh @atom:na @atom:cd + @dihedral:ho-oh-c2-c2 @atom:ho @atom:oh @atom:c2 @atom:c2 + @dihedral:ho-oh-c2-c3 @atom:ho @atom:oh @atom:c2 @atom:c3 + @dihedral:ho-oh-c3-h1 @atom:ho @atom:oh @atom:c3 @atom:h1 + @dihedral:ho-oh-ca-ca @atom:ho @atom:oh @atom:ca @atom:ca + @dihedral:ho-oh-n2-c2 @atom:ho @atom:oh @atom:n2 @atom:c2 + @dihedral:ho-oh-n3-c3 @atom:ho @atom:oh @atom:n3 @atom:c3 + @dihedral:ho-oh-n4-c3 @atom:ho @atom:oh @atom:n4 @atom:c3 + @dihedral:ho-oh-na-cc @atom:ho @atom:oh @atom:na @atom:cc + @dihedral:ho-oh-nh-c2 @atom:ho @atom:oh @atom:nh @atom:c2 + @dihedral:ho-oh-no-o @atom:ho @atom:oh @atom:no @atom:o + @dihedral:ho-oh-oh-ho @atom:ho @atom:oh @atom:oh @atom:ho + @dihedral:ho-oh-p2-c2 @atom:ho @atom:oh @atom:p2 @atom:c2 + @dihedral:ho-oh-p4-c3 @atom:ho @atom:oh @atom:p4 @atom:c3 + @dihedral:ho-oh-p5-o @atom:ho @atom:oh @atom:p5 @atom:o + @dihedral:hs-sh-c2-c2 @atom:hs @atom:sh @atom:c2 @atom:c2 + @dihedral:hs-sh-c2-c3 @atom:hs @atom:sh @atom:c2 @atom:c3 + @dihedral:hs-sh-c3-h1 @atom:hs @atom:sh @atom:c3 @atom:h1 + @dihedral:hs-sh-ca-ca @atom:hs @atom:sh @atom:ca @atom:ca + @dihedral:hs-sh-n2-c2 @atom:hs @atom:sh @atom:n2 @atom:c2 + @dihedral:hs-sh-n3-c3 @atom:hs @atom:sh @atom:n3 @atom:c3 + @dihedral:hs-sh-n4-c3 @atom:hs @atom:sh @atom:n4 @atom:c3 + @dihedral:hs-sh-na-cc @atom:hs @atom:sh @atom:na @atom:cc + @dihedral:hs-sh-nh-c2 @atom:hs @atom:sh @atom:nh @atom:c2 + @dihedral:hs-sh-no-o @atom:hs @atom:sh @atom:no @atom:o + @dihedral:hs-sh-oh-ho @atom:hs @atom:sh @atom:oh @atom:ho + @dihedral:hs-sh-os-c3 @atom:hs @atom:sh @atom:os @atom:c3 + @dihedral:hs-sh-p2-c2 @atom:hs @atom:sh @atom:p2 @atom:c2 + @dihedral:hs-sh-p3-c3 @atom:hs @atom:sh @atom:p3 @atom:c3 + @dihedral:hs-sh-p4-c3 @atom:hs @atom:sh @atom:p4 @atom:c3 + @dihedral:hs-sh-p5-os @atom:hs @atom:sh @atom:p5 @atom:os + @dihedral:hs-sh-p5-os @atom:hs @atom:sh @atom:p5 @atom:os + @dihedral:hs-sh-sh-hs @atom:hs @atom:sh @atom:sh @atom:hs + @dihedral:n2-c2-c3-c2 @atom:n2 @atom:c2 @atom:c3 @atom:c2 + @dihedral:n3-c3-c3-c3 @atom:n3 @atom:c3 @atom:c3 @atom:c3 + @dihedral:n3-c3-c3-ca @atom:n3 @atom:c3 @atom:c3 @atom:ca + @dihedral:n3-c3-n3-hn @atom:n3 @atom:c3 @atom:n3 @atom:hn + @dihedral:n4-c3-c3-c3 @atom:n4 @atom:c3 @atom:c3 @atom:c3 + @dihedral:n4-c3-n4-hn @atom:n4 @atom:c3 @atom:n4 @atom:hn + @dihedral:n-c3-c3-c3 @atom:n @atom:c3 @atom:c3 @atom:c3 + @dihedral:nh-c3-c3-c3 @atom:nh @atom:c3 @atom:c3 @atom:c3 + @dihedral:o-c-c3-c3 @atom:o @atom:c @atom:c3 @atom:c3 + @dihedral:oh-c3-c3-c3 @atom:oh @atom:c3 @atom:c3 @atom:c3 + @dihedral:oh-c3-c3-c @atom:oh @atom:c3 @atom:c3 @atom:c + @dihedral:oh-c3-c3-n @atom:oh @atom:c3 @atom:c3 @atom:n + @dihedral:oh-c3-oh-ho @atom:oh @atom:c3 @atom:oh @atom:ho + @dihedral:o-no-c2-c2 @atom:o @atom:no @atom:c2 @atom:c2 + @dihedral:o-no-c2-c3 @atom:o @atom:no @atom:c2 @atom:c3 + @dihedral:o-no-c3-no @atom:o @atom:no @atom:c3 @atom:no + @dihedral:o-no-ca-ca @atom:o @atom:no @atom:ca @atom:ca + @dihedral:o-no-cd-cc @atom:o @atom:no @atom:cd @atom:cc + @dihedral:o-no-n2-c2 @atom:o @atom:no @atom:n2 @atom:c2 + @dihedral:o-no-n3-c3 @atom:o @atom:no @atom:n3 @atom:c3 + @dihedral:o-no-n4-c3 @atom:o @atom:no @atom:n4 @atom:c3 + @dihedral:o-no-na-cc @atom:o @atom:no @atom:na @atom:cc + @dihedral:o-no-nh-c2 @atom:o @atom:no @atom:nh @atom:c2 + @dihedral:o-no-no-o @atom:o @atom:no @atom:no @atom:o + @dihedral:o-no-no-o @atom:o @atom:no @atom:no @atom:o + @dihedral:o-no-p2-c2 @atom:o @atom:no @atom:p2 @atom:c2 + @dihedral:o-no-p4-c3 @atom:o @atom:no @atom:p4 @atom:c3 + @dihedral:o-py-ne-c2 @atom:o @atom:py @atom:ne @atom:c2 + @dihedral:o-py-ne-c2 @atom:o @atom:py @atom:ne @atom:c2 + @dihedral:o-s4-c3-s4 @atom:o @atom:s4 @atom:c3 @atom:s4 + @dihedral:o-s6-c3-s6 @atom:o @atom:s6 @atom:c3 @atom:s6 + @dihedral:os-c-c3-c @atom:os @atom:c @atom:c3 @atom:c + @dihedral:os-c-c3-c @atom:os @atom:c @atom:c3 @atom:c + @dihedral:os-p3-os-c3 @atom:os @atom:p3 @atom:os @atom:c3 + @dihedral:os-p5-n3-c3 @atom:os @atom:p5 @atom:n3 @atom:c3 + @dihedral:os-p5-n4-c3 @atom:os @atom:p5 @atom:n4 @atom:c3 + @dihedral:os-p5-na-cc @atom:os @atom:p5 @atom:na @atom:cc + @dihedral:os-p5-nh-c2 @atom:os @atom:p5 @atom:nh @atom:c2 + @dihedral:os-p5-no-o @atom:os @atom:p5 @atom:no @atom:o + @dihedral:os-p5-no-o @atom:os @atom:p5 @atom:no @atom:o + @dihedral:os-p5-p3-c3 @atom:os @atom:p5 @atom:p3 @atom:c3 + @dihedral:os-p5-ss-c3 @atom:os @atom:p5 @atom:ss @atom:c3 + @dihedral:os-py-ca-ca @atom:os @atom:py @atom:ca @atom:ca + @dihedral:os-py-ce-c2 @atom:os @atom:py @atom:ce @atom:c2 + @dihedral:os-py-ce-c3 @atom:os @atom:py @atom:ce @atom:c3 + @dihedral:os-py-pe-c2 @atom:os @atom:py @atom:pe @atom:c2 + @dihedral:os-py-py-c3 @atom:os @atom:py @atom:py @atom:c3 + @dihedral:os-py-py-os @atom:os @atom:py @atom:py @atom:os + @dihedral:os-py-sx-c3 @atom:os @atom:py @atom:sx @atom:c3 + @dihedral:os-py-sy-c3 @atom:os @atom:py @atom:sy @atom:c3 + @dihedral:os-py-sy-c3 @atom:os @atom:py @atom:sy @atom:c3 + @dihedral:p3-c3-p3-hp @atom:p3 @atom:c3 @atom:p3 @atom:hp + @dihedral:s-c-c3-c @atom:s @atom:c @atom:c3 @atom:c + @dihedral:sh-c3-c3-n @atom:sh @atom:c3 @atom:c3 @atom:n + @dihedral:sh-c3-sh-hs @atom:sh @atom:c3 @atom:sh @atom:hs + @dihedral:ss-c3-ss-c3 @atom:ss @atom:c3 @atom:ss @atom:c3 + @dihedral:c3-c3-ca-ca @atom:c3 @atom:c3 @atom:ca @atom:ca + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 + @dihedral:ca-ca-c-o @atom:ca @atom:ca @atom:c @atom:o + @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c + @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o + @dihedral:c2-ce-cs-c3 @atom:c2 @atom:ce @atom:cs @atom:c3 + @dihedral:c2-ce-c-c3 @atom:c2 @atom:ce @atom:c @atom:c3 + @dihedral:c2-ce-ce-c2 @atom:c2 @atom:ce @atom:ce @atom:c2 + @dihedral:c2-n-c-c3 @atom:c2 @atom:n @atom:c @atom:c3 + @dihedral:c2-n-cs-c3 @atom:c2 @atom:n @atom:cs @atom:c3 + @dihedral:c2-ne-c-c3 @atom:c2 @atom:ne @atom:c @atom:c3 + @dihedral:c2-ne-cs-c3 @atom:c2 @atom:ne @atom:cs @atom:c3 + @dihedral:c2-pe-c-c3 @atom:c2 @atom:pe @atom:c @atom:c3 + @dihedral:c2-pe-cs-c3 @atom:c2 @atom:pe @atom:cs @atom:c3 + @dihedral:c3-cs-cs-c3 @atom:c3 @atom:cs @atom:cs @atom:c3 + @dihedral:c3-c-c-c3 @atom:c3 @atom:c @atom:c @atom:c3 + @dihedral:c3-c-cs-c3 @atom:c3 @atom:c @atom:cs @atom:c3 + @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca + @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca + @dihedral:c3-cs-n-ca @atom:c3 @atom:cs @atom:n @atom:ca + @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 + @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 + @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 + @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 + @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 + @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 + @dihedral:c3-nu-ca-ca @atom:c3 @atom:nu @atom:ca @atom:ca + @dihedral:c3-nh-ca-ca @atom:c3 @atom:nh @atom:ca @atom:ca + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 + @dihedral:c3-p3-c-c3 @atom:c3 @atom:p3 @atom:c @atom:c3 + @dihedral:c3-p3-cs-c3 @atom:c3 @atom:p3 @atom:cs @atom:c3 + @dihedral:c3-ss-c-c3 @atom:c3 @atom:ss @atom:c @atom:c3 + @dihedral:c3-ss-cs-c3 @atom:c3 @atom:ss @atom:cs @atom:c3 + @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 + @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 + @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 + @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 + @dihedral:c3-sy-cs-c3 @atom:c3 @atom:sy @atom:cs @atom:c3 + @dihedral:c3-sy-c-c3 @atom:c3 @atom:sy @atom:c @atom:c3 + @dihedral:ca-ca-c-c3 @atom:ca @atom:ca @atom:c @atom:c3 + @dihedral:ca-ca-cs-c3 @atom:ca @atom:ca @atom:cs @atom:c3 + @dihedral:c-c3-c3-c3 @atom:c @atom:c3 @atom:c3 @atom:c3 + @dihedral:c-n-cs-c3 @atom:c @atom:n @atom:cs @atom:c3 + @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 + @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 + @dihedral:hc-c3-c-c3 @atom:hc @atom:c3 @atom:c @atom:c3 + @dihedral:hc-c3-cs-c3 @atom:hc @atom:c3 @atom:cs @atom:c3 + @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 + @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 + @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 + @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 + @dihedral:ho-oh-c-c3 @atom:ho @atom:oh @atom:c @atom:c3 + @dihedral:ho-oh-cs-c3 @atom:ho @atom:oh @atom:cs @atom:c3 + @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 + @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 + @dihedral:o-n-c-c3 @atom:o @atom:n @atom:c @atom:c3 + @dihedral:o-n-cs-c3 @atom:o @atom:n @atom:cs @atom:c3 + @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 + @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 + @dihedral:os-py-c-c3 @atom:os @atom:py @atom:c @atom:c3 + @dihedral:os-py-cs-c3 @atom:os @atom:py @atom:cs @atom:c3 + } # (end of Dihedrals By Type) + + write_once("In Settings") { + improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes + improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 + improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 + improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 + improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 + improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 + improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 + improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 + improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!) + improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 + improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999 + improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 + improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 + improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 + } # (end of improper_coeffs) + + write_once("Data Impropers By Type (gaff_imp.py)") { + @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o + @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o + @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha + @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn + @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn + @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn + @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3 + @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2 + @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3 + @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3 + @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn + @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o + @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3 + @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 + @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc + @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc + @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o + @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh + @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2 + @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na + @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2 + @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na + @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 + @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 + @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f + @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl + @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br + @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i + @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh + @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3 + @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 + @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o + @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 + @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh + @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os + @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2 + @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2 + @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2 + } # (end of Impropers By Type) + + + write_once("In Init") { + # Default styles and settings for AMBER based force-fields: + units real + atom_style full + bond_style hybrid harmonic + angle_style hybrid harmonic + dihedral_style hybrid fourier + improper_style hybrid cvff + pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 + kspace_style pppm 0.0001 + + # NOTE: If you do not want to use long-range coulombic forces, + # comment out the two lines above and uncomment this line: + # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 + + pair_modify mix arithmetic + special_bonds amber + } + +} + + diff --git a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt b/tools/moltemplate/moltemplate/force_fields/loplsaa.lt index 0c9614632c6b38eab4c72debbcf8ee60368d7f14..017411a75f1ff3e9ed9a232cdc9792e6717b2254 100644 --- a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt +++ b/tools/moltemplate/moltemplate/force_fields/loplsaa.lt @@ -1,17 +1,17 @@ -########################################################################### -## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## -## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ## -## CREDIT: Sebastian Echeverri (file format conversion) ## -########################################################################### +############################################################################ +## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## +## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 +## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## +## CREDIT: Sebastian Echeverri (file format conversion) ## +############################################################################ # This file was generated using: -# tinkerparm2lt.py -name LOPLSAA -file loplsaa_ext.prm -dihedral-style opls -# (and then edited manually to make sure the -# bond, angle, and improper interactions for these atoms -# remain unchanged) +# tinkerparm2lt.py -name OPLSAA -file loplsaa_ext.prm -dihedral-style opls -zeropad 3 +# (...and then EDITED manually to make sure the default bond, angle, +# and improper interactions for these atoms remain unchanged) -import "oplsaa.lt" # <-- Load the ordinary OPLS parameters - # We will extend and override them below +import "oplsaa.lt" # <-- Load the ordinary OPLS parameters first + # We will augment and override them below @@ -22,12 +22,20 @@ OPLSAA { write_once("In Charges") { set type @atom:80L charge -0.222 # "Alkane CH3- (LOPLS CT_CH3)" set type @atom:81L charge -0.148 # "Alkane -CH2- (LOPLS CT_CH2)" + set type @atom:81LL charge 0.19 # "Alkane -CH2- (LOPLS ALT)" set type @atom:85LCH3 charge 0.074 # "Alkane H-C CH3 (LOPLS HC_CH3)" set type @atom:85LCH2 charge 0.074 # "Alkane H-C CH2 (LOPLS HC_CH2)" set type @atom:87L charge -0.16 # "Alkene RH-C= (LOPLS CM_CH)" set type @atom:89L charge 0.16 # "Alkene H-C= (LOPLS HC_CH)" set type @atom:86L charge 0.0 # "Alkene R2-C= (LOPLS)" set type @atom:88L charge -0.23 # "Alkene H2-C= (LOPLS)" + set type @atom:96L charge -0.683 # "Alcohol -OH (LOPLS)" + set type @atom:97L charge 0.418 # "Alcohol -OH (LOPLS)" + set type @atom:111L charge -0.7 # "Diol -OH (LOPLS)" + set type @atom:112L charge 0.435 # "Diol -OH (LOPLS)" + set type @atom:113L charge -0.73 # "Triol -OH (LOPLS)" + set type @atom:114L charge 0.465 # "Triol -OH (LOPLS)" + set type @atom:118L charge 0.06 # "Diol & Triol H-COH (LOPLS)" set type @atom:169L charge 0.005 # "Chloroalkene Cl-CH= (LOPLS)" set type @atom:266L charge -0.07 # "Uracil & Thymine C5 (LOPLS)" set type @atom:267L charge 0.08 # "Uracil & Thymine C6 (LOPLS)" @@ -37,9 +45,14 @@ OPLSAA { set type @atom:325L charge 0.1 # "CytosineH+ C6 (LOPLS)" set type @atom:340L charge 0.18 # "Trifluorothymine CF3- (LOPLS)" set type @atom:342L charge 0.12 # "Chloroalkene Cl2-C= (LOPLS)" + set type @atom:406L charge 0.75 # "Ester -COOR (LOPLS)" + set type @atom:407L charge -0.55 # "Ester C=O (LOPLS)" + set type @atom:408L charge -0.45 # "Ester CO-O-R (LOPLS)" set type @atom:458L charge -0.03 # "Vinyl Ether =CH-OR (LOPLS)" set type @atom:459L charge 0.085 # "Vinyl Ether =CR-OR (LOPLS)" set type @atom:649L charge -0.344 # "Cl..CH3..Cl- Sn2 TS (LOPLS)" + set type @atom:718L charge 0.06 # "Propylene Carbonate CH2 (LOPLS)" + set type @atom:718LL charge 0.03 # "Propylene Carbonate CH2 (LOPLS ALT)" set type @atom:900L charge -0.25 # "Allene/Ketene H2C=C=X (LOPLS)" set type @atom:901L charge -0.1 # "Allene/Ketene HRC=C=X (LOPLS)" set type @atom:902L charge 0.05 # "Allene/Ketene R2C=C=X (LOPLS)" @@ -49,12 +62,20 @@ OPLSAA { write_once("Data Masses") { @atom:80L 12.011 @atom:81L 12.011 + @atom:81LL 12.011 @atom:85LCH3 1.008 @atom:85LCH2 1.008 @atom:87L 12.011 @atom:89L 1.008 @atom:86L 12.011 @atom:88L 12.011 + @atom:96L 15.999 + @atom:97L 1.008 + @atom:111L 15.999 + @atom:112L 1.008 + @atom:113L 15.999 + @atom:114L 1.008 + @atom:118L 1.008 @atom:169L 12.011 @atom:266L 12.011 @atom:267L 12.011 @@ -64,66 +85,113 @@ OPLSAA { @atom:325L 12.011 @atom:340L 12.011 @atom:342L 12.011 + @atom:406L 12.011 + @atom:407L 15.999 + @atom:408L 15.999 @atom:458L 12.011 @atom:459L 12.011 @atom:649L 12.011 + @atom:718L 1.008 + @atom:718LL 1.008 @atom:900L 12.011 @atom:901L 12.011 @atom:902L 12.011 } #(end of atom masses) - # ------- force-field-IDs for bonded interaction lookup ------- - # (First append the "force-field-ID" to the atom type name. - # Later use these expanded names for force-field lookup.) - replace{ @atom:80L @atom:80L_b13_a13_d13L_i13 } - replace{ @atom:81L @atom:81L_b13_a13_d13L_i13 } - replace{ @atom:85LCH3 @atom:85LCH3_b46_a46_d46_i46 } - replace{ @atom:85LCH2 @atom:85LCH2_b46_a46_d46_i46 } - replace{ @atom:87L @atom:87L_b47_a47_d47L_i47 } - replace{ @atom:89L @atom:89L_b46_a46_d46_i46 } - replace{ @atom:86L @atom:86L_b47_a47_d47L_i47 } - replace{ @atom:88L @atom:88L_b47_a47_d47L_i47 } - replace{ @atom:169L @atom:169L_b47_a47_d47L_i47 } - replace{ @atom:266L @atom:266L_b47_a47_d47L_i47 } - replace{ @atom:267L @atom:267L_b47_a47_d47L_i47 } - replace{ @atom:280L @atom:280L_b47_a47_d47L_i47 } - replace{ @atom:281L @atom:281L_b47_a47_d47L_i47 } - replace{ @atom:324L @atom:324L_b47_a47_d47L_i47 } - replace{ @atom:325L @atom:325L_b47_a47_d47L_i47 } - replace{ @atom:340L @atom:340L_b47_a47_d47L_i47 } - replace{ @atom:342L @atom:342L_b47_a47_d47L_i47 } - replace{ @atom:458L @atom:458L_b47_a47_d47L_i47 } - replace{ @atom:459L @atom:459L_b47_a47_d47L_i47 } - replace{ @atom:649L @atom:649L_b47_a47_d47L_i47 } - replace{ @atom:900L @atom:900L_b47_a47_d47L_i47 } - replace{ @atom:901L @atom:901L_b47_a47_d47L_i47 } - replace{ @atom:902L @atom:902L_b47_a47_d47L_i47 } - #(end of force-field-IDs) + + # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- + # Each type of atom has a separate ID used for looking up bond parameters + # and a separate ID for looking up 3-body angle interaction parameters + # and a separate ID for looking up 4-body dihedral interaction parameters + # and a separate ID for looking up 4-body improper interaction parameters + # The complete @atom type name includes ALL of these ID numbers. There's + # no need to force the end-user to type the complete name of each atom. + # The "replace" command used below informs moltemplate that the short + # @atom names we have been using abovee are equivalent to the complete + # @atom names used below: + + replace{ @atom:80L @atom:80L_b013_a013_d013L_i013 } + replace{ @atom:81L @atom:81L_b013_a013_d013L_i013 } + replace{ @atom:81LL @atom:81LL_b013_a013_d013LL_i013 } + replace{ @atom:85LCH3 @atom:85LCH3_b046_a046_d046_i046 } + replace{ @atom:85LCH2 @atom:85LCH2_b046_a046_d046_i046 } + replace{ @atom:87L @atom:87L_b047_a047_d047L_i047 } + replace{ @atom:89L @atom:89L_b046_a046_d046_i046 } + replace{ @atom:86L @atom:86L_b047_a047_d047L_i047 } + replace{ @atom:88L @atom:88L_b047_a047_d047L_i047 } + replace{ @atom:96L @atom:96L_b005_a005_d005L_i005 } + replace{ @atom:97L @atom:97L_b007_a007_d007L_i007 } + replace{ @atom:111L @atom:111L_b005_a005_d005L_i005 } + replace{ @atom:112L @atom:112L_b007_a007_d007L_i007 } + replace{ @atom:113L @atom:113L_b005_a005_d005L_i005 } + replace{ @atom:114L @atom:114L_b007_a007_d007L_i007 } + replace{ @atom:118L @atom:118L_b046_a046_d046L_i046 } + replace{ @atom:169L @atom:169L_b047_a047_d047L_i047 } + replace{ @atom:266L @atom:266L_b047_a047_d047L_i047 } + replace{ @atom:267L @atom:267L_b047_a047_d047L_i047 } + replace{ @atom:280L @atom:280L_b047_a047_d047L_i047 } + replace{ @atom:281L @atom:281L_b047_a047_d047L_i047 } + replace{ @atom:324L @atom:324L_b047_a047_d047L_i047 } + replace{ @atom:325L @atom:325L_b047_a047_d047L_i047 } + replace{ @atom:340L @atom:340L_b047_a047_d047L_i047 } + replace{ @atom:342L @atom:342L_b047_a047_d047L_i047 } + replace{ @atom:406L @atom:406L_b003_a003_d003L_i003 } + replace{ @atom:407L @atom:407L_b004_a004_d004L_i004 } + replace{ @atom:408L @atom:408L_b020_a020_d020L_i020 } + replace{ @atom:458L @atom:458L_b047_a047_d047L_i047 } + replace{ @atom:459L @atom:459L_b047_a047_d047L_i047 } + replace{ @atom:649L @atom:649L_b047_a047_d047L_i047 } + replace{ @atom:718L @atom:718L_b046_a046_d046L_i046 } + replace{ @atom:718LL @atom:718LL_b046_a046_d046L_i046 } + replace{ @atom:900L @atom:900L_b047_a047_d047L_i047 } + replace{ @atom:901L @atom:901L_b047_a047_d047L_i047 } + replace{ @atom:902L @atom:902L_b047_a047_d047L_i047 } + + + + + # --------------- Non-Bonded interactions: --------------------- + # http://lammps.sandia.gov/doc/pair_lj.html + # Syntax: + # pair_coeff AtomType1 AtomType2 parameters... write_once("In Settings") { - pair_coeff @atom:80L_b13_a13_d13L_i13 @atom:80L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:81L_b13_a13_d13L_i13 @atom:81L_b13_a13_d13L_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:85LCH3_b46_a46_d46_i46 @atom:85LCH3_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:85LCH2_b46_a46_d46_i46 @atom:85LCH2_b46_a46_d46_i46 lj/cut/coul/long 0.026290630975 2.5 - pair_coeff @atom:87L_b47_a47_d47L_i47 @atom:87L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:89L_b46_a46_d46_i46 @atom:89L_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:86L_b47_a47_d47L_i47 @atom:86L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:88L_b47_a47_d47L_i47 @atom:88L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:169L_b47_a47_d47L_i47 @atom:169L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:266L_b47_a47_d47L_i47 @atom:266L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:267L_b47_a47_d47L_i47 @atom:267L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:280L_b47_a47_d47L_i47 @atom:280L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:281L_b47_a47_d47L_i47 @atom:281L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:324L_b47_a47_d47L_i47 @atom:324L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:325L_b47_a47_d47L_i47 @atom:325L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:340L_b47_a47_d47L_i47 @atom:340L_b47_a47_d47L_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:342L_b47_a47_d47L_i47 @atom:342L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:458L_b47_a47_d47L_i47 @atom:458L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:459L_b47_a47_d47L_i47 @atom:459L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:649L_b47_a47_d47L_i47 @atom:649L_b47_a47_d47L_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:900L_b47_a47_d47L_i47 @atom:900L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:901L_b47_a47_d47L_i47 @atom:901L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:902L_b47_a47_d47L_i47 @atom:902L_b47_a47_d47L_i47 lj/cut/coul/long 0.086 3.3 + pair_coeff @atom:80L_b013_a013_d013L_i013 @atom:80L_b013_a013_d013L_i013 0.066 3.5 + pair_coeff @atom:81L_b013_a013_d013L_i013 @atom:81L_b013_a013_d013L_i013 0.066 3.5 + pair_coeff @atom:81LL_b013_a013_d013LL_i013 @atom:81LL_b013_a013_d013LL_i013 0.066 0.35 + pair_coeff @atom:85LCH3_b046_a046_d046_i046 @atom:85LCH3_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:85LCH2_b046_a046_d046_i046 @atom:85LCH2_b046_a046_d046_i046 0.026290630975 2.5 + pair_coeff @atom:87L_b047_a047_d047L_i047 @atom:87L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:89L_b046_a046_d046_i046 @atom:89L_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:86L_b047_a047_d047L_i047 @atom:86L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:88L_b047_a047_d047L_i047 @atom:88L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:96L_b005_a005_d005L_i005 @atom:96L_b005_a005_d005L_i005 0.17 0.312 + pair_coeff @atom:97L_b007_a007_d007L_i007 @atom:97L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:111L_b005_a005_d005L_i005 @atom:111L_b005_a005_d005L_i005 0.17 0.307 + pair_coeff @atom:112L_b007_a007_d007L_i007 @atom:112L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:113L_b005_a005_d005L_i005 @atom:113L_b005_a005_d005L_i005 0.17 0.307 + pair_coeff @atom:114L_b007_a007_d007L_i007 @atom:114L_b007_a007_d007L_i007 0.0 0.0 + pair_coeff @atom:118L_b046_a046_d046L_i046 @atom:118L_b046_a046_d046L_i046 0.03 0.25 + pair_coeff @atom:169L_b047_a047_d047L_i047 @atom:169L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:266L_b047_a047_d047L_i047 @atom:266L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:267L_b047_a047_d047L_i047 @atom:267L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:280L_b047_a047_d047L_i047 @atom:280L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:281L_b047_a047_d047L_i047 @atom:281L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:324L_b047_a047_d047L_i047 @atom:324L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:325L_b047_a047_d047L_i047 @atom:325L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:340L_b047_a047_d047L_i047 @atom:340L_b047_a047_d047L_i047 0.08 3.5 + pair_coeff @atom:342L_b047_a047_d047L_i047 @atom:342L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:406L_b003_a003_d003L_i003 @atom:406L_b003_a003_d003L_i003 0.105 0.31875 + pair_coeff @atom:407L_b004_a004_d004L_i004 @atom:407L_b004_a004_d004L_i004 0.168 0.3108 + pair_coeff @atom:408L_b020_a020_d020L_i020 @atom:408L_b020_a020_d020L_i020 0.17 0.255 + pair_coeff @atom:458L_b047_a047_d047L_i047 @atom:458L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:459L_b047_a047_d047L_i047 @atom:459L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:649L_b047_a047_d047L_i047 @atom:649L_b047_a047_d047L_i047 0.076 3.55 + pair_coeff @atom:718L_b046_a046_d046L_i046 @atom:718L_b046_a046_d046L_i046 0.15 0.242 + pair_coeff @atom:718LL_b046_a046_d046L_i046 @atom:718LL_b046_a046_d046L_i046 0.15 0.242 + pair_coeff @atom:900L_b047_a047_d047L_i047 @atom:900L_b047_a047_d047L_i047 0.086 3.3 + pair_coeff @atom:901L_b047_a047_d047L_i047 @atom:901L_b047_a047_d047L_i047 0.086 3.3 + pair_coeff @atom:902L_b047_a047_d047L_i047 @atom:902L_b047_a047_d047L_i047 0.086 3.3 } #(end of pair_coeffs) @@ -135,499 +203,69 @@ OPLSAA { # Dihedral parameters for some of these atoms are modified: + # ----------- Dihedral Interactions: ------------ + # http://lammps.sandia.gov/doc/dihedral_opls.html + # Syntax: + # dihedral_coeff DihedralTypeName parameters... + write_once("In Settings") { - dihedral_coeff @dihedral:13L-13L-13L-13L opls 0.6446926386 -0.2143420172 0.1782194073 0.0 - dihedral_coeff @dihedral:X-47L-47L-X opls 0.0 12.2502629063 0.0 0.0 - dihedral_coeff @dihedral:47L-47L-13L-13L opls -0.8050121893 0.3218905354 -0.1032768881 0.0 - dihedral_coeff @dihedral:13L-13L-13L-47L opls 0.4821902486 0.1343683078 0.1777461759 0.0 + dihedral_coeff @dihedral:013L_013L_013L_013L 0.6446926386 -0.2143420172 0.1782194073 0.0 + dihedral_coeff @dihedral:X_047L_047L_X 0.0 12.2502629063 0.0 0.0 + dihedral_coeff @dihedral:047L_047L_013L_013L -0.8050121893 0.3218905354 -0.1032768881 0.0 + dihedral_coeff @dihedral:013L_013L_013L_047L 0.4821902486 0.1343683078 0.1777461759 0.0 + dihedral_coeff @dihedral:046L_013LL_005L_007L 0.00962596 -0.0145554 0.381091 0.0 + dihedral_coeff @dihedral:046L_013LL_013LL_005L 0.0143774 0.033021 0.26687 0.0 + dihedral_coeff @dihedral:013LL_013LL_005L_007L -0.675785 -0.0160421 0.373199 0.0 + dihedral_coeff @dihedral:013LL_013LL_013LL_005L 1.31261 -0.266307 0.637867 0.0 + dihedral_coeff @dihedral:005L_013LL_013LL_005L 2.69106 -0.849706 0.725731 0.0 + dihedral_coeff @dihedral:013LL_003L_020L_013LL 3.11923 5.73771 0.0 0.0 + dihedral_coeff @dihedral:013LL_020L_003L_004L 0.0 5.73772 0.0 0.0 + dihedral_coeff @dihedral:046L_013LL_003L_020L -0.00742471 0.00217734 0.111803 0.0 + dihedral_coeff @dihedral:003L_020L_013LL_013LL -1.7354 -1.24844 0.623897 0.0 + dihedral_coeff @dihedral:046L_013LL_013LL_020L 0.0113337 0.0236209 0.429747 0.0 + dihedral_coeff @dihedral:013LL_013LL_003L_020L 0.884988 -0.626905 -0.493344 0.0 + dihedral_coeff @dihedral:013LL_013LL_003L_004L -0.276019 1.23685 -0.670745 0.0 + dihedral_coeff @dihedral:003L_013LL_013LL_046L -0.0021152 0.0173542 -0.295208 0.0 + dihedral_coeff @dihedral:003L_013LL_013LL_013LL -2.30738 -0.627326 0.621951 0.0 + dihedral_coeff @dihedral:013LL_013LL_013LL_020L 2.25871 -1.02408 1.0071 0.0 + dihedral_coeff @dihedral:020L_013LL_013LL_020L 4.66787 -2.62698 1.3248 0.0 + dihedral_coeff @dihedral:005L_013LL_013LL_020L 5.03208 -2.37742 1.23809 0.0 } #(end of dihedral_coeffs) - - # First we must slightly loosen the requirements to generate dihedrals - # involving atom types d13 or d47. We want the same rules to apply - # for atoms of type d13L and d47L. To cover both of these cases, - # I replaced "d13_" with "d13*_" in the lines below: - # (Later I will add the custom dihedrals for these atom types.) + # Rules for creating dihedral interactions according to atom type: + # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4 + # (* = wildcard) write_once("Data Dihedrals By Type") { - @dihedral:2-2-2-13 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13*_i* - @dihedral:2-2-13-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d2_i* - @dihedral:4-3-3-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-3-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-3-24 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:13-3-3-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-5-7 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:1-3-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:1-3-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:* - @dihedral:4-3-13-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-13-21 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:4-3-13-44 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:4-3-13-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-13-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-3-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:5-3-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-13-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-13-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-3-13-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:20-3-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-3-13-13 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:21-3-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-13-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:24-3-13-21 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:24-3-13-24 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:24-3-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-13-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:48-3-13-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:52-3-13-13 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:52-3-13-44 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:52-3-13-46 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:65-3-13-13 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:65-3-13-46 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-13-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-20-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-20-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-20-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-20-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-20-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-3-20-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-3-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-24-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-24-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-24-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-24-5 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:13-3-24-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-24-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-24-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:24-3-24-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-3-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-3-24-45 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:X-3-47-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-47-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-47-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-47-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:24-3-47-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-47-47 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:107-3-47-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-47-47 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-50-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-50-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:5-3-50-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-50-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-3-56-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:13-3-56-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:4-3-107-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-3-107-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-13-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-13-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-13-46 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:7-5-13-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* - @dihedral:7-5-13-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-13-50 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* - @dihedral:7-5-44-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:7-5-47-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:7-5-79-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-13-3 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* - @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-13-24 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:1-13-13-1 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d1_i* - @dihedral:1-13-13-5 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:1-13-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:1-13-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-13-5 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:3-13-13-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-13-15 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* - @dihedral:3-13-13-16 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* - @dihedral:3-13-13-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:3-13-13-80 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:5-13-13-5 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d5_i* - @dihedral:5-13-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-13-13-20 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:5-13-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:5-13-13-24 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:5-13-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-13-15 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* - @dihedral:13-13-13-16 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* - @dihedral:13-13-13-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-13-21 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:13-13-13-44 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:13-13-13-24 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-13-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-51 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* - @dihedral:13-13-13-53 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-65 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d65_i* - @dihedral:13-13-13-66 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d66_i* - @dihedral:13-13-13-79 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-13-107 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* - @dihedral:13-13-13-108 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:15-13-13-46 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:16-13-13-46 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-13-13-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-13-13-20 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:20-13-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-13-13-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d21_i* - @dihedral:21-13-13-44 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:21-13-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-44 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* - @dihedral:44-13-13-46 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-48 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:24-13-13-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-80 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-13-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-13-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-13-53 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:46-13-13-55 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* - @dihedral:46-13-13-59 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* - @dihedral:46-13-13-62 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* - @dihedral:46-13-13-65 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d65_i* - @dihedral:46-13-13-66 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d66_i* - @dihedral:46-13-13-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* - @dihedral:46-13-13-80 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-82 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* - @dihedral:46-13-13-83 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:46-13-13-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-13-87 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* - @dihedral:46-13-13-88 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* - @dihedral:46-13-13-102 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* - @dihedral:46-13-13-104 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* - @dihedral:46-13-13-107 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* - @dihedral:46-13-13-108 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:46-13-13-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* - @dihedral:48-13-13-53 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:108-13-13-108 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* - @dihedral:13-13-15-17 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:46-13-15-17 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:13-13-16-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-16-16 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-16-16 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-18-19 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-18-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-19-18 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-19-19 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-19-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-19-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-20-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:56-13-20-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:57-13-20-13 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-20-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-20-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-20-64 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:46-13-20-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:* - @dihedral:46-13-20-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-20-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-20-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-20-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-20-64 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:13-13-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-44-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-24-45 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:3-13-24-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-24-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-24-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-59 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-24-79 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-24-91 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:46-13-24-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-24-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-24-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:48-13-24-59 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:X-13-47-50 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:1-13-47-47 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-47-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-47-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-47-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-110 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* - @dihedral:47-13-47-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-13-47-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-48-48 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-13-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:21-13-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:64-13-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:65-13-48-48 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-50-47 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-13-50-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-13-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:13-13-51-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:* - @dihedral:13-13-51-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-51-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-53-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-53-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-53-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-53-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-55-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-55-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-55-54 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-55-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-55-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-56-18 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-57-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-62 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-57-82 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-57-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:20-13-57-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-57-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:13-13-59-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:46-13-59-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-62-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-62-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-64-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-64-52 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-13-64-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:48-13-64-52 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:X-13-79-23 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:X-13-79-24 @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-79-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-79-23 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-5 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d5_i* - @dihedral:46-13-79-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-79-23 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-80-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:13-13-80-60 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:13-13-80-84 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-80-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:46-13-80-60 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:46-13-80-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:13-13-82-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:46-13-82-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:13-13-83-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:46-13-83-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:1-13-84-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-57 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* - @dihedral:21-13-84-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:46-13-84-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:1-13-87-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-87-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:21-13-87-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:46-13-87-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-88-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:46-13-88-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-13-90-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-90-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:13-13-95-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-95-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-102-103 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:46-13-102-103 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:13-13-104-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-104-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13*_i* - @dihedral:X-13-105-X @atom:* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-62 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-105-82 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-105-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:20-13-105-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-105-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:3-13-107-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-107-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-107-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-107-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-107-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-107-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-108-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-13-108-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-108-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-108-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-108-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-13-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-13-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-16-16-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-16-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-16-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:18-18-56-13 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-19-19-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-19-19-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d46_i* - @dihedral:13-19-19-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-19-19-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:46-19-19-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* - @dihedral:19-19-47-13 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:19-19-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-19-47-47 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-20-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-20-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-47-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-47-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-20-47-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* - @dihedral:13-20-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-20-51-5 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d5_i* - @dihedral:13-20-51-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-51-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-20-51-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-56-3 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:13-20-59-56 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:13-20-64-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-20-64-52 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:108-20-108-13 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-44-44-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-44-44-45 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-44-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-79-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-82-61 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:47-24-86-48 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:47-24-86-56 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:47-46-47-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-46-47-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:X-47-47-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:* - @dihedral:X-47-47-19 @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d19_i* - @dihedral:3-47-47-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-47-47-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:5-47-47-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:5-47-47-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-47-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-47-47-19 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d19_i* - @dihedral:13-47-47-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d20_i* - @dihedral:13-47-47-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:19-47-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:20-47-47-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:21-47-47-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d21_i* - @dihedral:21-47-47-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-56 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:47-47-48-48 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-47-50-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-50-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:13-47-50-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:24-47-50-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:46-47-50-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:46-47-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-50-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-47-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:X-47-84-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-47-86-48 @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-47-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-47-86-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:* - @dihedral:49-47-86-24 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d24_i* - @dihedral:X-47-87-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-47-88-X @atom:* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:13-47-110-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-47-110-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47*_i* - @dihedral:X-48-48-13 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-48-48-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-48-48-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-48-48-49 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:47-48-48-49 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-50-47 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:56-48-50-47 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:48-48-53-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:55-48-55-13 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-48-79-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13*_i* - @dihedral:56-48-101-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d101_i* @atom:*_b*_a*_d13*_i* - @dihedral:48-48-109-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-50-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-50-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-50-50-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:46-50-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:47-50-50-47 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47*_i* - @dihedral:13-50-109-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-50-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-50-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-50-109-13 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:47-50-109-46 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:47-50-109-109 @atom:*_b*_a*_d47*_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-53-82-61 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:13-56-56-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-56-56-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:4-89-90-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13*_i* - @dihedral:91-89-90-13 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-91-91-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-91-91-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-13 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13*_i* - @dihedral:13-109-109-46 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-48 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:13-109-109-50 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:13-109-109-109 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:24-3-13-53 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:52-3-13-24 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-53 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:3-13-13-83 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:3-13-13-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:3-13-13-85 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:5-13-13-53 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:15-13-13-53 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:16-13-13-53 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-55 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* - @dihedral:24-13-13-83 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:53-13-13-83 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d83_i* - @dihedral:24-13-13-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:53-13-13-84 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d84_i* - @dihedral:24-13-13-85 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:46-13-13-85 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:53-13-13-85 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* - @dihedral:3-13-53-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13*_i* - @dihedral:3-13-53-54 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-53-54 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-85-X @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-85-57 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d57_i* - @dihedral:46-13-85-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-13-20 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-13-47 @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d13*_i* @atom:*_b*_a*_d47*_i* + @dihedral:013L_013L_013L_013L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* + @dihedral:X_047L_047L_X @atom:* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:* + @dihedral:047L_047L_013L_013L @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* + @dihedral:013L_013L_013L_047L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d047L_i* + @dihedral:046L_013LL_005L_007L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* + @dihedral:046L_013LL_013LL_005L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:013LL_013LL_005L_007L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* + @dihedral:013LL_013LL_013LL_005L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:005L_013LL_013LL_005L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* + @dihedral:013LL_003L_020L_013LL @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* + @dihedral:013LL_020L_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* + @dihedral:046L_013LL_003L_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* + @dihedral:003L_020L_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* + @dihedral:046L_013LL_013LL_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:013LL_013LL_003L_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* + @dihedral:013LL_013LL_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* + @dihedral:003L_013LL_013LL_046L @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d046L_i* + @dihedral:003L_013LL_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* + @dihedral:013LL_013LL_013LL_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:020L_013LL_013LL_020L @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* + @dihedral:005L_013LL_013LL_020L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* } #(end of dihedrals by type) - # New dihedrals which have been customized: - # (These will override the rules above) + # ----------- New Dihedral Interactions: ------------ + # http://lammps.sandia.gov/doc/dihedral_opls.html + # Syntax: + # dihedral_coeff DihedralTypeName parameters... - write_once("Data Dihedrals By Type") { - @dihedral:13L-13L-13L-13L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* - @dihedral:X-47L-47L-X @atom:* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:* - @dihedral:47L-47L-13L-13L @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d47L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* - @dihedral:13L-13L-13L-47L @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d13L_i* @atom:*_b*_a*_d47L_i* - } #(end of dihedrals by type) -} # end of additional parameters appended to the "OPLSAA" object +} # OPLSAA + diff --git a/tools/moltemplate/moltemplate/force_fields/martini.lt b/tools/moltemplate/moltemplate/force_fields/martini.lt index 3279e55dbc026b2fb8c5119105ff857b47b0ed4a..9304de004a0f020b606a625f2dee7e32ac2bdb60 100644 --- a/tools/moltemplate/moltemplate/force_fields/martini.lt +++ b/tools/moltemplate/moltemplate/force_fields/martini.lt @@ -1,13 +1,25 @@ # Autogenerated by EMC 2 LT tool v0.1 on 2017-06-28 # # cd martini/ -# ./emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini +# emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini # mv -f martini.lt ../ # +# For details see the "README.txt" file (located in "force_fields/martini/") +# +# (Note: The rigid bond constraints used original MARTINI model for +# cholesterol have been replaced by stiff but flexible bonds. +# There is a trade-off between increasing the stiffness of the bonds, and +# using larger time steps. To alter the stiffness of the bonds, and edit +# the "ITEM BOND" section of the "cholesterol.prm", edit the "k" parameters +# (3rd column, for the "S..." entries), and run "emcprm2lt.py" again.) +# # Adapted from EMC by Pieter J. in 't Veld # Originally written as, FFNAME:MARTINI STYLE:COARSE VERSION:V2.0 on Feb 2014 +# "emcprm2lt.py" was written by David Stelter. + MARTINI { + write_once("Data Masses") { @atom:BP4 72.000000 # BP4 @atom:C1 72.000000 # C1 @@ -2210,4 +2222,6 @@ MARTINI { pair_style hybrid lj/gromacs/coul/gromacs 9.000000 12.000000 special_bonds lj/coul 0.0 0.0 0.0 } # end init + } # MARTINI + diff --git a/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py b/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py deleted file mode 100755 index 81ed2358aa14a0ab7dcfe8795ef00b45ca4d3062..0000000000000000000000000000000000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini/emcprm2lt.py +++ /dev/null @@ -1,580 +0,0 @@ -#!/usr/bin/python - -import os, sys, getopt -import datetime - -__version__ = 0.1 - -#################### UNITS #################### -# Only used with --units flag -econv = 1.0 # Additional Factor for unit conversion if needed (energies) -lconv = 1.0 # Additional Factor for unit conversion if neededa (lengths) -dconv = 1.0 # Additional Factor for unit conversion if neededa (densities) -############################################### - -print('\nEMC 2 LT conversion tool: v%s\n' % __version__) - -def helpme(): - print 'Help for the EMC 2 LT conversion tool\n' - print 'Input takes a list of files in EMC .prm format to be read.' - print 'Additional styles (bond, angle, etc) can be modified via the',\ - 'command line. Any valid LAMMPS style can be used.\n' - print 'Styles include:' - print '--pair-style=' - print '--bond-style=' - print '--angle-style=' - print '--dihedral-style=' - print '--improper-style=\n' - print 'Default styles are lj/cut/coul/long, harmonic, harmonic, harmonic,',\ - 'harmonic \n' - print 'Other commands:' - print '--name= provides basename for output file if desired\n' - print '--units flag for manual units (no parameter needed)\n' - print 'Usage example:' - print 'emcprm2lt.py file1 file2 --bond-style=harmonic --angle-style=harmonic' - print '' - -def Abort(): - print 'Aborting...' - sys.exit() - -def WriteInit(): -# Write generic LAMMPS settings, likely need additional on a per-ff basis - foutput.write(' write_once("In Init") {\n') - foutput.write(' # Warning: This is a very generic "In Init" section, further\n') - foutput.write(' # modification prior to any simulation is extremely likely\n') - foutput.write(' units real\n') - foutput.write(' atom_style full\n') - foutput.write(' bond_style hybrid %s\n' % bstyle) - if angle_flag: - foutput.write(' angle_style hybrid %s\n' % astyle) - if torsion_flag: - foutput.write(' dihedral_style hybrid %s\n' % dstyle) - if improp_flag: - foutput.write(' improper_style hybrid %s\n' % istyle) - foutput.write(' pair_style hybrid %s %f %f\n' % (pstyle, - float(inner[0])*lconv, float(cutoff[0])*lconv)) - if pair14[0] == 'OFF': - foutput.write(' special_bonds lj/coul 0.0 0.0 0.0\n') - else: - print 'Warning: special_bonds needed, add to "In Init" section\n' - foutput.write(' } # end init\n') - -def Units(length_flag, energy_flag, density_flag): -# Check flags for all units, determine what conversions are needed, hard-coded for LAMMPS 'real' - print 'Attempting to auto-convert units... This should always be double-checked',\ - ' especially for unique potential styles' - global lconv; global econv; global dconv - if length_flag: - print 'Warning: length scale does not match LAMMPS real units, attempting conversion to angstroms' - if length[0] == 'NANOMETER': - lconv = 10.0 - print ' nanometer -> angstrom' - elif length[0] == 'MICROMETER': - lconv = 10000.0 - print ' micrometer -> angstrom' - elif length[0] == 'METER': - lconv = 10000000000.0 - print ' meter -> angstrom' - else: - print 'Length units NOT converted' - if energy_flag: - print 'Warning: energy units do not match LAMMPS real units, attempting conversion to kcal/mol' - if energy[0] == 'KJ/MOL': - econv = 0.239006 - print ' kj/mol -> kcal/mol' - elif energy[0] == 'J/MOL': - econv = 0.000239006 - print ' j/mol -> kcal/mol' - elif energy[0] == 'CAL/MOL': - econv = 0.001 - print ' cal/mol -> kcal/mol' - else: - print 'Energy units NOT converted' - if density_flag: - print 'Warning: density units do not match LAMMPS real units, attempting conversion to gram/cm^3' - if density[0] == 'KG/M^3': - dconv = 0.001 - print ' kg/m^3 -> g/cm^3' - else: - print 'Density units NOT converted' - return lconv, econv, dconv - -def ChkPotential(manual_flag, angle_flag, torsion_flag, improp_flag): -# Check type of potential, determine type of unit conversion is necessary - global beconv - if angle_flag: - global aeconv - if torsion_flag: - global deconv - if improp_flag: - global ieconv - if manual_flag == False: - # Chk bond potential - if bstyle == '' or bstyle == 'harmonic': - beconv = econv / (2*pow(lconv,2)) - else: - print 'Cannot find bond potential type, use manual units' - Abort() - if angle_flag: - if astyle == '' or astyle == 'harmonic': - aeconv = econv - elif astyle == 'cosine/squared': - aeconv = econv / 2 - else: - print 'Cannot find angle potential type, use manual units' - Abort() - # torsion and improper not implemented fully - elif torsion_flag: - if dstyle == '' or dstyle == 'harmonic': - deconv = econv - else: - print 'Cannot find torsion potential type, use manual units' - Abort() - elif improp_flag: - if istyle == '' or istyle == 'harmonic': - ieconv = econv - else: - print 'Cannot find improper potential type, use manual units' - Abort() - else: - # Modify as needed - print 'Warning: Manual units used, set potential conversion units in script' - beconv = 1 - if angle_flag: - aeconv = 1 - if torsion_flag: - deconv = 1 - if improp_flag: - ieconv = 1 - - -### Parse input ### -if len(sys.argv) == 1: - helpme() - sys.exit() -manual_units = False # Turned on via command line -args = list(sys.argv[1:]) -myopts, args = getopt.gnu_getopt(args, 'fh', ['pair-style=', 'bond-style=', 'angle-style=', - 'dihedral-style=', 'improper-style=', 'name=', 'units']) -filenames = list(args) -pstyle = ''; bstyle = ''; astyle = ''; dstyle = ''; istyle = '' -name = '' -for opt, arg in myopts: - if opt in ('-f'): - filenames = arg - elif opt in ('--pair-style'): - pstyle = arg - elif opt in ('--bond-style'): - bstyle = arg - elif opt in ('--angle-style'): - astyle = arg - elif opt in ('--dihedral-style'): - dstyle = arg - elif opt in ('--improper-style'): - istyle = arg - elif opt in ('--name'): - name = arg - elif opt in ('--units'): - manual_units = True - print 'Manual units enabled, modify python script accordingly' - elif opt in ('-h', '--help'): - helpme() - sys.exit() - -### Check input filenames, make sure they exist ### -print 'Converting: ' -for i in range(len(filenames)): - if os.path.isfile(filenames[i]): - print '', filenames[i] - else: - print 'invalid filename:', filenames[i] - Abort() -print 'from EMC .prm to moltemplate .lt format\n' - -### Open all files ### -f = [open(fname, 'r') for fname in filenames] - -### All these settings from DEFINE should be list of fixed size ### -ffname = [[] for i in range(len(f))] -fftype = [[] for i in range(len(f))] -version = [[] for i in range(len(f))] -created1 = [[] for i in range(len(f))] -created2 = [[] for i in range(len(f))] -length = [[] for i in range(len(f))] -energy = [[] for i in range(len(f))] -density = [[] for i in range(len(f))] -mix = [[] for i in range(len(f))] -nbonded = [[] for i in range(len(f))] -inner = [[] for i in range(len(f))] -cutoff = [[] for i in range(len(f))] -pair14 = [[] for i in range(len(f))] -angle_def = [[] for i in range(len(f))] -torsion_def = [[] for i in range(len(f))] -improp_def = [[] for i in range(len(f))] # not all prm have this - -### Parse DEFINE section, save info for each file ### -for i in range(len(f)): - grab = False - for line in f[i]: - if line.strip() == 'ITEM DEFINE': - grab = True - elif line.strip() == 'ITEM END': - grab = False - elif grab: - if line.startswith('FFNAME'): - ffname[i] = line.split()[1].strip() - if line.startswith('FFTYPE'): - fftype[i] = line.split()[1].strip() - if line.startswith('VERSION'): - version[i] = line.split()[1].strip() - if line.startswith('CREATED'): - created1[i] = line.split()[1].strip() - created2[i] = line.split()[2].strip() - if line.startswith('LENGTH'): - length[i] = line.split()[1].strip() - if line.startswith('ENERGY'): - energy[i] = line.split()[1].strip() - if line.startswith('DENSITY'): - density[i] = line.split()[1].strip() - if line.startswith('MIX'): - mix[i] = line.split()[1].strip() - if line.startswith('NBONDED'): - nbonded[i] = line.split()[1].strip() - if line.startswith('INNER'): - inner[i] = line.split()[1].strip() - if line.startswith('CUTOFF'): - cutoff[i] = line.split()[1].strip() - if line.startswith('PAIR14'): - pair14[i] = line.split()[1].strip() - if line.startswith('ANGLE'): - angle_def[i] = line.split()[1].strip() - if line.startswith('TORSION'): - torsion_def[i] = line.split()[1].strip() - if line.startswith('IMPROP'): - improp_def[i] = line.split()[1].strip() - -### Sanity Checks ### -for i in range(len(f)): - for j in range(len(f)): - if ffname[j] != ffname[i]: - print 'force field files do not match' - Abort() - if length[j] != length[i]: - print 'units not identical between files' - Abort() - if energy[j] != energy[i]: - print 'units not identical between files' - Abort() - if density[j] != density[i]: - print 'units not identical between files' - Abort() - if inner[j] != inner[i]: - print 'inner cutoff not identical between files' - Abort() - if cutoff[j] != cutoff[i]: - print 'cutoff not identical between files' - Abort() - if pair14[j] != pair14[i]: - print '1-4 pair interaction not consistent between files' - Abort() - -### Check if sections exist in PRM file ### -angle_flag = False; torsion_flag = False; improp_flag = False -for i in range(len(f)): - if angle_def[i] == 'WARN': - angle_flag = True - if torsion_def[i] == 'WARN': - torsion_flag = True - if improp_def[i] == 'WARN': - improp_flag = True - -### Check which units to use, trip convert flags ### -length_flag = False; energy_flag = False; density_flag = False -if length[0] != 'ANGSTROM': - length_flag = True -if energy[0] != 'KCAL/MOL': - energy_flag = True -if density[0] != 'G/CC': - density_flag = True -if manual_units == True: - length_flag = False - energy_flag = False - density_flag = False -Units(length_flag, energy_flag, density_flag) - -### Read Whole File, save to lists ### -# Non-crucial sections include -# BONDS, ANGLE, TORSION, IMPROP, NONBOND -# Read all sections every time, only output sections when flags tripped -f = [open(fname, 'r') for fname in filenames] -masses = []; nonbond = []; bond = []; angle = []; torsion = []; improp = [] -equiv = [] -for i in range(len(f)): - MASS = False - NONBOND = False - BOND = False - ANGLE = False - TORSION = False - IMPROP = False - EQUIV = False - for line in f[i]: - if line.strip() == 'ITEM MASS': - MASS = True - elif line.strip() == 'ITEM END': - MASS = False - elif MASS: - if not line.startswith('#'): - if not line.startswith('\n'): - masses.append(line.strip().split()) - if line.strip() == 'ITEM NONBOND': - NONBOND = True - elif line.strip() == 'ITEM END': - NONBOND = False - elif NONBOND: - if not line.startswith('#'): - if not line.startswith('\n'): - nonbond.append(line.strip().split()) - if line.strip() == 'ITEM BOND': - BOND = True - elif line.strip() == 'ITEM END': - BOND = False - elif BOND: - if not line.startswith('#'): - if not line.startswith('\n'): - bond.append(line.strip().split()) - if line.strip() == 'ITEM ANGLE': - ANGLE = True - elif line.strip() == 'ITEM END': - ANGLE = False - elif ANGLE: - if not line.startswith('#'): - if not line.startswith('\n'): - angle.append(line.strip().split()) - if line.strip() == 'ITEM TORSION': - TORSION = True - elif line.strip() == 'ITEM END': - TORSION = False - elif TORSION: - if not line.startswith('#'): - if not line.startswith('\n'): - torsion.append(line.strip().split()) - if line.strip() == 'ITEM IMPROP': - IMPROP = True - elif line.strip() == 'ITEM END': - IMPROP = False - elif IMPROP: - if not line.startswith('#'): - if not line.startswith('\n'): - improp.append(line.strip().split()) - if line.strip() == 'ITEM EQUIVALENCE': - EQUIV = True - elif line.strip() == 'ITEM END': - EQUIV = False - elif EQUIV: - if not line.startswith('#'): - if not line.startswith('\n'): - equiv.append(line.strip().split()) -### Close prm files ### -for fname in f: - fname.close() - -### Sanity checks before writing LT files ### -# Check Equiv -for i in range(len(equiv)): - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and (equiv[i] != equiv[j]): - print 'Error: Identical atom types with different equivalences' - Abort() -# Check Masses -for i in range(len(masses)): - for j in range(len(masses)): - if (masses[i][0] == masses[j][0]) and (masses[i][1] != masses[j][1]): - print 'Error: Identical types with different mass' - Abort() -# Check Nonbond -for i in range(len(nonbond)): - for j in range(len(nonbond)): - if (nonbond[i][0] == nonbond[j][0]) and (nonbond[i][1] == nonbond[j][1]) and ((nonbond[i][2] != nonbond[j][2]) or (nonbond[i][3] != nonbond[j][3])): - print 'Error: Identical types with different pair-interactions' - Abort() - -### Remove double equivalences ### -for i in range(len(equiv)): - once = True - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and once: - once = False - elif (equiv[i][0] == equiv[j][0]): - equiv[j][1] = None - equiv[j][2] = 'duplicate' - if len(equiv[i]) != 6: - print 'Warning: Incorrect equivalence formatting for type %s' % equiv[i][0],\ - 'skipping type, topology may not be complete' - equiv[i][1] = None - equiv[i][2] = 'invalid_format' - -### Check Potential Styles and Set Units ### -ChkPotential(manual_units, angle_flag, torsion_flag, improp_flag) - -### Set output LT file ### -fname = 'ff_output.lt' -if name == '': - fname = ffname[0] + '.lt' -else: - fname = name + '.lt' -foutput = open(fname, 'w') - -### Output to LT format ### -foutput.write('# Autogenerated by EMC 2 LT tool v%s on %s\n' % (__version__, str(datetime.date.today()))) -foutput.write('#\n# ') -for i in range(len(sys.argv)): - foutput.write('%s ' % sys.argv[i]) -foutput.write('\n') -foutput.write('#\n') -foutput.write('# Adapted from EMC by Pieter J. in \'t Veld\n') -foutput.write('# Originally written as, FFNAME:%s STYLE:%s VERSION:%s on %s %s\n' % - (ffname[0], fftype[0], version[0], created1[0], created2[0])) -foutput.write('\n') -foutput.write('%s {\n' % ffname[0]) - -# Charges not necessary? emc file assign charges in smiles, which would -# be in the per-molecule files created by moltemplate user... not here - -### Mass Info ### -foutput.write(' write_once("Data Masses") {\n') -for i in range(len(masses)): - if equiv[i][1] != None: - foutput.write(' @atom:%s %f # %s\n' % - (masses[i][0], float(masses[i][1]), masses[i][0])) -foutput.write(' } # end of atom masses\n\n') - -### Equiv Info ### -# Write Equivalence -foutput.write(' # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup -----\n') -for i in range(len(equiv)): - if equiv[i][1] != None: - foutput.write(' replace{ @atom:%s @atom:%s_b%s_a%s_d%s_i%s}\n' % - (equiv[i][0], equiv[i][0], equiv[i][2], equiv[i][3], equiv[i][4], equiv[i][5])) -foutput.write(' # END EQUIVALENCE\n\n') - -### Nonbonded Info ### -if pstyle == '': - print 'Warning: no non-bonded potential provided, assuming lj/cut/coul/long' - pstyle = 'lj/cut/coul/long' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Non-Bonded interactions -----\n') -# Add new types from equivalence -for i in range(len(equiv)): - once = True - for j in range(len(nonbond)): - # Get terms for new types - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][0]): - if not equiv[i][1] == nonbond[j][1]: - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][1], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if once: - once = False - line = '%s %s %s %s' % (equiv[i][0], equiv[i][0], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][1]): - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][0], nonbond[j][2], nonbond[j][3]) - if line.split() != nonbond[-1]: - nonbond.append(line.split()) -for i in range(len(nonbond)): - atom1name = None - atom2name = None - # Cross Terms + Diagonal, normal - for j in range(len(equiv)): - if nonbond[i][0] == equiv[j][0]: - atom1name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][0], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - if nonbond[i][1] == equiv[j][0]: - atom2name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][1], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - #foutput.write(' pair_coeff @atom:%s @atom:%s %s %f %f' % - # (nonbond[i][0], nonbond[i][1], pstyle, float(nonbond[i][2])*econv, float(nonbond[i][2])*lconv)) - foutput.write(' pair_coeff @atom:%s @atom:%s %s %f %f' % - (atom1name, atom2name, pstyle, float(nonbond[i][3])*econv, float(nonbond[i][2])*lconv)) - foutput.write(' # %s-%s\n' % (nonbond[i][0], nonbond[i][1])) -foutput.write(' } # end of nonbonded parameters\n\n') - -### Bond Info ### -if bstyle == '': - print 'Warning: no bond potential provided, assuming harmonic' - bstyle == 'harmonic' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Bonds -----\n') -for i in range(len(bond)): - foutput.write(' bond_coeff @bond:%s-%s %s %f %f' % - (bond[i][0], bond[i][1], bstyle, float(bond[i][2])*beconv, float(bond[i][3])*lconv)) - foutput.write(' # %s-%s\n' % (bond[i][0], bond[i][1])) -foutput.write(' }\n\n') -foutput.write(' write_once("Data Bonds By Type") {\n') -for i in range(len(bond)): - foutput.write(' @bond:%s-%s @atom:*_b%s_a*_d*_i* @atom:*_b%s_a*_d*_i*\n' % - (bond[i][0], bond[i][1], bond[i][0], bond[i][1])) -foutput.write(' } # end of bonds\n\n') - -### Angle Info ### -if angle_flag: - if astyle == '': - print 'Warning: no angle potential provided, assuming harmonic' - astyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Angles -----\n') - for i in range(len(angle)): - foutput.write(' angle_coeff @angle:%s-%s-%s %s %f %f' % - (angle[i][0], angle[i][1], angle[i][2], astyle, float(angle[i][3])*aeconv, float(angle[i][4]))) - foutput.write(' # %s-%s-%s\n' % (angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Angles By Type") {\n') - for i in range(len(angle)): - foutput.write(' @angle:%s-%s-%s @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i*\n' % - (angle[i][0], angle[i][1], angle[i][2], angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' } # end of angles\n\n') - -### Torsion/Dihedral Info ###a -# Incomplete -if torsion_flag: - if dstyle == '': - print 'Warning: no dihedral/torsion potential provided, assuming harmonic' - dstyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Dihedrals -----\n') - for i in range(len(torsion)): - foutput.write(' dihedral_coeff @dihedral:%s-%s-%s-%s %s %f %f %f %f\n' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], dstyle, float(torsion[i][4])*deconv, float(torsion[i][5]), float(torsion[i][6]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Dihedrals By Type") {\n') - for i in range(len(torsion)): - foutput.write(' @dihedral:%s-%s-%s-%s @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i*' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3])) - foutput.write(' } # end of dihedrals\n\n') - -### Improper Info ### -# Incomplete -ieconv = econv # improper coeff conversion -if improp_flag: - if istyle == '': - print 'Warning: no improper potential provided, assuming harmonic' - istyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Impropers -----\n') - # As discussed, a check for convention of impropers is probably needed here - for i in range(len(improp)): - foutput.write(' improper_coeff @improper:%s-%s-%s-%s %s %f %f\n' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], istyle, - float(improp[i][4]), float(improp[i][5]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Impropers By Type") {\n') - for i in range(len(improp)): - foutput.write(' @improper:%s-%s-%s-%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], improp[i][0], improp[i][1], improp[i][2], improp[i][3])) - foutput.write(' } # end of impropers\n\n') - -### Initialization Info ### -print 'Warning: Attempting to write generic "In Init" section,',\ - 'further modification after this script is extremely likely' -WriteInit() - -foutput.write('} # %s\n' % ffname[0]) -sys.exit() diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..2e20697a439f63ffce9992c2c242d7cea4bd85e1 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt @@ -0,0 +1,42 @@ +The files in this directory are used to create the "martini.lt" file +(containing MARTINI force field parameters for moltemplate). +These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. +The original MARTINI files are distributed at http://cgmartini.nl + +Conversion from EMC (.PRM) format to moltemplate (.LT) format was +done using the "emcprm2lt.py" script written by David Stelter. +Here is an example how to use the emcprm2lt.py script: + +emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini + +This will generate a file named "martini.lt" which (in this example) +only includes the force field parameters for lipids and cholestrol. +Later you can define new molecules in moltemplate using: + +import "martini.lt" +NewMolecule inherits MARTINI { + write("Data Atoms") {...atom coordinates and types go here...} + write("Data Bond List") {...list of bonds goes here...} +} + +See "DOPC.lt" in /examples/coarse_grained/MARTINI_examples/ for more details. + +(Note: The rigid bond constraints used for cholesterol in the original MARTINI + model for cholesterol have been replaced by stiff but flexible bonds. + There is a trade-off between increasing the stiffness of the bonds + and using larger time steps. To alter the stiffness of the bonds + edit the "ITEM BOND" section of the "cholesterol.prm", edit the "k" + parameters (3rd column, for the "S..." entries, and run "emcprm2lt.py" again.) + +---- Credits: ---- +emcprm2lt.py was written by David Stelter +EMC was written by Pieter J. in 't Veld +MARTINI was created by S.J. Marrink and coworkers (http://cgmartini.nl) + +---- additional citation request ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + diff --git a/tools/moltemplate/moltemplate/force_fields/martini/aminoacids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/aminoacids.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm index 7d78eed759b161f9edb9f5f141d5de6822b0093e..f9b4f7b8d017cee41a48dbf888aaa4fd8998c54f 100644 --- a/tools/moltemplate/moltemplate/force_fields/martini/cholesterol.prm +++ b/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm @@ -78,6 +78,7 @@ SP12 SP1 SP12 SP12 SP12 SP12 ITEM END # Bond parameters +# To change the bond stiffness, edit the "k" parameter ITEM BOND diff --git a/tools/moltemplate/moltemplate/force_fields/martini/lipids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/lipids.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/martini.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/martini.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/polymers.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/polymers.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm diff --git a/tools/moltemplate/moltemplate/force_fields/martini/sugars.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/martini/sugars.prm rename to tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt b/tools/moltemplate/moltemplate/force_fields/oplsaa.lt index 92b2628df5688c65175142883f56baca52cd5f20..7bb69a7445333d46dde6c65c60a76be55ba8d183 100644 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa.lt @@ -1,6 +1,18 @@ -# This file contains OPLSAA parameters and rules for creating -# angle, dihedral, and improper interactions according to OPLSAA conventions. -# These parameters are taken from those distributed with BOSS Version 4.8. +# This file contains OPLSAA parameters and rules for creating angle, dihedral, +# and improper interactions according to OPLSAA conventions, taken from +# "OPLS All-Atom Parameters for Organic Molecules, Ions, +# Peptides & Nucleic Acids, July 2008" and distributed with BOSS Version 4.8. +# This file was generated automatically using this script: +# +# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls -zeropad 3 +# +# The "oplsaa.prm" file was downloaded on 2018-6-15 from the TINKER website +# https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm +# (Corrections to imrpopers were added by David Huang (adelaide.edu.au)) +# (Additional conversion details are explained at the end of this file.) +# Urey-Bradley parameters are not included, and a quadratic energy function +# is used (rather than a cosine) for the improper interactions (in order +# to take advantage of available GPU acceleration in LAMMPS at this time). # # USAGE: You can create molecules using this force-field this way: # @@ -13,6 +25,8 @@ # } # } # +# You can omit the atom charge in your molecule definition. +# (Partial charges will be assigned later according to the force field rules.) # Responsibility for choosing the atom types (eg "@atom:88", "@atom:89") falls # on the user. You must select the type of each atom in the molecule carefully # by looking at the description in the "In Charges" section of this file @@ -23,7 +37,6 @@ - OPLSAA { # Below we will use lammps "set" command to assign atom charges @@ -1860,912 +1873,912 @@ OPLSAA { # @atom names we have been using abovee are equivalent to the complete # @atom names used below: - replace{ @atom:1 @atom:1_b1_a1_d1_i1 } - replace{ @atom:2 @atom:2_b2_a2_d2_i2 } - replace{ @atom:3 @atom:3_b3_a3_d3_i3 } - replace{ @atom:4 @atom:4_b4_a4_d4_i4 } - replace{ @atom:5 @atom:5_b5_a5_d5_i5 } - replace{ @atom:6 @atom:6_b6_a6_d6_i6 } - replace{ @atom:7 @atom:7_b7_a7_d7_i7 } - replace{ @atom:8 @atom:8_b8_a8_d8_i8 } - replace{ @atom:9 @atom:9_b6_a6_d6_i6 } - replace{ @atom:10 @atom:10_b6_a6_d6_i6 } - replace{ @atom:11 @atom:11_b6_a6_d6_i6 } - replace{ @atom:12 @atom:12_b6_a6_d6_i6 } - replace{ @atom:13 @atom:13_b2_a2_d2_i2 } - replace{ @atom:14 @atom:14_b9_a9_d9_i9 } - replace{ @atom:15 @atom:15_b10_a10_d10_i10 } - replace{ @atom:16 @atom:16_b11_a11_d11_i11 } - replace{ @atom:17 @atom:17_b12_a12_d12_i12 } - replace{ @atom:18 @atom:18_b13_a13_d13_i13 } - replace{ @atom:19 @atom:19_b14_a14_d14_i14 } - replace{ @atom:20 @atom:20_b5_a5_d5_i5 } - replace{ @atom:21 @atom:21_b7_a7_d7_i7 } - replace{ @atom:22 @atom:22_b6_a6_d6_i6 } - replace{ @atom:23 @atom:23_b2_a2_d2_i2 } - replace{ @atom:24 @atom:24_b15_a15_d15_i15 } - replace{ @atom:25 @atom:25_b15_a15_d15_i15 } - replace{ @atom:26 @atom:26_b16_a16_d16_i16 } - replace{ @atom:27 @atom:27_b16_a16_d16_i16 } - replace{ @atom:28 @atom:28_b17_a17_d17_i17 } - replace{ @atom:29 @atom:29_b17_a17_d17_i17 } - replace{ @atom:30 @atom:30_b6_a6_d6_i6 } - replace{ @atom:31 @atom:31_b2_a2_d2_i2 } - replace{ @atom:32 @atom:32_b6_a6_d6_i6 } - replace{ @atom:33 @atom:33_b2_a2_d2_i2 } - replace{ @atom:34 @atom:34_b6_a6_d6_i6 } - replace{ @atom:35 @atom:35_b2_a2_d2_i2 } - replace{ @atom:36 @atom:36_b18_a18_d18_i18 } - replace{ @atom:37 @atom:37_b19_a19_d19_i19 } - replace{ @atom:38 @atom:38_b6_a6_d6_i6 } - replace{ @atom:39 @atom:39_b10_a10_d10_i10 } - replace{ @atom:40 @atom:40_b13_a13_d13_i13 } - replace{ @atom:41 @atom:41_b20_a20_d20_i20 } - replace{ @atom:42 @atom:42_b6_a6_d6_i6 } - replace{ @atom:43 @atom:43_b2_a2_d2_i2 } - replace{ @atom:44 @atom:44_b2_a2_d2_i2 } - replace{ @atom:45 @atom:45_b21_a21_d21_i21 } - replace{ @atom:46 @atom:46_b10_a10_d10_i10 } - replace{ @atom:47 @atom:47_b21_a21_d21_i21 } - replace{ @atom:48 @atom:48_b13_a13_d13_i13 } - replace{ @atom:49 @atom:49_b21_a21_d21_i21 } - replace{ @atom:50 @atom:50_b22_a22_d22_i22 } - replace{ @atom:51 @atom:51_b23_a23_d23_i23 } - replace{ @atom:52 @atom:52_b6_a6_d6_i6 } - replace{ @atom:53 @atom:53_b4_a4_d4_i4 } - replace{ @atom:54 @atom:54_b24_a24_d24_i24 } - replace{ @atom:55 @atom:55_b3_a3_d3_i3 } - replace{ @atom:56 @atom:56_b6_a6_d6_i6 } - replace{ @atom:57 @atom:57_b25_a25_d25_i25 } - replace{ @atom:58 @atom:58_b26_a26_d26_i26 } - replace{ @atom:59 @atom:59_b27_a27_d27_i27 } - replace{ @atom:60 @atom:60_b28_a28_d28_i28 } - replace{ @atom:61 @atom:61_b29_a29_d29_i29 } - replace{ @atom:62 @atom:62_b30_a30_d30_i30 } - replace{ @atom:63 @atom:63_b31_a31_d31_i31 } - replace{ @atom:64 @atom:64_b32_a32_d32_i32 } - replace{ @atom:65 @atom:65_b31_a31_d31_i31 } - replace{ @atom:66 @atom:66_b32_a32_d32_i32 } - replace{ @atom:67 @atom:67_b33_a33_d33_i33 } - replace{ @atom:68 @atom:68_b34_a34_d34_i34 } - replace{ @atom:69 @atom:69_b35_a35_d35_i35 } - replace{ @atom:70 @atom:70_b36_a36_d36_i36 } - replace{ @atom:71 @atom:71_b37_a37_d37_i37 } - replace{ @atom:72 @atom:72_b38_a38_d38_i38 } - replace{ @atom:73 @atom:73_b39_a39_d39_i39 } - replace{ @atom:74 @atom:74_b40_a40_d40_i40 } - replace{ @atom:75 @atom:75_b41_a41_d41_i41 } - replace{ @atom:76 @atom:76_b42_a42_d42_i42 } - replace{ @atom:77 @atom:77_b43_a43_d43_i43 } - replace{ @atom:78 @atom:78_b44_a44_d44_i44 } - replace{ @atom:79 @atom:79_b45_a45_d45_i45 } - replace{ @atom:80 @atom:80_b13_a13_d13_i13 } - replace{ 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@atom:164_b16_a16_d16_i16 } - replace{ @atom:165 @atom:165_b13_a13_d13_i13 } - replace{ @atom:166 @atom:166_b13_a13_d13_i13 } - replace{ @atom:167 @atom:167_b13_a13_d13_i13 } - replace{ @atom:168 @atom:168_b21_a21_d21_i21 } - replace{ @atom:169 @atom:169_b47_a47_d47_i47 } - replace{ @atom:170 @atom:170_b48_a48_d48_i48 } - replace{ @atom:171 @atom:171_b13_a13_d13_i13 } - replace{ @atom:172 @atom:172_b13_a13_d13_i13 } - replace{ @atom:173 @atom:173_b3_a3_d3_i3 } - replace{ @atom:174 @atom:174_b3_a3_d3_i3 } - replace{ @atom:175 @atom:175_b3_a3_d3_i3 } - replace{ @atom:176 @atom:176_b3_a3_d3_i3 } - replace{ @atom:177 @atom:177_b3_a3_d3_i3 } - replace{ @atom:178 @atom:178_b4_a4_d4_i4 } - replace{ @atom:179 @atom:179_b24_a24_d24_i24 } - replace{ @atom:180 @atom:180_b24_a24_d24_i24 } - replace{ @atom:181 @atom:181_b24_a24_d24_i24 } - replace{ @atom:182 @atom:182_b45_a45_d45_i45 } - replace{ @atom:183 @atom:183_b45_a45_d45_i45 } - replace{ @atom:184 @atom:184_b13_a13_d13_i13 } - replace{ 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} - replace{ @atom:206 @atom:206_b21_a21_d21_i21 } - replace{ @atom:207 @atom:207_b24_a24_d24_i24 } - replace{ @atom:208 @atom:208_b48_a48_d48_i48 } - replace{ @atom:209 @atom:209_b3_a3_d3_i3 } - replace{ @atom:210 @atom:210_b4_a4_d4_i4 } - replace{ @atom:211 @atom:211_b5_a5_d5_i5 } - replace{ @atom:212 @atom:212_b7_a7_d7_i7 } - replace{ @atom:213 @atom:213_b3_a3_d3_i3 } - replace{ @atom:214 @atom:214_b52_a52_d52_i52 } - replace{ @atom:215 @atom:215_b13_a13_d13_i13 } - replace{ @atom:216 @atom:216_b13_a13_d13_i13 } - replace{ @atom:217 @atom:217_b13_a13_d13_i13 } - replace{ @atom:218 @atom:218_b13_a13_d13_i13 } - replace{ @atom:219 @atom:219_b3_a3_d3_i3 } - replace{ @atom:220 @atom:220_b4_a4_d4_i4 } - replace{ @atom:221 @atom:221_b46_a46_d46_i46 } - replace{ @atom:222 @atom:222_b3_a3_d3_i3 } - replace{ @atom:223 @atom:223_b4_a4_d4_i4 } - replace{ @atom:224 @atom:224_b46_a46_d46_i46 } - replace{ @atom:225 @atom:225_b13_a13_d13_i13 } - replace{ @atom:226 @atom:226_b13_a13_d13_i13 } - 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@atom:247_b54_a54_d54_i54 } - replace{ @atom:248 @atom:248_b13_a13_d13_i13 } - replace{ @atom:249 @atom:249_b13_a13_d13_i13 } - replace{ @atom:250 @atom:250_b13_a13_d13_i13 } - replace{ @atom:251 @atom:251_b13_a13_d13_i13 } - replace{ @atom:252 @atom:252_b53_a53_d53_i53 } - replace{ @atom:253 @atom:253_b54_a54_d54_i54 } - replace{ @atom:254 @atom:254_b56_a56_d56_i56 } - replace{ @atom:255 @atom:255_b48_a48_d48_i48 } - replace{ @atom:256 @atom:256_b55_a55_d55_i55 } - replace{ @atom:257 @atom:257_b45_a45_d45_i45 } - replace{ @atom:258 @atom:258_b48_a48_d48_i48 } - replace{ @atom:259 @atom:259_b49_a49_d49_i49 } - replace{ @atom:260 @atom:260_b48_a48_d48_i48 } - replace{ @atom:261 @atom:261_b49_a49_d49_i49 } - replace{ @atom:262 @atom:262_b57_a57_d57_i57 } - replace{ @atom:263 @atom:263_b3_a3_d3_i3 } - replace{ @atom:264 @atom:264_b57_a57_d57_i57 } - replace{ @atom:265 @atom:265_b3_a3_d3_i3 } - replace{ @atom:266 @atom:266_b47_a47_d47_i47 } - replace{ @atom:267 @atom:267_b47_a47_d47_i47 } - replace{ @atom:268 @atom:268_b45_a45_d45_i45 } - replace{ @atom:269 @atom:269_b4_a4_d4_i4 } - replace{ @atom:270 @atom:270_b45_a45_d45_i45 } - replace{ @atom:271 @atom:271_b4_a4_d4_i4 } - replace{ @atom:272 @atom:272_b46_a46_d46_i46 } - replace{ @atom:273 @atom:273_b46_a46_d46_i46 } - replace{ @atom:274 @atom:274_b13_a13_d13_i13 } - replace{ @atom:275 @atom:275_b46_a46_d46_i46 } - replace{ @atom:276 @atom:276_b57_a57_d57_i57 } - replace{ @atom:277 @atom:277_b3_a3_d3_i3 } - replace{ @atom:278 @atom:278_b56_a56_d56_i56 } - replace{ @atom:279 @atom:279_b48_a48_d48_i48 } - replace{ @atom:280 @atom:280_b47_a47_d47_i47 } - replace{ @atom:281 @atom:281_b47_a47_d47_i47 } - replace{ @atom:282 @atom:282_b45_a45_d45_i45 } - replace{ @atom:283 @atom:283_b4_a4_d4_i4 } - replace{ @atom:284 @atom:284_b55_a55_d55_i55 } - replace{ @atom:285 @atom:285_b45_a45_d45_i45 } - replace{ @atom:286 @atom:286_b45_a45_d45_i45 } - replace{ @atom:287 @atom:287_b46_a46_d46_i46 } - replace{ @atom:288 @atom:288_b58_a58_d58_i58 } - replace{ @atom:289 @atom:289_b56_a56_d56_i56 } - replace{ @atom:290 @atom:290_b59_a59_d59_i59 } - replace{ @atom:291 @atom:291_b56_a56_d56_i56 } - replace{ @atom:292 @atom:292_b60_a60_d60_i60 } - replace{ @atom:293 @atom:293_b60_a60_d60_i60 } - replace{ @atom:294 @atom:294_b48_a48_d48_i48 } - replace{ @atom:295 @atom:295_b61_a61_d61_i61 } - replace{ @atom:296 @atom:296_b62_a62_d62_i62 } - replace{ @atom:297 @atom:297_b57_a57_d57_i57 } - replace{ @atom:298 @atom:298_b63_a63_d63_i63 } - replace{ @atom:299 @atom:299_b55_a55_d55_i55 } - replace{ @atom:300 @atom:300_b45_a45_d45_i45 } - replace{ @atom:301 @atom:301_b45_a45_d45_i45 } - replace{ @atom:302 @atom:302_b63_a63_d63_i63 } - replace{ @atom:303 @atom:303_b45_a45_d45_i45 } - replace{ @atom:304 @atom:304_b57_a57_d57_i57 } - replace{ @atom:305 @atom:305_b48_a48_d48_i48 } - replace{ @atom:306 @atom:306_b56_a56_d56_i56 } - replace{ @atom:307 @atom:307_b60_a60_d60_i60 } - replace{ @atom:308 @atom:308_b60_a60_d60_i60 } - replace{ @atom:309 @atom:309_b3_a3_d3_i3 } - replace{ @atom:310 @atom:310_b45_a45_d45_i45 } - replace{ @atom:311 @atom:311_b55_a55_d55_i55 } - replace{ @atom:312 @atom:312_b45_a45_d45_i45 } - replace{ @atom:313 @atom:313_b4_a4_d4_i4 } - replace{ @atom:314 @atom:314_b13_a13_d13_i13 } - replace{ @atom:315 @atom:315_b46_a46_d46_i46 } - replace{ @atom:316 @atom:316_b13_a13_d13_i13 } - replace{ @atom:317 @atom:317_b46_a46_d46_i46 } - replace{ @atom:318 @atom:318_b13_a13_d13_i13 } - replace{ @atom:319 @atom:319_b46_a46_d46_i46 } - replace{ @atom:320 @atom:320_b57_a57_d57_i57 } - replace{ @atom:321 @atom:321_b3_a3_d3_i3 } - replace{ @atom:322 @atom:322_b57_a57_d57_i57 } - replace{ @atom:323 @atom:323_b48_a48_d48_i48 } - replace{ @atom:324 @atom:324_b47_a47_d47_i47 } - replace{ @atom:325 @atom:325_b47_a47_d47_i47 } - replace{ @atom:326 @atom:326_b45_a45_d45_i45 } - replace{ @atom:327 @atom:327_b4_a4_d4_i4 } - replace{ @atom:328 @atom:328_b45_a45_d45_i45 } - 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@atom:349_b69_a69_d69_i69 } - replace{ @atom:350 @atom:350_b70_a70_d70_i70 } - replace{ @atom:351 @atom:351_b71_a71_d71_i71 } - replace{ @atom:352 @atom:352_b72_a72_d72_i72 } - replace{ @atom:353 @atom:353_b73_a73_d73_i73 } - replace{ @atom:354 @atom:354_b74_a74_d74_i74 } - replace{ @atom:355 @atom:355_b75_a75_d75_i75 } - replace{ @atom:356 @atom:356_b76_a76_d76_i76 } - replace{ @atom:357 @atom:357_b6_a6_d6_i6 } - replace{ @atom:358 @atom:358_b46_a46_d46_i46 } - replace{ @atom:359 @atom:359_b15_a15_d15_i15 } - replace{ @atom:360 @atom:360_b6_a6_d6_i6 } - replace{ @atom:361 @atom:361_b46_a46_d46_i46 } - replace{ @atom:362 @atom:362_b5_a5_d5_i5 } - replace{ @atom:363 @atom:363_b13_a13_d13_i13 } - replace{ @atom:364 @atom:364_b46_a46_d46_i46 } - replace{ @atom:365 @atom:365_b19_a19_d19_i19 } - replace{ @atom:366 @atom:366_b18_a18_d18_i18 } - replace{ @atom:367 @atom:367_b6_a6_d6_i6 } - replace{ @atom:368 @atom:368_b46_a46_d46_i46 } - replace{ @atom:369 @atom:369_b53_a53_d53_i53 } - replace{ @atom:370 @atom:370_b45_a45_d45_i45 } - replace{ @atom:371 @atom:371_b6_a6_d6_i6 } - replace{ @atom:372 @atom:372_b46_a46_d46_i46 } - replace{ @atom:373 @atom:373_b13_a13_d13_i13 } - replace{ @atom:374 @atom:374_b46_a46_d46_i46 } - replace{ @atom:375 @atom:375_b33_a33_d33_i33 } - replace{ @atom:376 @atom:376_b5_a5_d5_i5 } - replace{ @atom:377 @atom:377_b7_a7_d7_i7 } - replace{ @atom:378 @atom:378_b77_a77_d77_i77 } - replace{ @atom:379 @atom:379_b78_a78_d78_i78 } - replace{ @atom:380 @atom:380_b20_a20_d20_i20 } - replace{ @atom:381 @atom:381_b64_a64_d64_i64 } - replace{ @atom:382 @atom:382_b52_a52_d52_i52 } - replace{ @atom:383 @atom:383_b20_a20_d20_i20 } - replace{ @atom:384 @atom:384_b13_a13_d13_i13 } - replace{ @atom:385 @atom:385_b46_a46_d46_i46 } - replace{ @atom:386 @atom:386_b64_a64_d64_i64 } - replace{ @atom:387 @atom:387_b52_a52_d52_i52 } - replace{ @atom:388 @atom:388_b20_a20_d20_i20 } - replace{ @atom:389 @atom:389_b13_a13_d13_i13 } - replace{ @atom:390 @atom:390_b46_a46_d46_i46 } - replace{ @atom:391 @atom:391_b64_a64_d64_i64 } - replace{ @atom:392 @atom:392_b52_a52_d52_i52 } - replace{ @atom:393 @atom:393_b20_a20_d20_i20 } - replace{ @atom:394 @atom:394_b13_a13_d13_i13 } - replace{ @atom:395 @atom:395_b46_a46_d46_i46 } - replace{ @atom:396 @atom:396_b13_a13_d13_i13 } - replace{ @atom:397 @atom:397_b46_a46_d46_i46 } - replace{ @atom:398 @atom:398_b48_a48_d48_i48 } - replace{ @atom:399 @atom:399_b13_a13_d13_i13 } - replace{ @atom:400 @atom:400_b46_a46_d46_i46 } - replace{ @atom:401 @atom:401_b48_a48_d48_i48 } - replace{ @atom:402 @atom:402_b13_a13_d13_i13 } - replace{ @atom:403 @atom:403_b46_a46_d46_i46 } - replace{ @atom:404 @atom:404_b48_a48_d48_i48 } - replace{ @atom:405 @atom:405_b13_a13_d13_i13 } - replace{ @atom:406 @atom:406_b3_a3_d3_i3 } - replace{ @atom:407 @atom:407_b4_a4_d4_i4 } - replace{ @atom:408 @atom:408_b20_a20_d20_i20 } - replace{ @atom:409 @atom:409_b13_a13_d13_i13 } - replace{ @atom:410 @atom:410_b46_a46_d46_i46 } - replace{ @atom:411 @atom:411_b3_a3_d3_i3 } - replace{ @atom:412 @atom:412_b3_a3_d3_i3 } - replace{ @atom:413 @atom:413_b48_a48_d48_i48 } - replace{ @atom:414 @atom:414_b20_a20_d20_i20 } - replace{ @atom:415 @atom:415_b79_a79_d79_i79 } - replace{ @atom:416 @atom:416_b23_a23_d23_i23 } - replace{ @atom:417 @atom:417_b13_a13_d13_i13 } - replace{ @atom:418 @atom:418_b46_a46_d46_i46 } - replace{ @atom:419 @atom:419_b24_a24_d24_i24 } - replace{ @atom:420 @atom:420_b45_a45_d45_i45 } - replace{ @atom:421 @atom:421_b24_a24_d24_i24 } - replace{ @atom:422 @atom:422_b45_a45_d45_i45 } - replace{ @atom:423 @atom:423_b13_a13_d13_i13 } - replace{ @atom:424 @atom:424_b46_a46_d46_i46 } - replace{ @atom:425 @atom:425_b13_a13_d13_i13 } - replace{ @atom:426 @atom:426_b46_a46_d46_i46 } - replace{ @atom:427 @atom:427_b13_a13_d13_i13 } - replace{ @atom:428 @atom:428_b46_a46_d46_i46 } - replace{ @atom:429 @atom:429_b48_a48_d48_i48 } - replace{ @atom:430 @atom:430_b48_a48_d48_i48 } - replace{ @atom:431 @atom:431_b13_a13_d13_i13 } - replace{ @atom:432 @atom:432_b13_a13_d13_i13 } - replace{ @atom:433 @atom:433_b13_a13_d13_i13 } - replace{ @atom:434 @atom:434_b79_a79_d79_i79 } - replace{ @atom:435 @atom:435_b23_a23_d23_i23 } - replace{ @atom:436 @atom:436_b22_a22_d22_i22 } - replace{ @atom:437 @atom:437_b22_a22_d22_i22 } - replace{ @atom:438 @atom:438_b23_a23_d23_i23 } - replace{ @atom:439 @atom:439_b13_a13_d13_i13 } - replace{ @atom:440 @atom:440_b13_a13_d13_i13 } - replace{ @atom:441 @atom:441_b80_a80_d80_i80 } - replace{ @atom:442 @atom:442_b60_a60_d60_i60 } - replace{ @atom:443 @atom:443_b81_a81_d81_i81 } - replace{ @atom:444 @atom:444_b57_a57_d57_i57 } - replace{ @atom:445 @atom:445_b45_a45_d45_i45 } - replace{ @atom:446 @atom:446_b13_a13_d13_i13 } - replace{ @atom:447 @atom:447_b82_a82_d82_i82 } - replace{ @atom:448 @atom:448_b83_a83_d83_i83 } - replace{ @atom:449 @atom:449_b84_a84_d84_i84 } - replace{ @atom:450 @atom:450_b82_a82_d82_i82 } - replace{ @atom:451 @atom:451_b85_a85_d85_i85 } - replace{ @atom:452 @atom:452_b61_a61_d61_i61 } - replace{ @atom:453 @atom:453_b57_a57_d57_i57 } - replace{ @atom:454 @atom:454_b45_a45_d45_i45 } - replace{ @atom:455 @atom:455_b84_a84_d84_i84 } - replace{ @atom:456 @atom:456_b13_a13_d13_i13 } - replace{ @atom:457 @atom:457_b13_a13_d13_i13 } - replace{ @atom:458 @atom:458_b47_a47_d47_i47 } - replace{ @atom:459 @atom:459_b47_a47_d47_i47 } - replace{ @atom:460 @atom:460_b86_a86_d86_i86 } - replace{ @atom:461 @atom:461_b56_a56_d56_i56 } - replace{ @atom:462 @atom:462_b48_a48_d48_i48 } - replace{ @atom:463 @atom:463_b48_a48_d48_i48 } - replace{ @atom:464 @atom:464_b48_a48_d48_i48 } - replace{ @atom:465 @atom:465_b49_a49_d49_i49 } - replace{ @atom:466 @atom:466_b49_a49_d49_i49 } - replace{ @atom:467 @atom:467_b49_a49_d49_i49 } - replace{ @atom:468 @atom:468_b56_a56_d56_i56 } - replace{ @atom:469 @atom:469_b48_a48_d48_i48 } - replace{ @atom:470 @atom:470_b49_a49_d49_i49 } - replace{ @atom:471 @atom:471_b56_a56_d56_i56 } - replace{ @atom:472 @atom:472_b59_a59_d59_i59 } - replace{ @atom:473 @atom:473_b48_a48_d48_i48 } - replace{ @atom:474 @atom:474_b48_a48_d48_i48 } - replace{ @atom:475 @atom:475_b49_a49_d49_i49 } - replace{ @atom:476 @atom:476_b49_a49_d49_i49 } - replace{ @atom:477 @atom:477_b49_a49_d49_i49 } - replace{ @atom:478 @atom:478_b56_a56_d56_i56 } - replace{ @atom:479 @atom:479_b48_a48_d48_i48 } - replace{ @atom:480 @atom:480_b48_a48_d48_i48 } - replace{ @atom:481 @atom:481_b49_a49_d49_i49 } - replace{ @atom:482 @atom:482_b49_a49_d49_i49 } - replace{ @atom:483 @atom:483_b57_a57_d57_i57 } - replace{ @atom:484 @atom:484_b84_a84_d84_i84 } - replace{ @atom:485 @atom:485_b87_a87_d87_i87 } - replace{ @atom:486 @atom:486_b45_a45_d45_i45 } - replace{ @atom:487 @atom:487_b49_a49_d49_i49 } - replace{ @atom:488 @atom:488_b49_a49_d49_i49 } - replace{ @atom:489 @atom:489_b57_a57_d57_i57 } - replace{ @atom:490 @atom:490_b61_a61_d61_i61 } - replace{ @atom:491 @atom:491_b88_a88_d88_i88 } - replace{ @atom:492 @atom:492_b87_a87_d87_i87 } - replace{ @atom:493 @atom:493_b84_a84_d84_i84 } - replace{ @atom:494 @atom:494_b45_a45_d45_i45 } - replace{ @atom:495 @atom:495_b49_a49_d49_i49 } - replace{ @atom:496 @atom:496_b49_a49_d49_i49 } - replace{ @atom:497 @atom:497_b49_a49_d49_i49 } - replace{ @atom:498 @atom:498_b57_a57_d57_i57 } - replace{ @atom:499 @atom:499_b82_a82_d82_i82 } - replace{ @atom:500 @atom:500_b61_a61_d61_i61 } - replace{ @atom:501 @atom:501_b83_a83_d83_i83 } - replace{ @atom:502 @atom:502_b84_a84_d84_i84 } - replace{ @atom:503 @atom:503_b45_a45_d45_i45 } - replace{ @atom:504 @atom:504_b49_a49_d49_i49 } - replace{ @atom:505 @atom:505_b49_a49_d49_i49 } - replace{ @atom:506 @atom:506_b49_a49_d49_i49 } - replace{ @atom:507 @atom:507_b20_a20_d20_i20 } - replace{ @atom:508 @atom:508_b84_a84_d84_i84 } - replace{ @atom:509 @atom:509_b87_a87_d87_i87 } - replace{ @atom:510 @atom:510_b49_a49_d49_i49 } - replace{ @atom:511 @atom:511_b49_a49_d49_i49 } - replace{ @atom:512 @atom:512_b20_a20_d20_i20 } - replace{ @atom:513 @atom:513_b82_a82_d82_i82 } - replace{ @atom:514 @atom:514_b61_a61_d61_i61 } - replace{ @atom:515 @atom:515_b83_a83_d83_i83 } - replace{ @atom:516 @atom:516_b84_a84_d84_i84 } - replace{ @atom:517 @atom:517_b49_a49_d49_i49 } - replace{ @atom:518 @atom:518_b49_a49_d49_i49 } - replace{ @atom:519 @atom:519_b49_a49_d49_i49 } - replace{ @atom:520 @atom:520_b20_a20_d20_i20 } - replace{ @atom:521 @atom:521_b61_a61_d61_i61 } - replace{ @atom:522 @atom:522_b88_a88_d88_i88 } - replace{ @atom:523 @atom:523_b87_a87_d87_i87 } - replace{ @atom:524 @atom:524_b84_a84_d84_i84 } - replace{ @atom:525 @atom:525_b49_a49_d49_i49 } - replace{ @atom:526 @atom:526_b49_a49_d49_i49 } - replace{ @atom:527 @atom:527_b49_a49_d49_i49 } - replace{ @atom:528 @atom:528_b57_a57_d57_i57 } - replace{ @atom:529 @atom:529_b84_a84_d84_i84 } - replace{ @atom:530 @atom:530_b87_a87_d87_i87 } - replace{ @atom:531 @atom:531_b48_a48_d48_i48 } - replace{ @atom:532 @atom:532_b48_a48_d48_i48 } - replace{ @atom:533 @atom:533_b48_a48_d48_i48 } - replace{ @atom:534 @atom:534_b48_a48_d48_i48 } - replace{ @atom:535 @atom:535_b81_a81_d81_i81 } - replace{ @atom:536 @atom:536_b60_a60_d60_i60 } - replace{ @atom:537 @atom:537_b45_a45_d45_i45 } - replace{ @atom:538 @atom:538_b49_a49_d49_i49 } - replace{ @atom:539 @atom:539_b49_a49_d49_i49 } - replace{ @atom:540 @atom:540_b49_a49_d49_i49 } - replace{ @atom:541 @atom:541_b49_a49_d49_i49 } - replace{ @atom:542 @atom:542_b49_a49_d49_i49 } - replace{ @atom:543 @atom:543_b49_a49_d49_i49 } - replace{ @atom:544 @atom:544_b56_a56_d56_i56 } - replace{ @atom:545 @atom:545_b48_a48_d48_i48 } - replace{ @atom:546 @atom:546_b48_a48_d48_i48 } - replace{ @atom:547 @atom:547_b48_a48_d48_i48 } - replace{ @atom:548 @atom:548_b48_a48_d48_i48 } - replace{ @atom:549 @atom:549_b48_a48_d48_i48 } - replace{ @atom:550 @atom:550_b48_a48_d48_i48 } - replace{ @atom:551 @atom:551_b48_a48_d48_i48 } - replace{ @atom:552 @atom:552_b48_a48_d48_i48 } - replace{ @atom:553 @atom:553_b48_a48_d48_i48 } - replace{ @atom:554 @atom:554_b49_a49_d49_i49 } - replace{ @atom:555 @atom:555_b49_a49_d49_i49 } - replace{ @atom:556 @atom:556_b49_a49_d49_i49 } - replace{ @atom:557 @atom:557_b49_a49_d49_i49 } - replace{ @atom:558 @atom:558_b49_a49_d49_i49 } - replace{ @atom:559 @atom:559_b49_a49_d49_i49 } - replace{ @atom:560 @atom:560_b49_a49_d49_i49 } - replace{ @atom:561 @atom:561_b56_a56_d56_i56 } - replace{ @atom:562 @atom:562_b59_a59_d59_i59 } - replace{ @atom:563 @atom:563_b56_a56_d56_i56 } - replace{ @atom:564 @atom:564_b60_a60_d60_i60 } - replace{ @atom:565 @atom:565_b60_a60_d60_i60 } - replace{ @atom:566 @atom:566_b48_a48_d48_i48 } - replace{ @atom:567 @atom:567_b61_a61_d61_i61 } - replace{ @atom:568 @atom:568_b62_a62_d62_i62 } - replace{ @atom:569 @atom:569_b57_a57_d57_i57 } - replace{ @atom:570 @atom:570_b49_a49_d49_i49 } - replace{ @atom:571 @atom:571_b49_a49_d49_i49 } - replace{ @atom:572 @atom:572_b49_a49_d49_i49 } - replace{ @atom:573 @atom:573_b45_a45_d45_i45 } - replace{ @atom:574 @atom:574_b16_a16_d16_i16 } - replace{ @atom:575 @atom:575_b82_a82_d82_i82 } - replace{ @atom:576 @atom:576_b61_a61_d61_i61 } - replace{ @atom:577 @atom:577_b83_a83_d83_i83 } - replace{ @atom:578 @atom:578_b84_a84_d84_i84 } - replace{ @atom:579 @atom:579_b49_a49_d49_i49 } - replace{ @atom:580 @atom:580_b49_a49_d49_i49 } - replace{ @atom:581 @atom:581_b49_a49_d49_i49 } - replace{ @atom:582 @atom:582_b56_a56_d56_i56 } - replace{ @atom:583 @atom:583_b59_a59_d59_i59 } - replace{ @atom:584 @atom:584_b49_a49_d49_i49 } - replace{ @atom:585 @atom:585_b48_a48_d48_i48 } - replace{ @atom:586 @atom:586_b13_a13_d13_i13 } - replace{ @atom:587 @atom:587_b56_a56_d56_i56 } - replace{ @atom:588 @atom:588_b48_a48_d48_i48 } - replace{ @atom:589 @atom:589_b48_a48_d48_i48 } - replace{ @atom:590 @atom:590_b48_a48_d48_i48 } - replace{ @atom:591 @atom:591_b48_a48_d48_i48 } - replace{ @atom:592 @atom:592_b48_a48_d48_i48 } - replace{ @atom:593 @atom:593_b48_a48_d48_i48 } - replace{ @atom:594 @atom:594_b49_a49_d49_i49 } - replace{ @atom:595 @atom:595_b49_a49_d49_i49 } - replace{ @atom:596 @atom:596_b49_a49_d49_i49 } - replace{ @atom:597 @atom:597_b49_a49_d49_i49 } - replace{ @atom:598 @atom:598_b57_a57_d57_i57 } - replace{ @atom:599 @atom:599_b82_a82_d82_i82 } - replace{ @atom:600 @atom:600_b61_a61_d61_i61 } - replace{ @atom:601 @atom:601_b83_a83_d83_i83 } - replace{ @atom:602 @atom:602_b84_a84_d84_i84 } - replace{ @atom:603 @atom:603_b13_a13_d13_i13 } - replace{ @atom:604 @atom:604_b49_a49_d49_i49 } - replace{ @atom:605 @atom:605_b49_a49_d49_i49 } - replace{ @atom:606 @atom:606_b49_a49_d49_i49 } - replace{ @atom:607 @atom:607_b46_a46_d46_i46 } - replace{ @atom:608 @atom:608_b13_a13_d13_i13 } - replace{ @atom:609 @atom:609_b13_a13_d13_i13 } - replace{ @atom:610 @atom:610_b13_a13_d13_i13 } - replace{ @atom:611 @atom:611_b13_a13_d13_i13 } - replace{ @atom:612 @atom:612_b13_a13_d13_i13 } - replace{ @atom:613 @atom:613_b13_a13_d13_i13 } - replace{ @atom:614 @atom:614_b13_a13_d13_i13 } - replace{ @atom:615 @atom:615_b13_a13_d13_i13 } - replace{ @atom:616 @atom:616_b13_a13_d13_i13 } - replace{ @atom:617 @atom:617_b13_a13_d13_i13 } - replace{ @atom:618 @atom:618_b13_a13_d13_i13 } - replace{ @atom:619 @atom:619_b13_a13_d13_i13 } - replace{ @atom:620 @atom:620_b13_a13_d13_i13 } - replace{ @atom:621 @atom:621_b13_a13_d13_i13 } - replace{ @atom:622 @atom:622_b13_a13_d13_i13 } - replace{ @atom:623 @atom:623_b15_a15_d15_i15 } - replace{ @atom:624 @atom:624_b17_a17_d17_i17 } - replace{ @atom:625 @atom:625_b48_a48_d48_i48 } - replace{ @atom:626 @atom:626_b89_a89_d89_i89 } - replace{ @atom:627 @atom:627_b90_a90_d90_i90 } - replace{ @atom:628 @atom:628_b91_a91_d91_i91 } - replace{ @atom:629 @atom:629_b91_a91_d91_i91 } - replace{ @atom:630 @atom:630_b13_a13_d13_i13 } - replace{ @atom:631 @atom:631_b86_a86_d86_i86 } - replace{ @atom:632 @atom:632_b86_a86_d86_i86 } - replace{ @atom:633 @atom:633_b86_a86_d86_i86 } - replace{ @atom:634 @atom:634_b86_a86_d86_i86 } - replace{ @atom:635 @atom:635_b86_a86_d86_i86 } - replace{ @atom:636 @atom:636_b86_a86_d86_i86 } - replace{ @atom:637 @atom:637_b16_a16_d16_i16 } - replace{ @atom:638 @atom:638_b92_a92_d92_i92 } - replace{ @atom:639 @atom:639_b93_a93_d93_i93 } - replace{ @atom:640 @atom:640_b94_a94_d94_i94 } - replace{ @atom:641 @atom:641_b95_a95_d95_i95 } - replace{ @atom:642 @atom:642_b13_a13_d13_i13 } - replace{ @atom:643 @atom:643_b46_a46_d46_i46 } - replace{ @atom:644 @atom:644_b96_a96_d96_i96 } - replace{ @atom:645 @atom:645_b97_a97_d97_i97 } - replace{ @atom:646 @atom:646_b98_a98_d98_i98 } - replace{ @atom:647 @atom:647_b99_a99_d99_i99 } + replace{ @atom:1 @atom:1_b001_a001_d001_i001 } + replace{ @atom:2 @atom:2_b002_a002_d002_i002 } + replace{ @atom:3 @atom:3_b003_a003_d003_i003 } + replace{ @atom:4 @atom:4_b004_a004_d004_i004 } + replace{ @atom:5 @atom:5_b005_a005_d005_i005 } + replace{ @atom:6 @atom:6_b006_a006_d006_i006 } + replace{ @atom:7 @atom:7_b007_a007_d007_i007 } + replace{ @atom:8 @atom:8_b008_a008_d008_i008 } + replace{ @atom:9 @atom:9_b006_a006_d006_i006 } + replace{ @atom:10 @atom:10_b006_a006_d006_i006 } + replace{ @atom:11 @atom:11_b006_a006_d006_i006 } + replace{ @atom:12 @atom:12_b006_a006_d006_i006 } + replace{ @atom:13 @atom:13_b002_a002_d002_i002 } + replace{ @atom:14 @atom:14_b009_a009_d009_i009 } + replace{ @atom:15 @atom:15_b010_a010_d010_i010 } + replace{ @atom:16 @atom:16_b011_a011_d011_i011 } + replace{ @atom:17 @atom:17_b012_a012_d012_i012 } + replace{ @atom:18 @atom:18_b013_a013_d013_i013 } + replace{ @atom:19 @atom:19_b014_a014_d014_i014 } + replace{ @atom:20 @atom:20_b005_a005_d005_i005 } + replace{ @atom:21 @atom:21_b007_a007_d007_i007 } + replace{ @atom:22 @atom:22_b006_a006_d006_i006 } + replace{ @atom:23 @atom:23_b002_a002_d002_i002 } + replace{ @atom:24 @atom:24_b015_a015_d015_i015 } + replace{ @atom:25 @atom:25_b015_a015_d015_i015 } + replace{ @atom:26 @atom:26_b016_a016_d016_i016 } + replace{ @atom:27 @atom:27_b016_a016_d016_i016 } + replace{ @atom:28 @atom:28_b017_a017_d017_i017 } + replace{ @atom:29 @atom:29_b017_a017_d017_i017 } + replace{ @atom:30 @atom:30_b006_a006_d006_i006 } + replace{ @atom:31 @atom:31_b002_a002_d002_i002 } + replace{ @atom:32 @atom:32_b006_a006_d006_i006 } + replace{ @atom:33 @atom:33_b002_a002_d002_i002 } + replace{ @atom:34 @atom:34_b006_a006_d006_i006 } + replace{ @atom:35 @atom:35_b002_a002_d002_i002 } + replace{ @atom:36 @atom:36_b018_a018_d018_i018 } + replace{ @atom:37 @atom:37_b019_a019_d019_i019 } + replace{ @atom:38 @atom:38_b006_a006_d006_i006 } + replace{ @atom:39 @atom:39_b010_a010_d010_i010 } + replace{ @atom:40 @atom:40_b013_a013_d013_i013 } + replace{ @atom:41 @atom:41_b020_a020_d020_i020 } + replace{ @atom:42 @atom:42_b006_a006_d006_i006 } + replace{ @atom:43 @atom:43_b002_a002_d002_i002 } + replace{ @atom:44 @atom:44_b002_a002_d002_i002 } + replace{ @atom:45 @atom:45_b021_a021_d021_i021 } + replace{ @atom:46 @atom:46_b010_a010_d010_i010 } + replace{ @atom:47 @atom:47_b021_a021_d021_i021 } + replace{ @atom:48 @atom:48_b013_a013_d013_i013 } + replace{ @atom:49 @atom:49_b021_a021_d021_i021 } + replace{ @atom:50 @atom:50_b022_a022_d022_i022 } + replace{ @atom:51 @atom:51_b023_a023_d023_i023 } + replace{ @atom:52 @atom:52_b006_a006_d006_i006 } + replace{ @atom:53 @atom:53_b004_a004_d004_i004 } + replace{ @atom:54 @atom:54_b024_a024_d024_i024 } + replace{ @atom:55 @atom:55_b003_a003_d003_i003 } + replace{ @atom:56 @atom:56_b006_a006_d006_i006 } + replace{ @atom:57 @atom:57_b025_a025_d025_i025 } + replace{ @atom:58 @atom:58_b026_a026_d026_i026 } + replace{ @atom:59 @atom:59_b027_a027_d027_i027 } + replace{ @atom:60 @atom:60_b028_a028_d028_i028 } + replace{ @atom:61 @atom:61_b029_a029_d029_i029 } + replace{ @atom:62 @atom:62_b030_a030_d030_i030 } + replace{ @atom:63 @atom:63_b031_a031_d031_i031 } + replace{ @atom:64 @atom:64_b032_a032_d032_i032 } + replace{ @atom:65 @atom:65_b031_a031_d031_i031 } + replace{ @atom:66 @atom:66_b032_a032_d032_i032 } + replace{ @atom:67 @atom:67_b033_a033_d033_i033 } + replace{ @atom:68 @atom:68_b034_a034_d034_i034 } + replace{ @atom:69 @atom:69_b035_a035_d035_i035 } + replace{ @atom:70 @atom:70_b036_a036_d036_i036 } + replace{ @atom:71 @atom:71_b037_a037_d037_i037 } + replace{ @atom:72 @atom:72_b038_a038_d038_i038 } + replace{ @atom:73 @atom:73_b039_a039_d039_i039 } + replace{ @atom:74 @atom:74_b040_a040_d040_i040 } + replace{ @atom:75 @atom:75_b041_a041_d041_i041 } + replace{ @atom:76 @atom:76_b042_a042_d042_i042 } + replace{ @atom:77 @atom:77_b043_a043_d043_i043 } + replace{ @atom:78 @atom:78_b044_a044_d044_i044 } + replace{ @atom:79 @atom:79_b045_a045_d045_i045 } + replace{ @atom:80 @atom:80_b013_a013_d013_i013 } + replace{ @atom:81 @atom:81_b013_a013_d013_i013 } + replace{ @atom:82 @atom:82_b013_a013_d013_i013 } + replace{ @atom:83 @atom:83_b013_a013_d013_i013 } + replace{ @atom:84 @atom:84_b013_a013_d013_i013 } + replace{ @atom:85 @atom:85_b046_a046_d046_i046 } + replace{ @atom:86 @atom:86_b047_a047_d047_i047 } + replace{ @atom:87 @atom:87_b047_a047_d047_i047 } + replace{ @atom:88 @atom:88_b047_a047_d047_i047 } + replace{ @atom:89 @atom:89_b046_a046_d046_i046 } + replace{ @atom:90 @atom:90_b048_a048_d048_i048 } + replace{ @atom:91 @atom:91_b049_a049_d049_i049 } + replace{ @atom:92 @atom:92_b048_a048_d048_i048 } + replace{ @atom:93 @atom:93_b013_a013_d013_i013 } + replace{ @atom:94 @atom:94_b013_a013_d013_i013 } + replace{ @atom:95 @atom:95_b050_a050_d050_i050 } + replace{ @atom:96 @atom:96_b005_a005_d005_i005 } + replace{ @atom:97 @atom:97_b007_a007_d007_i007 } + replace{ @atom:98 @atom:98_b046_a046_d046_i046 } + replace{ @atom:99 @atom:99_b013_a013_d013_i013 } + replace{ @atom:100 @atom:100_b013_a013_d013_i013 } + replace{ @atom:101 @atom:101_b013_a013_d013_i013 } + replace{ @atom:102 @atom:102_b013_a013_d013_i013 } + replace{ @atom:103 @atom:103_b013_a013_d013_i013 } + replace{ @atom:104 @atom:104_b005_a005_d005_i005 } + replace{ @atom:105 @atom:105_b007_a007_d007_i007 } + replace{ @atom:106 @atom:106_b001_a001_d001_i001 } + replace{ @atom:107 @atom:107_b046_a046_d046_i046 } + replace{ @atom:108 @atom:108_b048_a048_d048_i048 } + replace{ @atom:109 @atom:109_b005_a005_d005_i005 } + replace{ @atom:110 @atom:110_b007_a007_d007_i007 } + replace{ @atom:111 @atom:111_b005_a005_d005_i005 } + replace{ @atom:112 @atom:112_b007_a007_d007_i007 } + replace{ @atom:113 @atom:113_b005_a005_d005_i005 } + replace{ @atom:114 @atom:114_b007_a007_d007_i007 } + replace{ @atom:115 @atom:115_b013_a013_d013_i013 } + replace{ @atom:116 @atom:116_b013_a013_d013_i013 } + replace{ @atom:117 @atom:117_b013_a013_d013_i013 } + replace{ @atom:118 @atom:118_b046_a046_d046_i046 } + replace{ @atom:119 @atom:119_b020_a020_d020_i020 } + replace{ @atom:120 @atom:120_b050_a050_d050_i050 } + replace{ @atom:121 @atom:121_b020_a020_d020_i020 } + replace{ @atom:122 @atom:122_b020_a020_d020_i020 } + replace{ @atom:123 @atom:123_b013_a013_d013_i013 } + replace{ @atom:124 @atom:124_b013_a013_d013_i013 } + replace{ @atom:125 @atom:125_b013_a013_d013_i013 } + replace{ @atom:126 @atom:126_b013_a013_d013_i013 } + replace{ @atom:127 @atom:127_b046_a046_d046_i046 } + replace{ @atom:128 @atom:128_b020_a020_d020_i020 } + replace{ @atom:129 @atom:129_b005_a005_d005_i005 } + replace{ @atom:130 @atom:130_b007_a007_d007_i007 } + replace{ @atom:131 @atom:131_b051_a051_d051_i051 } + replace{ @atom:132 @atom:132_b046_a046_d046_i046 } + replace{ @atom:133 @atom:133_b051_a051_d051_i051 } + replace{ @atom:134 @atom:134_b046_a046_d046_i046 } + replace{ @atom:135 @atom:135_b051_a051_d051_i051 } + replace{ @atom:136 @atom:136_b046_a046_d046_i046 } + replace{ @atom:137 @atom:137_b051_a051_d051_i051 } + replace{ @atom:138 @atom:138_b046_a046_d046_i046 } + replace{ @atom:139 @atom:139_b051_a051_d051_i051 } + replace{ @atom:140 @atom:140_b051_a051_d051_i051 } + replace{ @atom:141 @atom:141_b048_a048_d048_i048 } + replace{ @atom:142 @atom:142_b015_a015_d015_i015 } + replace{ @atom:143 @atom:143_b015_a015_d015_i015 } + replace{ @atom:144 @atom:144_b016_a016_d016_i016 } + replace{ @atom:145 @atom:145_b016_a016_d016_i016 } + replace{ @atom:146 @atom:146_b017_a017_d017_i017 } + replace{ @atom:147 @atom:147_b017_a017_d017_i017 } + replace{ @atom:148 @atom:148_b013_a013_d013_i013 } + replace{ @atom:149 @atom:149_b013_a013_d013_i013 } + replace{ @atom:150 @atom:150_b013_a013_d013_i013 } + replace{ @atom:151 @atom:151_b013_a013_d013_i013 } + replace{ @atom:152 @atom:152_b013_a013_d013_i013 } + replace{ @atom:153 @atom:153_b013_a013_d013_i013 } + replace{ @atom:154 @atom:154_b013_a013_d013_i013 } + replace{ @atom:155 @atom:155_b013_a013_d013_i013 } + replace{ @atom:156 @atom:156_b013_a013_d013_i013 } + replace{ @atom:157 @atom:157_b013_a013_d013_i013 } + replace{ @atom:158 @atom:158_b013_a013_d013_i013 } + replace{ @atom:159 @atom:159_b013_a013_d013_i013 } + replace{ @atom:160 @atom:160_b013_a013_d013_i013 } + replace{ @atom:161 @atom:161_b013_a013_d013_i013 } + replace{ @atom:162 @atom:162_b013_a013_d013_i013 } + replace{ @atom:163 @atom:163_b048_a048_d048_i048 } + replace{ @atom:164 @atom:164_b016_a016_d016_i016 } + replace{ @atom:165 @atom:165_b013_a013_d013_i013 } + replace{ @atom:166 @atom:166_b013_a013_d013_i013 } + replace{ @atom:167 @atom:167_b013_a013_d013_i013 } + replace{ @atom:168 @atom:168_b021_a021_d021_i021 } + replace{ @atom:169 @atom:169_b047_a047_d047_i047 } + replace{ @atom:170 @atom:170_b048_a048_d048_i048 } + replace{ @atom:171 @atom:171_b013_a013_d013_i013 } + replace{ @atom:172 @atom:172_b013_a013_d013_i013 } + replace{ @atom:173 @atom:173_b003_a003_d003_i003 } + replace{ @atom:174 @atom:174_b003_a003_d003_i003 } + replace{ @atom:175 @atom:175_b003_a003_d003_i003 } + replace{ @atom:176 @atom:176_b003_a003_d003_i003 } + replace{ @atom:177 @atom:177_b003_a003_d003_i003 } + replace{ @atom:178 @atom:178_b004_a004_d004_i004 } + replace{ @atom:179 @atom:179_b024_a024_d024_i024 } + replace{ @atom:180 @atom:180_b024_a024_d024_i024 } + replace{ @atom:181 @atom:181_b024_a024_d024_i024 } + replace{ @atom:182 @atom:182_b045_a045_d045_i045 } + replace{ @atom:183 @atom:183_b045_a045_d045_i045 } + replace{ @atom:184 @atom:184_b013_a013_d013_i013 } + replace{ @atom:185 @atom:185_b013_a013_d013_i013 } + replace{ @atom:186 @atom:186_b013_a013_d013_i013 } + replace{ @atom:187 @atom:187_b013_a013_d013_i013 } + replace{ @atom:188 @atom:188_b013_a013_d013_i013 } + replace{ @atom:189 @atom:189_b003_a003_d003_i003 } + replace{ @atom:190 @atom:190_b004_a004_d004_i004 } + replace{ @atom:191 @atom:191_b024_a024_d024_i024 } + replace{ @atom:192 @atom:192_b045_a045_d045_i045 } + replace{ @atom:193 @atom:193_b024_a024_d024_i024 } + replace{ @atom:194 @atom:194_b003_a003_d003_i003 } + replace{ @atom:195 @atom:195_b004_a004_d004_i004 } + replace{ @atom:196 @atom:196_b045_a045_d045_i045 } + replace{ @atom:197 @atom:197_b046_a046_d046_i046 } + replace{ @atom:198 @atom:198_b013_a013_d013_i013 } + replace{ @atom:199 @atom:199_b013_a013_d013_i013 } + replace{ @atom:200 @atom:200_b013_a013_d013_i013 } + replace{ @atom:201 @atom:201_b013_a013_d013_i013 } + replace{ @atom:202 @atom:202_b048_a048_d048_i048 } + replace{ @atom:203 @atom:203_b019_a019_d019_i019 } + replace{ @atom:204 @atom:204_b018_a018_d018_i018 } + replace{ @atom:205 @atom:205_b048_a048_d048_i048 } + replace{ @atom:206 @atom:206_b021_a021_d021_i021 } + replace{ @atom:207 @atom:207_b024_a024_d024_i024 } + replace{ @atom:208 @atom:208_b048_a048_d048_i048 } + replace{ @atom:209 @atom:209_b003_a003_d003_i003 } + replace{ @atom:210 @atom:210_b004_a004_d004_i004 } + replace{ @atom:211 @atom:211_b005_a005_d005_i005 } + replace{ @atom:212 @atom:212_b007_a007_d007_i007 } + replace{ @atom:213 @atom:213_b003_a003_d003_i003 } + replace{ @atom:214 @atom:214_b052_a052_d052_i052 } + replace{ @atom:215 @atom:215_b013_a013_d013_i013 } + replace{ @atom:216 @atom:216_b013_a013_d013_i013 } + replace{ @atom:217 @atom:217_b013_a013_d013_i013 } + replace{ @atom:218 @atom:218_b013_a013_d013_i013 } + replace{ @atom:219 @atom:219_b003_a003_d003_i003 } + replace{ @atom:220 @atom:220_b004_a004_d004_i004 } + replace{ @atom:221 @atom:221_b046_a046_d046_i046 } + replace{ @atom:222 @atom:222_b003_a003_d003_i003 } + replace{ @atom:223 @atom:223_b004_a004_d004_i004 } + replace{ @atom:224 @atom:224_b046_a046_d046_i046 } + replace{ @atom:225 @atom:225_b013_a013_d013_i013 } + replace{ @atom:226 @atom:226_b013_a013_d013_i013 } + replace{ @atom:227 @atom:227_b013_a013_d013_i013 } + replace{ @atom:228 @atom:228_b013_a013_d013_i013 } + replace{ @atom:229 @atom:229_b053_a053_d053_i053 } + replace{ @atom:230 @atom:230_b053_a053_d053_i053 } + replace{ @atom:231 @atom:231_b053_a053_d053_i053 } + replace{ @atom:232 @atom:232_b054_a054_d054_i054 } + replace{ @atom:233 @atom:233_b054_a054_d054_i054 } + replace{ @atom:234 @atom:234_b013_a013_d013_i013 } + replace{ @atom:235 @atom:235_b013_a013_d013_i013 } + replace{ @atom:236 @atom:236_b013_a013_d013_i013 } + replace{ @atom:237 @atom:237_b013_a013_d013_i013 } + replace{ @atom:238 @atom:238_b013_a013_d013_i013 } + replace{ @atom:239 @atom:239_b013_a013_d013_i013 } + replace{ @atom:240 @atom:240_b013_a013_d013_i013 } + replace{ @atom:241 @atom:241_b013_a013_d013_i013 } + replace{ @atom:242 @atom:242_b013_a013_d013_i013 } + replace{ @atom:243 @atom:243_b055_a055_d055_i055 } + replace{ @atom:244 @atom:244_b054_a054_d054_i054 } + replace{ @atom:245 @atom:245_b048_a048_d048_i048 } + replace{ @atom:246 @atom:246_b055_a055_d055_i055 } + replace{ @atom:247 @atom:247_b054_a054_d054_i054 } + replace{ @atom:248 @atom:248_b013_a013_d013_i013 } + replace{ @atom:249 @atom:249_b013_a013_d013_i013 } + replace{ @atom:250 @atom:250_b013_a013_d013_i013 } + replace{ @atom:251 @atom:251_b013_a013_d013_i013 } + replace{ @atom:252 @atom:252_b053_a053_d053_i053 } + replace{ @atom:253 @atom:253_b054_a054_d054_i054 } + replace{ @atom:254 @atom:254_b056_a056_d056_i056 } + replace{ @atom:255 @atom:255_b048_a048_d048_i048 } + replace{ @atom:256 @atom:256_b055_a055_d055_i055 } + replace{ @atom:257 @atom:257_b045_a045_d045_i045 } + replace{ @atom:258 @atom:258_b048_a048_d048_i048 } + replace{ @atom:259 @atom:259_b049_a049_d049_i049 } + replace{ @atom:260 @atom:260_b048_a048_d048_i048 } + replace{ @atom:261 @atom:261_b049_a049_d049_i049 } + replace{ @atom:262 @atom:262_b057_a057_d057_i057 } + replace{ @atom:263 @atom:263_b003_a003_d003_i003 } + replace{ @atom:264 @atom:264_b057_a057_d057_i057 } + replace{ @atom:265 @atom:265_b003_a003_d003_i003 } + replace{ @atom:266 @atom:266_b047_a047_d047_i047 } + replace{ @atom:267 @atom:267_b047_a047_d047_i047 } + replace{ @atom:268 @atom:268_b045_a045_d045_i045 } + replace{ @atom:269 @atom:269_b004_a004_d004_i004 } + replace{ @atom:270 @atom:270_b045_a045_d045_i045 } + replace{ @atom:271 @atom:271_b004_a004_d004_i004 } + replace{ @atom:272 @atom:272_b046_a046_d046_i046 } + replace{ @atom:273 @atom:273_b046_a046_d046_i046 } + replace{ @atom:274 @atom:274_b013_a013_d013_i013 } + replace{ @atom:275 @atom:275_b046_a046_d046_i046 } + replace{ @atom:276 @atom:276_b057_a057_d057_i057 } + replace{ @atom:277 @atom:277_b003_a003_d003_i003 } + replace{ @atom:278 @atom:278_b056_a056_d056_i056 } + replace{ @atom:279 @atom:279_b048_a048_d048_i048 } + replace{ @atom:280 @atom:280_b047_a047_d047_i047 } + replace{ @atom:281 @atom:281_b047_a047_d047_i047 } + replace{ @atom:282 @atom:282_b045_a045_d045_i045 } + replace{ @atom:283 @atom:283_b004_a004_d004_i004 } + replace{ @atom:284 @atom:284_b055_a055_d055_i055 } + replace{ @atom:285 @atom:285_b045_a045_d045_i045 } + replace{ @atom:286 @atom:286_b045_a045_d045_i045 } + replace{ @atom:287 @atom:287_b046_a046_d046_i046 } + replace{ @atom:288 @atom:288_b058_a058_d058_i058 } + replace{ @atom:289 @atom:289_b056_a056_d056_i056 } + replace{ @atom:290 @atom:290_b059_a059_d059_i059 } + replace{ @atom:291 @atom:291_b056_a056_d056_i056 } + replace{ @atom:292 @atom:292_b060_a060_d060_i060 } + replace{ @atom:293 @atom:293_b060_a060_d060_i060 } + replace{ @atom:294 @atom:294_b048_a048_d048_i048 } + replace{ @atom:295 @atom:295_b061_a061_d061_i061 } + replace{ @atom:296 @atom:296_b062_a062_d062_i062 } + replace{ @atom:297 @atom:297_b057_a057_d057_i057 } + replace{ @atom:298 @atom:298_b063_a063_d063_i063 } + replace{ @atom:299 @atom:299_b055_a055_d055_i055 } + replace{ @atom:300 @atom:300_b045_a045_d045_i045 } + replace{ @atom:301 @atom:301_b045_a045_d045_i045 } + replace{ @atom:302 @atom:302_b063_a063_d063_i063 } + replace{ @atom:303 @atom:303_b045_a045_d045_i045 } + replace{ @atom:304 @atom:304_b057_a057_d057_i057 } + replace{ @atom:305 @atom:305_b048_a048_d048_i048 } + replace{ @atom:306 @atom:306_b056_a056_d056_i056 } + replace{ @atom:307 @atom:307_b060_a060_d060_i060 } + replace{ @atom:308 @atom:308_b060_a060_d060_i060 } + replace{ @atom:309 @atom:309_b003_a003_d003_i003 } + replace{ @atom:310 @atom:310_b045_a045_d045_i045 } + replace{ @atom:311 @atom:311_b055_a055_d055_i055 } + replace{ @atom:312 @atom:312_b045_a045_d045_i045 } + replace{ @atom:313 @atom:313_b004_a004_d004_i004 } + replace{ @atom:314 @atom:314_b013_a013_d013_i013 } + replace{ @atom:315 @atom:315_b046_a046_d046_i046 } + replace{ @atom:316 @atom:316_b013_a013_d013_i013 } + replace{ @atom:317 @atom:317_b046_a046_d046_i046 } + replace{ @atom:318 @atom:318_b013_a013_d013_i013 } + replace{ @atom:319 @atom:319_b046_a046_d046_i046 } + replace{ @atom:320 @atom:320_b057_a057_d057_i057 } + replace{ @atom:321 @atom:321_b003_a003_d003_i003 } + replace{ @atom:322 @atom:322_b057_a057_d057_i057 } + replace{ @atom:323 @atom:323_b048_a048_d048_i048 } + replace{ @atom:324 @atom:324_b047_a047_d047_i047 } + replace{ @atom:325 @atom:325_b047_a047_d047_i047 } + replace{ @atom:326 @atom:326_b045_a045_d045_i045 } + replace{ @atom:327 @atom:327_b004_a004_d004_i004 } + replace{ @atom:328 @atom:328_b045_a045_d045_i045 } + replace{ @atom:329 @atom:329_b055_a055_d055_i055 } + replace{ @atom:330 @atom:330_b045_a045_d045_i045 } + replace{ @atom:331 @atom:331_b045_a045_d045_i045 } + replace{ @atom:332 @atom:332_b049_a049_d049_i049 } + replace{ @atom:333 @atom:333_b058_a058_d058_i058 } + replace{ @atom:334 @atom:334_b013_a013_d013_i013 } + replace{ @atom:335 @atom:335_b046_a046_d046_i046 } + replace{ @atom:336 @atom:336_b064_a064_d064_i064 } + replace{ @atom:337 @atom:337_b052_a052_d052_i052 } + replace{ @atom:338 @atom:338_b020_a020_d020_i020 } + replace{ @atom:339 @atom:339_b013_a013_d013_i013 } + replace{ @atom:340 @atom:340_b047_a047_d047_i047 } + replace{ @atom:341 @atom:341_b021_a021_d021_i021 } + replace{ @atom:342 @atom:342_b047_a047_d047_i047 } + replace{ @atom:343 @atom:343_b001_a001_d001_i001 } + replace{ @atom:344 @atom:344_b021_a021_d021_i021 } + replace{ @atom:345 @atom:345_b065_a065_d065_i065 } + replace{ @atom:346 @atom:346_b066_a066_d066_i066 } + replace{ @atom:347 @atom:347_b067_a067_d067_i067 } + replace{ @atom:348 @atom:348_b068_a068_d068_i068 } + replace{ @atom:349 @atom:349_b069_a069_d069_i069 } + replace{ @atom:350 @atom:350_b070_a070_d070_i070 } + replace{ @atom:351 @atom:351_b071_a071_d071_i071 } + replace{ @atom:352 @atom:352_b072_a072_d072_i072 } + replace{ @atom:353 @atom:353_b073_a073_d073_i073 } + replace{ @atom:354 @atom:354_b074_a074_d074_i074 } + replace{ @atom:355 @atom:355_b075_a075_d075_i075 } + replace{ @atom:356 @atom:356_b076_a076_d076_i076 } + replace{ @atom:357 @atom:357_b006_a006_d006_i006 } + replace{ @atom:358 @atom:358_b046_a046_d046_i046 } + replace{ @atom:359 @atom:359_b015_a015_d015_i015 } + replace{ @atom:360 @atom:360_b006_a006_d006_i006 } + replace{ @atom:361 @atom:361_b046_a046_d046_i046 } + replace{ @atom:362 @atom:362_b005_a005_d005_i005 } + replace{ @atom:363 @atom:363_b013_a013_d013_i013 } + replace{ @atom:364 @atom:364_b046_a046_d046_i046 } + replace{ @atom:365 @atom:365_b019_a019_d019_i019 } + replace{ @atom:366 @atom:366_b018_a018_d018_i018 } + replace{ @atom:367 @atom:367_b006_a006_d006_i006 } + replace{ @atom:368 @atom:368_b046_a046_d046_i046 } + replace{ @atom:369 @atom:369_b053_a053_d053_i053 } + replace{ @atom:370 @atom:370_b045_a045_d045_i045 } + replace{ @atom:371 @atom:371_b006_a006_d006_i006 } + replace{ @atom:372 @atom:372_b046_a046_d046_i046 } + replace{ @atom:373 @atom:373_b013_a013_d013_i013 } + replace{ @atom:374 @atom:374_b046_a046_d046_i046 } + replace{ @atom:375 @atom:375_b033_a033_d033_i033 } + replace{ @atom:376 @atom:376_b005_a005_d005_i005 } + replace{ @atom:377 @atom:377_b007_a007_d007_i007 } + replace{ @atom:378 @atom:378_b077_a077_d077_i077 } + replace{ @atom:379 @atom:379_b078_a078_d078_i078 } + replace{ @atom:380 @atom:380_b020_a020_d020_i020 } + replace{ @atom:381 @atom:381_b064_a064_d064_i064 } + replace{ @atom:382 @atom:382_b052_a052_d052_i052 } + replace{ @atom:383 @atom:383_b020_a020_d020_i020 } + replace{ @atom:384 @atom:384_b013_a013_d013_i013 } + replace{ @atom:385 @atom:385_b046_a046_d046_i046 } + replace{ @atom:386 @atom:386_b064_a064_d064_i064 } + replace{ @atom:387 @atom:387_b052_a052_d052_i052 } + replace{ @atom:388 @atom:388_b020_a020_d020_i020 } + replace{ @atom:389 @atom:389_b013_a013_d013_i013 } + replace{ @atom:390 @atom:390_b046_a046_d046_i046 } + replace{ @atom:391 @atom:391_b064_a064_d064_i064 } + replace{ @atom:392 @atom:392_b052_a052_d052_i052 } + replace{ @atom:393 @atom:393_b020_a020_d020_i020 } + replace{ @atom:394 @atom:394_b013_a013_d013_i013 } + replace{ @atom:395 @atom:395_b046_a046_d046_i046 } + replace{ @atom:396 @atom:396_b013_a013_d013_i013 } + replace{ @atom:397 @atom:397_b046_a046_d046_i046 } + replace{ @atom:398 @atom:398_b048_a048_d048_i048 } + replace{ @atom:399 @atom:399_b013_a013_d013_i013 } + replace{ @atom:400 @atom:400_b046_a046_d046_i046 } + replace{ @atom:401 @atom:401_b048_a048_d048_i048 } + replace{ @atom:402 @atom:402_b013_a013_d013_i013 } + replace{ @atom:403 @atom:403_b046_a046_d046_i046 } + replace{ @atom:404 @atom:404_b048_a048_d048_i048 } + replace{ @atom:405 @atom:405_b013_a013_d013_i013 } + replace{ @atom:406 @atom:406_b003_a003_d003_i003 } + replace{ @atom:407 @atom:407_b004_a004_d004_i004 } + replace{ @atom:408 @atom:408_b020_a020_d020_i020 } + replace{ @atom:409 @atom:409_b013_a013_d013_i013 } + replace{ @atom:410 @atom:410_b046_a046_d046_i046 } + replace{ @atom:411 @atom:411_b003_a003_d003_i003 } + replace{ @atom:412 @atom:412_b003_a003_d003_i003 } + replace{ @atom:413 @atom:413_b048_a048_d048_i048 } + replace{ @atom:414 @atom:414_b020_a020_d020_i020 } + replace{ @atom:415 @atom:415_b079_a079_d079_i079 } + replace{ @atom:416 @atom:416_b023_a023_d023_i023 } + replace{ @atom:417 @atom:417_b013_a013_d013_i013 } + replace{ @atom:418 @atom:418_b046_a046_d046_i046 } + replace{ @atom:419 @atom:419_b024_a024_d024_i024 } + replace{ @atom:420 @atom:420_b045_a045_d045_i045 } + replace{ @atom:421 @atom:421_b024_a024_d024_i024 } + replace{ @atom:422 @atom:422_b045_a045_d045_i045 } + replace{ @atom:423 @atom:423_b013_a013_d013_i013 } + replace{ @atom:424 @atom:424_b046_a046_d046_i046 } + replace{ @atom:425 @atom:425_b013_a013_d013_i013 } + replace{ @atom:426 @atom:426_b046_a046_d046_i046 } + replace{ @atom:427 @atom:427_b013_a013_d013_i013 } + replace{ @atom:428 @atom:428_b046_a046_d046_i046 } + replace{ @atom:429 @atom:429_b048_a048_d048_i048 } + replace{ @atom:430 @atom:430_b048_a048_d048_i048 } + replace{ @atom:431 @atom:431_b013_a013_d013_i013 } + replace{ @atom:432 @atom:432_b013_a013_d013_i013 } + replace{ @atom:433 @atom:433_b013_a013_d013_i013 } + replace{ @atom:434 @atom:434_b079_a079_d079_i079 } + replace{ @atom:435 @atom:435_b023_a023_d023_i023 } + replace{ @atom:436 @atom:436_b022_a022_d022_i022 } + replace{ @atom:437 @atom:437_b022_a022_d022_i022 } + replace{ @atom:438 @atom:438_b023_a023_d023_i023 } + replace{ @atom:439 @atom:439_b013_a013_d013_i013 } + replace{ @atom:440 @atom:440_b013_a013_d013_i013 } + replace{ @atom:441 @atom:441_b080_a080_d080_i080 } + replace{ @atom:442 @atom:442_b060_a060_d060_i060 } + replace{ @atom:443 @atom:443_b081_a081_d081_i081 } + replace{ @atom:444 @atom:444_b057_a057_d057_i057 } + replace{ @atom:445 @atom:445_b045_a045_d045_i045 } + replace{ @atom:446 @atom:446_b013_a013_d013_i013 } + replace{ @atom:447 @atom:447_b082_a082_d082_i082 } + replace{ @atom:448 @atom:448_b083_a083_d083_i083 } + replace{ @atom:449 @atom:449_b084_a084_d084_i084 } + replace{ @atom:450 @atom:450_b082_a082_d082_i082 } + replace{ @atom:451 @atom:451_b085_a085_d085_i085 } + replace{ @atom:452 @atom:452_b061_a061_d061_i061 } + replace{ @atom:453 @atom:453_b057_a057_d057_i057 } + replace{ @atom:454 @atom:454_b045_a045_d045_i045 } + replace{ @atom:455 @atom:455_b084_a084_d084_i084 } + replace{ @atom:456 @atom:456_b013_a013_d013_i013 } + replace{ @atom:457 @atom:457_b013_a013_d013_i013 } + replace{ @atom:458 @atom:458_b047_a047_d047_i047 } + replace{ @atom:459 @atom:459_b047_a047_d047_i047 } + replace{ @atom:460 @atom:460_b086_a086_d086_i086 } + replace{ @atom:461 @atom:461_b056_a056_d056_i056 } + replace{ @atom:462 @atom:462_b048_a048_d048_i048 } + replace{ @atom:463 @atom:463_b048_a048_d048_i048 } + replace{ @atom:464 @atom:464_b048_a048_d048_i048 } + replace{ @atom:465 @atom:465_b049_a049_d049_i049 } + replace{ @atom:466 @atom:466_b049_a049_d049_i049 } + replace{ @atom:467 @atom:467_b049_a049_d049_i049 } + replace{ @atom:468 @atom:468_b056_a056_d056_i056 } + replace{ @atom:469 @atom:469_b048_a048_d048_i048 } + replace{ @atom:470 @atom:470_b049_a049_d049_i049 } + replace{ @atom:471 @atom:471_b056_a056_d056_i056 } + replace{ @atom:472 @atom:472_b059_a059_d059_i059 } + replace{ @atom:473 @atom:473_b048_a048_d048_i048 } + replace{ @atom:474 @atom:474_b048_a048_d048_i048 } + replace{ @atom:475 @atom:475_b049_a049_d049_i049 } + replace{ @atom:476 @atom:476_b049_a049_d049_i049 } + replace{ @atom:477 @atom:477_b049_a049_d049_i049 } + replace{ @atom:478 @atom:478_b056_a056_d056_i056 } + replace{ @atom:479 @atom:479_b048_a048_d048_i048 } + replace{ @atom:480 @atom:480_b048_a048_d048_i048 } + replace{ @atom:481 @atom:481_b049_a049_d049_i049 } + replace{ @atom:482 @atom:482_b049_a049_d049_i049 } + replace{ @atom:483 @atom:483_b057_a057_d057_i057 } + replace{ @atom:484 @atom:484_b084_a084_d084_i084 } + replace{ @atom:485 @atom:485_b087_a087_d087_i087 } + replace{ @atom:486 @atom:486_b045_a045_d045_i045 } + replace{ @atom:487 @atom:487_b049_a049_d049_i049 } + replace{ @atom:488 @atom:488_b049_a049_d049_i049 } + replace{ @atom:489 @atom:489_b057_a057_d057_i057 } + replace{ @atom:490 @atom:490_b061_a061_d061_i061 } + replace{ @atom:491 @atom:491_b088_a088_d088_i088 } + replace{ @atom:492 @atom:492_b087_a087_d087_i087 } + replace{ @atom:493 @atom:493_b084_a084_d084_i084 } + replace{ @atom:494 @atom:494_b045_a045_d045_i045 } + replace{ @atom:495 @atom:495_b049_a049_d049_i049 } + replace{ @atom:496 @atom:496_b049_a049_d049_i049 } + replace{ @atom:497 @atom:497_b049_a049_d049_i049 } + replace{ @atom:498 @atom:498_b057_a057_d057_i057 } + replace{ @atom:499 @atom:499_b082_a082_d082_i082 } + replace{ @atom:500 @atom:500_b061_a061_d061_i061 } + replace{ @atom:501 @atom:501_b083_a083_d083_i083 } + replace{ @atom:502 @atom:502_b084_a084_d084_i084 } + replace{ @atom:503 @atom:503_b045_a045_d045_i045 } + replace{ @atom:504 @atom:504_b049_a049_d049_i049 } + replace{ @atom:505 @atom:505_b049_a049_d049_i049 } + replace{ @atom:506 @atom:506_b049_a049_d049_i049 } + replace{ @atom:507 @atom:507_b020_a020_d020_i020 } + replace{ @atom:508 @atom:508_b084_a084_d084_i084 } + replace{ @atom:509 @atom:509_b087_a087_d087_i087 } + replace{ @atom:510 @atom:510_b049_a049_d049_i049 } + replace{ @atom:511 @atom:511_b049_a049_d049_i049 } + replace{ @atom:512 @atom:512_b020_a020_d020_i020 } + replace{ @atom:513 @atom:513_b082_a082_d082_i082 } + replace{ @atom:514 @atom:514_b061_a061_d061_i061 } + replace{ @atom:515 @atom:515_b083_a083_d083_i083 } + replace{ @atom:516 @atom:516_b084_a084_d084_i084 } + replace{ @atom:517 @atom:517_b049_a049_d049_i049 } + replace{ @atom:518 @atom:518_b049_a049_d049_i049 } + replace{ @atom:519 @atom:519_b049_a049_d049_i049 } + replace{ @atom:520 @atom:520_b020_a020_d020_i020 } + replace{ @atom:521 @atom:521_b061_a061_d061_i061 } + replace{ @atom:522 @atom:522_b088_a088_d088_i088 } + replace{ @atom:523 @atom:523_b087_a087_d087_i087 } + replace{ @atom:524 @atom:524_b084_a084_d084_i084 } + replace{ @atom:525 @atom:525_b049_a049_d049_i049 } + replace{ @atom:526 @atom:526_b049_a049_d049_i049 } + replace{ @atom:527 @atom:527_b049_a049_d049_i049 } + replace{ @atom:528 @atom:528_b057_a057_d057_i057 } + replace{ @atom:529 @atom:529_b084_a084_d084_i084 } + replace{ @atom:530 @atom:530_b087_a087_d087_i087 } + replace{ @atom:531 @atom:531_b048_a048_d048_i048 } + replace{ @atom:532 @atom:532_b048_a048_d048_i048 } + replace{ @atom:533 @atom:533_b048_a048_d048_i048 } + replace{ @atom:534 @atom:534_b048_a048_d048_i048 } + replace{ @atom:535 @atom:535_b081_a081_d081_i081 } + replace{ @atom:536 @atom:536_b060_a060_d060_i060 } + replace{ @atom:537 @atom:537_b045_a045_d045_i045 } + replace{ @atom:538 @atom:538_b049_a049_d049_i049 } + replace{ @atom:539 @atom:539_b049_a049_d049_i049 } + replace{ @atom:540 @atom:540_b049_a049_d049_i049 } + replace{ @atom:541 @atom:541_b049_a049_d049_i049 } + replace{ @atom:542 @atom:542_b049_a049_d049_i049 } + replace{ @atom:543 @atom:543_b049_a049_d049_i049 } + replace{ @atom:544 @atom:544_b056_a056_d056_i056 } + replace{ @atom:545 @atom:545_b048_a048_d048_i048 } + replace{ @atom:546 @atom:546_b048_a048_d048_i048 } + replace{ @atom:547 @atom:547_b048_a048_d048_i048 } + replace{ @atom:548 @atom:548_b048_a048_d048_i048 } + replace{ @atom:549 @atom:549_b048_a048_d048_i048 } + replace{ @atom:550 @atom:550_b048_a048_d048_i048 } + replace{ @atom:551 @atom:551_b048_a048_d048_i048 } + replace{ @atom:552 @atom:552_b048_a048_d048_i048 } + replace{ @atom:553 @atom:553_b048_a048_d048_i048 } + replace{ @atom:554 @atom:554_b049_a049_d049_i049 } + replace{ @atom:555 @atom:555_b049_a049_d049_i049 } + replace{ @atom:556 @atom:556_b049_a049_d049_i049 } + replace{ @atom:557 @atom:557_b049_a049_d049_i049 } + replace{ @atom:558 @atom:558_b049_a049_d049_i049 } + replace{ @atom:559 @atom:559_b049_a049_d049_i049 } + replace{ @atom:560 @atom:560_b049_a049_d049_i049 } + replace{ @atom:561 @atom:561_b056_a056_d056_i056 } + replace{ @atom:562 @atom:562_b059_a059_d059_i059 } + replace{ @atom:563 @atom:563_b056_a056_d056_i056 } + replace{ @atom:564 @atom:564_b060_a060_d060_i060 } + replace{ @atom:565 @atom:565_b060_a060_d060_i060 } + replace{ @atom:566 @atom:566_b048_a048_d048_i048 } + replace{ @atom:567 @atom:567_b061_a061_d061_i061 } + replace{ @atom:568 @atom:568_b062_a062_d062_i062 } + replace{ @atom:569 @atom:569_b057_a057_d057_i057 } + replace{ @atom:570 @atom:570_b049_a049_d049_i049 } + replace{ @atom:571 @atom:571_b049_a049_d049_i049 } + replace{ @atom:572 @atom:572_b049_a049_d049_i049 } + replace{ @atom:573 @atom:573_b045_a045_d045_i045 } + replace{ @atom:574 @atom:574_b016_a016_d016_i016 } + replace{ @atom:575 @atom:575_b082_a082_d082_i082 } + replace{ @atom:576 @atom:576_b061_a061_d061_i061 } + replace{ @atom:577 @atom:577_b083_a083_d083_i083 } + replace{ @atom:578 @atom:578_b084_a084_d084_i084 } + replace{ @atom:579 @atom:579_b049_a049_d049_i049 } + replace{ @atom:580 @atom:580_b049_a049_d049_i049 } + replace{ @atom:581 @atom:581_b049_a049_d049_i049 } + replace{ @atom:582 @atom:582_b056_a056_d056_i056 } + replace{ @atom:583 @atom:583_b059_a059_d059_i059 } + replace{ @atom:584 @atom:584_b049_a049_d049_i049 } + replace{ @atom:585 @atom:585_b048_a048_d048_i048 } + replace{ @atom:586 @atom:586_b013_a013_d013_i013 } + replace{ @atom:587 @atom:587_b056_a056_d056_i056 } + replace{ @atom:588 @atom:588_b048_a048_d048_i048 } + replace{ @atom:589 @atom:589_b048_a048_d048_i048 } + replace{ @atom:590 @atom:590_b048_a048_d048_i048 } + replace{ @atom:591 @atom:591_b048_a048_d048_i048 } + replace{ @atom:592 @atom:592_b048_a048_d048_i048 } + replace{ @atom:593 @atom:593_b048_a048_d048_i048 } + replace{ @atom:594 @atom:594_b049_a049_d049_i049 } + replace{ @atom:595 @atom:595_b049_a049_d049_i049 } + replace{ @atom:596 @atom:596_b049_a049_d049_i049 } + replace{ @atom:597 @atom:597_b049_a049_d049_i049 } + replace{ @atom:598 @atom:598_b057_a057_d057_i057 } + replace{ @atom:599 @atom:599_b082_a082_d082_i082 } + replace{ @atom:600 @atom:600_b061_a061_d061_i061 } + replace{ @atom:601 @atom:601_b083_a083_d083_i083 } + replace{ @atom:602 @atom:602_b084_a084_d084_i084 } + replace{ @atom:603 @atom:603_b013_a013_d013_i013 } + replace{ @atom:604 @atom:604_b049_a049_d049_i049 } + replace{ @atom:605 @atom:605_b049_a049_d049_i049 } + replace{ @atom:606 @atom:606_b049_a049_d049_i049 } + replace{ @atom:607 @atom:607_b046_a046_d046_i046 } + replace{ @atom:608 @atom:608_b013_a013_d013_i013 } + replace{ @atom:609 @atom:609_b013_a013_d013_i013 } + replace{ @atom:610 @atom:610_b013_a013_d013_i013 } + replace{ @atom:611 @atom:611_b013_a013_d013_i013 } + replace{ @atom:612 @atom:612_b013_a013_d013_i013 } + replace{ @atom:613 @atom:613_b013_a013_d013_i013 } + replace{ @atom:614 @atom:614_b013_a013_d013_i013 } + replace{ @atom:615 @atom:615_b013_a013_d013_i013 } + replace{ @atom:616 @atom:616_b013_a013_d013_i013 } + replace{ @atom:617 @atom:617_b013_a013_d013_i013 } + replace{ @atom:618 @atom:618_b013_a013_d013_i013 } + replace{ @atom:619 @atom:619_b013_a013_d013_i013 } + replace{ @atom:620 @atom:620_b013_a013_d013_i013 } + replace{ @atom:621 @atom:621_b013_a013_d013_i013 } + replace{ @atom:622 @atom:622_b013_a013_d013_i013 } + replace{ @atom:623 @atom:623_b015_a015_d015_i015 } + replace{ @atom:624 @atom:624_b017_a017_d017_i017 } + replace{ @atom:625 @atom:625_b048_a048_d048_i048 } + replace{ @atom:626 @atom:626_b089_a089_d089_i089 } + replace{ @atom:627 @atom:627_b090_a090_d090_i090 } + replace{ @atom:628 @atom:628_b091_a091_d091_i091 } + replace{ @atom:629 @atom:629_b091_a091_d091_i091 } + replace{ @atom:630 @atom:630_b013_a013_d013_i013 } + replace{ @atom:631 @atom:631_b086_a086_d086_i086 } + replace{ @atom:632 @atom:632_b086_a086_d086_i086 } + replace{ @atom:633 @atom:633_b086_a086_d086_i086 } + replace{ @atom:634 @atom:634_b086_a086_d086_i086 } + replace{ @atom:635 @atom:635_b086_a086_d086_i086 } + replace{ @atom:636 @atom:636_b086_a086_d086_i086 } + replace{ @atom:637 @atom:637_b016_a016_d016_i016 } + replace{ @atom:638 @atom:638_b092_a092_d092_i092 } + replace{ @atom:639 @atom:639_b093_a093_d093_i093 } + replace{ @atom:640 @atom:640_b094_a094_d094_i094 } + replace{ @atom:641 @atom:641_b095_a095_d095_i095 } + replace{ @atom:642 @atom:642_b013_a013_d013_i013 } + replace{ @atom:643 @atom:643_b046_a046_d046_i046 } + replace{ @atom:644 @atom:644_b096_a096_d096_i096 } + replace{ @atom:645 @atom:645_b097_a097_d097_i097 } + replace{ @atom:646 @atom:646_b098_a098_d098_i098 } + replace{ @atom:647 @atom:647_b099_a099_d099_i099 } replace{ @atom:648 @atom:648_b100_a100_d100_i100 } - replace{ @atom:649 @atom:649_b47_a47_d47_i47 } - replace{ @atom:650 @atom:650_b21_a21_d21_i21 } - replace{ @atom:651 @atom:651_b46_a46_d46_i46 } - replace{ @atom:652 @atom:652_b91_a91_d91_i91 } - replace{ @atom:653 @atom:653_b91_a91_d91_i91 } - replace{ @atom:654 @atom:654_b91_a91_d91_i91 } - replace{ @atom:655 @atom:655_b48_a48_d48_i48 } - replace{ @atom:656 @atom:656_b49_a49_d49_i49 } - replace{ @atom:657 @atom:657_b48_a48_d48_i48 } - replace{ @atom:658 @atom:658_b49_a49_d49_i49 } - replace{ @atom:659 @atom:659_b48_a48_d48_i48 } - replace{ @atom:660 @atom:660_b1_a1_d1_i1 } - replace{ @atom:661 @atom:661_b48_a48_d48_i48 } - replace{ @atom:662 @atom:662_b1_a1_d1_i1 } - replace{ @atom:663 @atom:663_b65_a65_d65_i65 } - replace{ @atom:664 @atom:664_b2_a2_d2_i2 } - replace{ @atom:665 @atom:665_b48_a48_d48_i48 } - replace{ @atom:666 @atom:666_b13_a13_d13_i13 } - replace{ @atom:667 @atom:667_b1_a1_d1_i1 } - replace{ @atom:668 @atom:668_b48_a48_d48_i48 } - replace{ @atom:669 @atom:669_b1_a1_d1_i1 } - replace{ @atom:670 @atom:670_b48_a48_d48_i48 } - replace{ @atom:671 @atom:671_b65_a65_d65_i65 } - replace{ @atom:672 @atom:672_b48_a48_d48_i48 } - replace{ @atom:673 @atom:673_b66_a66_d66_i66 } - replace{ @atom:674 @atom:674_b91_a91_d91_i91 } - replace{ @atom:675 @atom:675_b15_a15_d15_i15 } - replace{ @atom:676 @atom:676_b48_a48_d48_i48 } - replace{ @atom:677 @atom:677_b48_a48_d48_i48 } - replace{ @atom:678 @atom:678_b48_a48_d48_i48 } - replace{ @atom:679 @atom:679_b48_a48_d48_i48 } - replace{ @atom:680 @atom:680_b48_a48_d48_i48 } - replace{ @atom:681 @atom:681_b49_a49_d49_i49 } - replace{ @atom:682 @atom:682_b49_a49_d49_i49 } - replace{ @atom:683 @atom:683_b48_a48_d48_i48 } - replace{ @atom:684 @atom:684_b55_a55_d55_i55 } - replace{ @atom:685 @atom:685_b45_a45_d45_i45 } - replace{ @atom:686 @atom:686_b45_a45_d45_i45 } - replace{ @atom:687 @atom:687_b49_a49_d49_i49 } - replace{ @atom:688 @atom:688_b13_a13_d13_i13 } - replace{ @atom:689 @atom:689_b13_a13_d13_i13 } + replace{ @atom:649 @atom:649_b047_a047_d047_i047 } + replace{ @atom:650 @atom:650_b021_a021_d021_i021 } + replace{ @atom:651 @atom:651_b046_a046_d046_i046 } + replace{ @atom:652 @atom:652_b091_a091_d091_i091 } + replace{ @atom:653 @atom:653_b091_a091_d091_i091 } + replace{ @atom:654 @atom:654_b091_a091_d091_i091 } + replace{ @atom:655 @atom:655_b048_a048_d048_i048 } + replace{ @atom:656 @atom:656_b049_a049_d049_i049 } + replace{ @atom:657 @atom:657_b048_a048_d048_i048 } + replace{ @atom:658 @atom:658_b049_a049_d049_i049 } + replace{ @atom:659 @atom:659_b048_a048_d048_i048 } + replace{ @atom:660 @atom:660_b001_a001_d001_i001 } + replace{ @atom:661 @atom:661_b048_a048_d048_i048 } + replace{ @atom:662 @atom:662_b001_a001_d001_i001 } + replace{ @atom:663 @atom:663_b065_a065_d065_i065 } + replace{ @atom:664 @atom:664_b002_a002_d002_i002 } + replace{ @atom:665 @atom:665_b048_a048_d048_i048 } + replace{ @atom:666 @atom:666_b013_a013_d013_i013 } + replace{ @atom:667 @atom:667_b001_a001_d001_i001 } + replace{ @atom:668 @atom:668_b048_a048_d048_i048 } + replace{ @atom:669 @atom:669_b001_a001_d001_i001 } + replace{ @atom:670 @atom:670_b048_a048_d048_i048 } + replace{ @atom:671 @atom:671_b065_a065_d065_i065 } + replace{ @atom:672 @atom:672_b048_a048_d048_i048 } + replace{ @atom:673 @atom:673_b066_a066_d066_i066 } + replace{ @atom:674 @atom:674_b091_a091_d091_i091 } + replace{ @atom:675 @atom:675_b015_a015_d015_i015 } + replace{ @atom:676 @atom:676_b048_a048_d048_i048 } + replace{ @atom:677 @atom:677_b048_a048_d048_i048 } + replace{ @atom:678 @atom:678_b048_a048_d048_i048 } + replace{ @atom:679 @atom:679_b048_a048_d048_i048 } + replace{ @atom:680 @atom:680_b048_a048_d048_i048 } + replace{ @atom:681 @atom:681_b049_a049_d049_i049 } + replace{ @atom:682 @atom:682_b049_a049_d049_i049 } + replace{ @atom:683 @atom:683_b048_a048_d048_i048 } + replace{ @atom:684 @atom:684_b055_a055_d055_i055 } + replace{ @atom:685 @atom:685_b045_a045_d045_i045 } + replace{ @atom:686 @atom:686_b045_a045_d045_i045 } + replace{ @atom:687 @atom:687_b049_a049_d049_i049 } + replace{ @atom:688 @atom:688_b013_a013_d013_i013 } + replace{ @atom:689 @atom:689_b013_a013_d013_i013 } replace{ @atom:690 @atom:690_b101_a101_d101_i101 } - replace{ @atom:691 @atom:691_b56_a56_d56_i56 } + replace{ @atom:691 @atom:691_b056_a056_d056_i056 } replace{ @atom:692 @atom:692_b101_a101_d101_i101 } - replace{ @atom:693 @atom:693_b48_a48_d48_i48 } - replace{ @atom:694 @atom:694_b18_a18_d18_i18 } - replace{ @atom:695 @atom:695_b19_a19_d19_i19 } - replace{ @atom:696 @atom:696_b13_a13_d13_i13 } - replace{ @atom:697 @atom:697_b13_a13_d13_i13 } - replace{ @atom:698 @atom:698_b13_a13_d13_i13 } - replace{ @atom:699 @atom:699_b13_a13_d13_i13 } - replace{ @atom:700 @atom:700_b46_a46_d46_i46 } + replace{ @atom:693 @atom:693_b048_a048_d048_i048 } + replace{ @atom:694 @atom:694_b018_a018_d018_i018 } + replace{ @atom:695 @atom:695_b019_a019_d019_i019 } + replace{ @atom:696 @atom:696_b013_a013_d013_i013 } + replace{ @atom:697 @atom:697_b013_a013_d013_i013 } + replace{ @atom:698 @atom:698_b013_a013_d013_i013 } + replace{ @atom:699 @atom:699_b013_a013_d013_i013 } + replace{ @atom:700 @atom:700_b046_a046_d046_i046 } replace{ @atom:701 @atom:701_b102_a102_d102_i102 } replace{ @atom:702 @atom:702_b103_a103_d103_i103 } - replace{ @atom:703 @atom:703_b13_a13_d13_i13 } - replace{ @atom:704 @atom:704_b46_a46_d46_i46 } - replace{ @atom:705 @atom:705_b13_a13_d13_i13 } - replace{ @atom:706 @atom:706_b13_a13_d13_i13 } - replace{ @atom:707 @atom:707_b13_a13_d13_i13 } + replace{ @atom:703 @atom:703_b013_a013_d013_i013 } + replace{ @atom:704 @atom:704_b046_a046_d046_i046 } + replace{ @atom:705 @atom:705_b013_a013_d013_i013 } + replace{ @atom:706 @atom:706_b013_a013_d013_i013 } + replace{ @atom:707 @atom:707_b013_a013_d013_i013 } replace{ @atom:708 @atom:708_b102_a102_d102_i102 } - replace{ @atom:709 @atom:709_b48_a48_d48_i48 } - replace{ @atom:710 @atom:710_b13_a13_d13_i13 } - replace{ @atom:711 @atom:711_b56_a56_d56_i56 } - replace{ @atom:712 @atom:712_b4_a4_d4_i4 } - replace{ @atom:713 @atom:713_b3_a3_d3_i3 } - replace{ @atom:714 @atom:714_b20_a20_d20_i20 } - replace{ @atom:715 @atom:715_b13_a13_d13_i13 } - replace{ @atom:716 @atom:716_b13_a13_d13_i13 } - replace{ @atom:717 @atom:717_b13_a13_d13_i13 } - replace{ @atom:718 @atom:718_b46_a46_d46_i46 } - replace{ @atom:719 @atom:719_b46_a46_d46_i46 } - replace{ @atom:720 @atom:720_b46_a46_d46_i46 } - replace{ @atom:721 @atom:721_b20_a20_d20_i20 } + replace{ @atom:709 @atom:709_b048_a048_d048_i048 } + replace{ @atom:710 @atom:710_b013_a013_d013_i013 } + replace{ @atom:711 @atom:711_b056_a056_d056_i056 } + replace{ @atom:712 @atom:712_b004_a004_d004_i004 } + replace{ @atom:713 @atom:713_b003_a003_d003_i003 } + replace{ @atom:714 @atom:714_b020_a020_d020_i020 } + replace{ @atom:715 @atom:715_b013_a013_d013_i013 } + replace{ @atom:716 @atom:716_b013_a013_d013_i013 } + replace{ @atom:717 @atom:717_b013_a013_d013_i013 } + replace{ @atom:718 @atom:718_b046_a046_d046_i046 } + replace{ @atom:719 @atom:719_b046_a046_d046_i046 } + replace{ @atom:720 @atom:720_b046_a046_d046_i046 } + replace{ @atom:721 @atom:721_b020_a020_d020_i020 } replace{ @atom:722 @atom:722_b104_a104_d104_i104 } - replace{ @atom:723 @atom:723_b13_a13_d13_i13 } - replace{ @atom:724 @atom:724_b13_a13_d13_i13 } - replace{ @atom:725 @atom:725_b46_a46_d46_i46 } - replace{ @atom:726 @atom:726_b64_a64_d64_i64 } - replace{ @atom:727 @atom:727_b1_a1_d1_i1 } - replace{ @atom:728 @atom:728_b24_a24_d24_i24 } - replace{ @atom:729 @atom:729_b4_a4_d4_i4 } - replace{ @atom:730 @atom:730_b44_a44_d44_i44 } - replace{ @atom:731 @atom:731_b44_a44_d44_i44 } - replace{ @atom:732 @atom:732_b44_a44_d44_i44 } - replace{ @atom:733 @atom:733_b13_a13_d13_i13 } - replace{ @atom:734 @atom:734_b13_a13_d13_i13 } - replace{ @atom:735 @atom:735_b13_a13_d13_i13 } - replace{ @atom:736 @atom:736_b13_a13_d13_i13 } - replace{ @atom:737 @atom:737_b13_a13_d13_i13 } - replace{ @atom:738 @atom:738_b13_a13_d13_i13 } - replace{ @atom:739 @atom:739_b45_a45_d45_i45 } - replace{ @atom:740 @atom:740_b45_a45_d45_i45 } - replace{ @atom:741 @atom:741_b46_a46_d46_i46 } - replace{ @atom:742 @atom:742_b13_a13_d13_i13 } - replace{ @atom:743 @atom:743_b13_a13_d13_i13 } - replace{ @atom:744 @atom:744_b13_a13_d13_i13 } - replace{ @atom:745 @atom:745_b13_a13_d13_i13 } - replace{ @atom:746 @atom:746_b48_a48_d48_i48 } - replace{ @atom:747 @atom:747_b48_a48_d48_i48 } - replace{ @atom:748 @atom:748_b48_a48_d48_i48 } - replace{ @atom:749 @atom:749_b13_a13_d13_i13 } - replace{ @atom:750 @atom:750_b13_a13_d13_i13 } - replace{ @atom:751 @atom:751_b13_a13_d13_i13 } - replace{ @atom:752 @atom:752_b13_a13_d13_i13 } - replace{ @atom:753 @atom:753_b13_a13_d13_i13 } - replace{ @atom:754 @atom:754_b13_a13_d13_i13 } - replace{ @atom:755 @atom:755_b19_a19_d19_i19 } - replace{ @atom:756 @atom:756_b46_a46_d46_i46 } - replace{ @atom:757 @atom:757_b19_a19_d19_i19 } - replace{ @atom:758 @atom:758_b19_a19_d19_i19 } - replace{ @atom:759 @atom:759_b19_a19_d19_i19 } - replace{ @atom:760 @atom:760_b46_a46_d46_i46 } - replace{ @atom:761 @atom:761_b51_a51_d51_i51 } - replace{ @atom:762 @atom:762_b51_a51_d51_i51 } - replace{ @atom:763 @atom:763_b51_a51_d51_i51 } - replace{ @atom:764 @atom:764_b5_a5_d5_i5 } - replace{ @atom:765 @atom:765_b7_a7_d7_i7 } + replace{ @atom:723 @atom:723_b013_a013_d013_i013 } + replace{ @atom:724 @atom:724_b013_a013_d013_i013 } + replace{ @atom:725 @atom:725_b046_a046_d046_i046 } + replace{ @atom:726 @atom:726_b064_a064_d064_i064 } + replace{ @atom:727 @atom:727_b001_a001_d001_i001 } + replace{ @atom:728 @atom:728_b024_a024_d024_i024 } + replace{ @atom:729 @atom:729_b004_a004_d004_i004 } + replace{ @atom:730 @atom:730_b044_a044_d044_i044 } + replace{ @atom:731 @atom:731_b044_a044_d044_i044 } + replace{ @atom:732 @atom:732_b044_a044_d044_i044 } + replace{ @atom:733 @atom:733_b013_a013_d013_i013 } + replace{ @atom:734 @atom:734_b013_a013_d013_i013 } + replace{ @atom:735 @atom:735_b013_a013_d013_i013 } + replace{ @atom:736 @atom:736_b013_a013_d013_i013 } + replace{ @atom:737 @atom:737_b013_a013_d013_i013 } + replace{ @atom:738 @atom:738_b013_a013_d013_i013 } + replace{ @atom:739 @atom:739_b045_a045_d045_i045 } + replace{ @atom:740 @atom:740_b045_a045_d045_i045 } + replace{ @atom:741 @atom:741_b046_a046_d046_i046 } + replace{ @atom:742 @atom:742_b013_a013_d013_i013 } + replace{ @atom:743 @atom:743_b013_a013_d013_i013 } + replace{ @atom:744 @atom:744_b013_a013_d013_i013 } + replace{ @atom:745 @atom:745_b013_a013_d013_i013 } + replace{ @atom:746 @atom:746_b048_a048_d048_i048 } + replace{ @atom:747 @atom:747_b048_a048_d048_i048 } + replace{ @atom:748 @atom:748_b048_a048_d048_i048 } + replace{ @atom:749 @atom:749_b013_a013_d013_i013 } + replace{ @atom:750 @atom:750_b013_a013_d013_i013 } + replace{ @atom:751 @atom:751_b013_a013_d013_i013 } + replace{ @atom:752 @atom:752_b013_a013_d013_i013 } + replace{ @atom:753 @atom:753_b013_a013_d013_i013 } + replace{ @atom:754 @atom:754_b013_a013_d013_i013 } + replace{ @atom:755 @atom:755_b019_a019_d019_i019 } + replace{ @atom:756 @atom:756_b046_a046_d046_i046 } + replace{ @atom:757 @atom:757_b019_a019_d019_i019 } + replace{ @atom:758 @atom:758_b019_a019_d019_i019 } + replace{ @atom:759 @atom:759_b019_a019_d019_i019 } + replace{ @atom:760 @atom:760_b046_a046_d046_i046 } + replace{ @atom:761 @atom:761_b051_a051_d051_i051 } + replace{ @atom:762 @atom:762_b051_a051_d051_i051 } + replace{ @atom:763 @atom:763_b051_a051_d051_i051 } + replace{ @atom:764 @atom:764_b005_a005_d005_i005 } + replace{ @atom:765 @atom:765_b007_a007_d007_i007 } replace{ @atom:766 @atom:766_b105_a105_d105_i105 } replace{ @atom:767 @atom:767_b105_a105_d105_i105 } replace{ @atom:768 @atom:768_b105_a105_d105_i105 } - replace{ @atom:769 @atom:769_b19_a19_d19_i19 } - replace{ @atom:770 @atom:770_b53_a53_d53_i53 } - replace{ @atom:771 @atom:771_b54_a54_d54_i54 } - replace{ @atom:772 @atom:772_b13_a13_d13_i13 } - replace{ @atom:773 @atom:773_b13_a13_d13_i13 } - replace{ @atom:774 @atom:774_b13_a13_d13_i13 } - replace{ @atom:775 @atom:775_b13_a13_d13_i13 } - replace{ @atom:776 @atom:776_b84_a84_d84_i84 } - replace{ @atom:777 @atom:777_b87_a87_d87_i87 } - replace{ @atom:778 @atom:778_b86_a86_d86_i86 } - replace{ @atom:779 @atom:779_b86_a86_d86_i86 } - replace{ @atom:780 @atom:780_b46_a46_d46_i46 } - replace{ @atom:781 @atom:781_b13_a13_d13_i13 } - replace{ @atom:782 @atom:782_b3_a3_d3_i3 } - replace{ @atom:783 @atom:783_b53_a53_d53_i53 } - replace{ @atom:784 @atom:784_b52_a52_d52_i52 } - replace{ @atom:785 @atom:785_b54_a54_d54_i54 } - replace{ @atom:786 @atom:786_b1_a1_d1_i1 } - replace{ @atom:787 @atom:787_b13_a13_d13_i13 } - replace{ @atom:788 @atom:788_b46_a46_d46_i46 } - replace{ @atom:789 @atom:789_b13_a13_d13_i13 } - replace{ @atom:790 @atom:790_b13_a13_d13_i13 } - replace{ @atom:791 @atom:791_b13_a13_d13_i13 } - replace{ @atom:792 @atom:792_b13_a13_d13_i13 } - replace{ @atom:793 @atom:793_b13_a13_d13_i13 } - replace{ @atom:794 @atom:794_b13_a13_d13_i13 } - replace{ @atom:795 @atom:795_b1_a1_d1_i1 } - replace{ @atom:796 @atom:796_b13_a13_d13_i13 } - replace{ @atom:797 @atom:797_b46_a46_d46_i46 } - replace{ @atom:798 @atom:798_b13_a13_d13_i13 } - replace{ @atom:799 @atom:799_b13_a13_d13_i13 } - replace{ @atom:800 @atom:800_b21_a21_d21_i21 } - replace{ @atom:801 @atom:801_b13_a13_d13_i13 } - replace{ @atom:802 @atom:802_b46_a46_d46_i46 } - replace{ @atom:803 @atom:803_b13_a13_d13_i13 } - replace{ @atom:804 @atom:804_b13_a13_d13_i13 } - replace{ @atom:805 @atom:805_b65_a65_d65_i65 } - replace{ @atom:806 @atom:806_b13_a13_d13_i13 } - replace{ @atom:807 @atom:807_b46_a46_d46_i46 } - replace{ @atom:808 @atom:808_b13_a13_d13_i13 } - replace{ @atom:809 @atom:809_b13_a13_d13_i13 } - replace{ @atom:810 @atom:810_b1_a1_d1_i1 } - replace{ @atom:811 @atom:811_b21_a21_d21_i21 } - replace{ @atom:812 @atom:812_b65_a65_d65_i65 } - replace{ @atom:813 @atom:813_b48_a48_d48_i48 } - replace{ @atom:814 @atom:814_b20_a20_d20_i20 } - replace{ @atom:815 @atom:815_b13_a13_d13_i13 } - replace{ @atom:816 @atom:816_b1_a1_d1_i1 } - replace{ @atom:817 @atom:817_b24_a24_d24_i24 } - replace{ @atom:818 @atom:818_b48_a48_d48_i48 } - replace{ @atom:819 @atom:819_b13_a13_d13_i13 } - replace{ @atom:820 @atom:820_b3_a3_d3_i3 } - replace{ @atom:821 @atom:821_b3_a3_d3_i3 } - replace{ @atom:822 @atom:822_b4_a4_d4_i4 } - replace{ @atom:823 @atom:823_b24_a24_d24_i24 } - replace{ @atom:824 @atom:824_b45_a45_d45_i45 } - replace{ @atom:825 @atom:825_b5_a5_d5_i5 } - replace{ @atom:826 @atom:826_b7_a7_d7_i7 } - replace{ @atom:827 @atom:827_b13_a13_d13_i13 } - replace{ @atom:828 @atom:828_b13_a13_d13_i13 } - replace{ @atom:829 @atom:829_b86_a86_d86_i86 } - replace{ @atom:830 @atom:830_b86_a86_d86_i86 } - replace{ @atom:831 @atom:831_b86_a86_d86_i86 } - replace{ @atom:832 @atom:832_b86_a86_d86_i86 } - replace{ @atom:833 @atom:833_b48_a48_d48_i48 } + replace{ @atom:769 @atom:769_b019_a019_d019_i019 } + replace{ @atom:770 @atom:770_b053_a053_d053_i053 } + replace{ @atom:771 @atom:771_b054_a054_d054_i054 } + replace{ @atom:772 @atom:772_b013_a013_d013_i013 } + replace{ @atom:773 @atom:773_b013_a013_d013_i013 } + replace{ @atom:774 @atom:774_b013_a013_d013_i013 } + replace{ @atom:775 @atom:775_b013_a013_d013_i013 } + replace{ @atom:776 @atom:776_b084_a084_d084_i084 } + replace{ @atom:777 @atom:777_b087_a087_d087_i087 } + replace{ @atom:778 @atom:778_b086_a086_d086_i086 } + replace{ @atom:779 @atom:779_b086_a086_d086_i086 } + replace{ @atom:780 @atom:780_b046_a046_d046_i046 } + replace{ @atom:781 @atom:781_b013_a013_d013_i013 } + replace{ @atom:782 @atom:782_b003_a003_d003_i003 } + replace{ @atom:783 @atom:783_b053_a053_d053_i053 } + replace{ @atom:784 @atom:784_b052_a052_d052_i052 } + replace{ @atom:785 @atom:785_b054_a054_d054_i054 } + replace{ @atom:786 @atom:786_b001_a001_d001_i001 } + replace{ @atom:787 @atom:787_b013_a013_d013_i013 } + replace{ @atom:788 @atom:788_b046_a046_d046_i046 } + replace{ @atom:789 @atom:789_b013_a013_d013_i013 } + replace{ @atom:790 @atom:790_b013_a013_d013_i013 } + replace{ @atom:791 @atom:791_b013_a013_d013_i013 } + replace{ @atom:792 @atom:792_b013_a013_d013_i013 } + replace{ @atom:793 @atom:793_b013_a013_d013_i013 } + replace{ @atom:794 @atom:794_b013_a013_d013_i013 } + replace{ @atom:795 @atom:795_b001_a001_d001_i001 } + replace{ @atom:796 @atom:796_b013_a013_d013_i013 } + replace{ @atom:797 @atom:797_b046_a046_d046_i046 } + replace{ @atom:798 @atom:798_b013_a013_d013_i013 } + replace{ @atom:799 @atom:799_b013_a013_d013_i013 } + replace{ @atom:800 @atom:800_b021_a021_d021_i021 } + replace{ @atom:801 @atom:801_b013_a013_d013_i013 } + replace{ @atom:802 @atom:802_b046_a046_d046_i046 } + replace{ @atom:803 @atom:803_b013_a013_d013_i013 } + replace{ @atom:804 @atom:804_b013_a013_d013_i013 } + replace{ @atom:805 @atom:805_b065_a065_d065_i065 } + replace{ @atom:806 @atom:806_b013_a013_d013_i013 } + replace{ @atom:807 @atom:807_b046_a046_d046_i046 } + replace{ @atom:808 @atom:808_b013_a013_d013_i013 } + replace{ @atom:809 @atom:809_b013_a013_d013_i013 } + replace{ @atom:810 @atom:810_b001_a001_d001_i001 } + replace{ @atom:811 @atom:811_b021_a021_d021_i021 } + replace{ @atom:812 @atom:812_b065_a065_d065_i065 } + replace{ @atom:813 @atom:813_b048_a048_d048_i048 } + replace{ @atom:814 @atom:814_b020_a020_d020_i020 } + replace{ @atom:815 @atom:815_b013_a013_d013_i013 } + replace{ @atom:816 @atom:816_b001_a001_d001_i001 } + replace{ @atom:817 @atom:817_b024_a024_d024_i024 } + replace{ @atom:818 @atom:818_b048_a048_d048_i048 } + replace{ @atom:819 @atom:819_b013_a013_d013_i013 } + replace{ @atom:820 @atom:820_b003_a003_d003_i003 } + replace{ @atom:821 @atom:821_b003_a003_d003_i003 } + replace{ @atom:822 @atom:822_b004_a004_d004_i004 } + replace{ @atom:823 @atom:823_b024_a024_d024_i024 } + replace{ @atom:824 @atom:824_b045_a045_d045_i045 } + replace{ @atom:825 @atom:825_b005_a005_d005_i005 } + replace{ @atom:826 @atom:826_b007_a007_d007_i007 } + replace{ @atom:827 @atom:827_b013_a013_d013_i013 } + replace{ @atom:828 @atom:828_b013_a013_d013_i013 } + replace{ @atom:829 @atom:829_b086_a086_d086_i086 } + replace{ @atom:830 @atom:830_b086_a086_d086_i086 } + replace{ @atom:831 @atom:831_b086_a086_d086_i086 } + replace{ @atom:832 @atom:832_b086_a086_d086_i086 } + replace{ @atom:833 @atom:833_b048_a048_d048_i048 } replace{ @atom:834 @atom:834_b106_a106_d106_i106 } - replace{ @atom:835 @atom:835_b13_a13_d13_i13 } - replace{ @atom:836 @atom:836_b13_a13_d13_i13 } - replace{ @atom:837 @atom:837_b13_a13_d13_i13 } - replace{ @atom:838 @atom:838_b66_a66_d66_i66 } - replace{ @atom:839 @atom:839_b46_a46_d46_i46 } - replace{ @atom:840 @atom:840_b24_a24_d24_i24 } - replace{ @atom:841 @atom:841_b48_a48_d48_i48 } - replace{ @atom:842 @atom:842_b48_a48_d48_i48 } - replace{ @atom:843 @atom:843_b24_a24_d24_i24 } - replace{ @atom:844 @atom:844_b48_a48_d48_i48 } - replace{ @atom:845 @atom:845_b3_a3_d3_i3 } - replace{ @atom:846 @atom:846_b4_a4_d4_i4 } + replace{ @atom:835 @atom:835_b013_a013_d013_i013 } + replace{ @atom:836 @atom:836_b013_a013_d013_i013 } + replace{ @atom:837 @atom:837_b013_a013_d013_i013 } + replace{ @atom:838 @atom:838_b066_a066_d066_i066 } + replace{ @atom:839 @atom:839_b046_a046_d046_i046 } + replace{ @atom:840 @atom:840_b024_a024_d024_i024 } + replace{ @atom:841 @atom:841_b048_a048_d048_i048 } + replace{ @atom:842 @atom:842_b048_a048_d048_i048 } + replace{ @atom:843 @atom:843_b024_a024_d024_i024 } + replace{ @atom:844 @atom:844_b048_a048_d048_i048 } + replace{ @atom:845 @atom:845_b003_a003_d003_i003 } + replace{ @atom:846 @atom:846_b004_a004_d004_i004 } replace{ @atom:847 @atom:847_b107_a107_d107_i107 } - replace{ @atom:848 @atom:848_b13_a13_d13_i13 } - replace{ @atom:849 @atom:849_b13_a13_d13_i13 } - replace{ @atom:850 @atom:850_b13_a13_d13_i13 } - replace{ @atom:851 @atom:851_b13_a13_d13_i13 } - replace{ @atom:852 @atom:852_b46_a46_d46_i46 } - replace{ @atom:853 @atom:853_b3_a3_d3_i3 } - replace{ @atom:854 @atom:854_b4_a4_d4_i4 } - replace{ @atom:855 @atom:855_b46_a46_d46_i46 } - replace{ @atom:856 @atom:856_b13_a13_d13_i13 } - replace{ @atom:857 @atom:857_b13_a13_d13_i13 } - replace{ @atom:858 @atom:858_b13_a13_d13_i13 } - replace{ @atom:859 @atom:859_b13_a13_d13_i13 } - replace{ @atom:860 @atom:860_b13_a13_d13_i13 } - replace{ @atom:861 @atom:861_b13_a13_d13_i13 } - replace{ @atom:862 @atom:862_b13_a13_d13_i13 } - replace{ @atom:863 @atom:863_b13_a13_d13_i13 } - replace{ @atom:864 @atom:864_b13_a13_d13_i13 } - replace{ @atom:865 @atom:865_b13_a13_d13_i13 } + replace{ @atom:848 @atom:848_b013_a013_d013_i013 } + replace{ @atom:849 @atom:849_b013_a013_d013_i013 } + replace{ @atom:850 @atom:850_b013_a013_d013_i013 } + replace{ @atom:851 @atom:851_b013_a013_d013_i013 } + replace{ @atom:852 @atom:852_b046_a046_d046_i046 } + replace{ @atom:853 @atom:853_b003_a003_d003_i003 } + replace{ @atom:854 @atom:854_b004_a004_d004_i004 } + replace{ @atom:855 @atom:855_b046_a046_d046_i046 } + replace{ @atom:856 @atom:856_b013_a013_d013_i013 } + replace{ @atom:857 @atom:857_b013_a013_d013_i013 } + replace{ @atom:858 @atom:858_b013_a013_d013_i013 } + replace{ @atom:859 @atom:859_b013_a013_d013_i013 } + replace{ @atom:860 @atom:860_b013_a013_d013_i013 } + replace{ @atom:861 @atom:861_b013_a013_d013_i013 } + replace{ @atom:862 @atom:862_b013_a013_d013_i013 } + replace{ @atom:863 @atom:863_b013_a013_d013_i013 } + replace{ @atom:864 @atom:864_b013_a013_d013_i013 } + replace{ @atom:865 @atom:865_b013_a013_d013_i013 } replace{ @atom:866 @atom:866_b108_a108_d108_i108 } replace{ @atom:867 @atom:867_b108_a108_d108_i108 } replace{ @atom:868 @atom:868_b108_a108_d108_i108 } replace{ @atom:869 @atom:869_b108_a108_d108_i108 } - replace{ @atom:870 @atom:870_b45_a45_d45_i45 } - replace{ @atom:871 @atom:871_b13_a13_d13_i13 } - replace{ @atom:872 @atom:872_b13_a13_d13_i13 } - replace{ @atom:873 @atom:873_b13_a13_d13_i13 } - replace{ @atom:874 @atom:874_b13_a13_d13_i13 } - replace{ @atom:875 @atom:875_b1_a1_d1_i1 } - replace{ @atom:876 @atom:876_b21_a21_d21_i21 } - replace{ @atom:877 @atom:877_b65_a65_d65_i65 } - replace{ @atom:878 @atom:878_b66_a66_d66_i66 } - replace{ @atom:879 @atom:879_b68_a68_d68_i68 } - replace{ @atom:880 @atom:880_b69_a69_d69_i69 } - replace{ @atom:881 @atom:881_b70_a70_d70_i70 } - replace{ @atom:882 @atom:882_b71_a71_d71_i71 } - replace{ @atom:883 @atom:883_b72_a72_d72_i72 } - replace{ @atom:884 @atom:884_b73_a73_d73_i73 } - replace{ @atom:885 @atom:885_b74_a74_d74_i74 } - replace{ @atom:886 @atom:886_b75_a75_d75_i75 } - replace{ @atom:887 @atom:887_b76_a76_d76_i76 } - replace{ @atom:888 @atom:888_b13_a13_d13_i13 } - replace{ @atom:889 @atom:889_b13_a13_d13_i13 } - replace{ @atom:890 @atom:890_b13_a13_d13_i13 } - replace{ @atom:891 @atom:891_b13_a13_d13_i13 } - replace{ @atom:892 @atom:892_b46_a46_d46_i46 } - replace{ @atom:893 @atom:893_b53_a53_d53_i53 } - replace{ @atom:894 @atom:894_b48_a48_d48_i48 } - replace{ @atom:895 @atom:895_b53_a53_d53_i53 } - replace{ @atom:896 @atom:896_b48_a48_d48_i48 } + replace{ @atom:870 @atom:870_b045_a045_d045_i045 } + replace{ @atom:871 @atom:871_b013_a013_d013_i013 } + replace{ @atom:872 @atom:872_b013_a013_d013_i013 } + replace{ @atom:873 @atom:873_b013_a013_d013_i013 } + replace{ @atom:874 @atom:874_b013_a013_d013_i013 } + replace{ @atom:875 @atom:875_b001_a001_d001_i001 } + replace{ @atom:876 @atom:876_b021_a021_d021_i021 } + replace{ @atom:877 @atom:877_b065_a065_d065_i065 } + replace{ @atom:878 @atom:878_b066_a066_d066_i066 } + replace{ @atom:879 @atom:879_b068_a068_d068_i068 } + replace{ @atom:880 @atom:880_b069_a069_d069_i069 } + replace{ @atom:881 @atom:881_b070_a070_d070_i070 } + replace{ @atom:882 @atom:882_b071_a071_d071_i071 } + replace{ @atom:883 @atom:883_b072_a072_d072_i072 } + replace{ @atom:884 @atom:884_b073_a073_d073_i073 } + replace{ @atom:885 @atom:885_b074_a074_d074_i074 } + replace{ @atom:886 @atom:886_b075_a075_d075_i075 } + replace{ @atom:887 @atom:887_b076_a076_d076_i076 } + replace{ @atom:888 @atom:888_b013_a013_d013_i013 } + replace{ @atom:889 @atom:889_b013_a013_d013_i013 } + replace{ @atom:890 @atom:890_b013_a013_d013_i013 } + replace{ @atom:891 @atom:891_b013_a013_d013_i013 } + replace{ @atom:892 @atom:892_b046_a046_d046_i046 } + replace{ @atom:893 @atom:893_b053_a053_d053_i053 } + replace{ @atom:894 @atom:894_b048_a048_d048_i048 } + replace{ @atom:895 @atom:895_b053_a053_d053_i053 } + replace{ @atom:896 @atom:896_b048_a048_d048_i048 } replace{ @atom:897 @atom:897_b109_a109_d109_i109 } replace{ @atom:898 @atom:898_b109_a109_d109_i109 } - replace{ @atom:899 @atom:899_b46_a46_d46_i46 } - replace{ @atom:900 @atom:900_b47_a47_d47_i47 } - replace{ @atom:901 @atom:901_b47_a47_d47_i47 } - replace{ @atom:902 @atom:902_b47_a47_d47_i47 } + replace{ @atom:899 @atom:899_b046_a046_d046_i046 } + replace{ @atom:900 @atom:900_b047_a047_d047_i047 } + replace{ @atom:901 @atom:901_b047_a047_d047_i047 } + replace{ @atom:902 @atom:902_b047_a047_d047_i047 } replace{ @atom:903 @atom:903_b110_a110_d110_i110 } replace{ @atom:904 @atom:904_b110_a110_d110_i110 } - replace{ @atom:905 @atom:905_b4_a4_d4_i4 } - replace{ @atom:906 @atom:906_b13_a13_d13_i13 } + replace{ @atom:905 @atom:905_b004_a004_d004_i004 } + replace{ @atom:906 @atom:906_b013_a013_d013_i013 } @@ -2773,915 +2786,915 @@ OPLSAA { # --------------- Non-Bonded interactions: --------------------- # http://lammps.sandia.gov/doc/pair_lj.html # Syntax: - # pair_coeff AtomType1 AtomType2 pair_style_name parameters... + # pair_coeff AtomType1 AtomType2 parameters... write_once("In Settings") { - pair_coeff @atom:1_b1_a1_d1_i1 @atom:1_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:2_b2_a2_d2_i2 @atom:2_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:3_b3_a3_d3_i3 @atom:3_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:4_b4_a4_d4_i4 @atom:4_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:5_b5_a5_d5_i5 @atom:5_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:6_b6_a6_d6_i6 @atom:6_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91 - pair_coeff @atom:7_b7_a7_d7_i7 @atom:7_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:8_b8_a8_d8_i8 @atom:8_b8_a8_d8_i8 lj/cut/coul/long 0.294 3.73 - pair_coeff @atom:9_b6_a6_d6_i6 @atom:9_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:10_b6_a6_d6_i6 @atom:10_b6_a6_d6_i6 lj/cut/coul/long 0.175 3.905 - pair_coeff @atom:11_b6_a6_d6_i6 @atom:11_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.91 - pair_coeff @atom:12_b6_a6_d6_i6 @atom:12_b6_a6_d6_i6 lj/cut/coul/long 0.145 3.96 - pair_coeff @atom:13_b2_a2_d2_i2 @atom:13_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:14_b9_a9_d9_i9 @atom:14_b9_a9_d9_i9 lj/cut/coul/long 0.14 3.85 - pair_coeff @atom:15_b10_a10_d10_i10 @atom:15_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85 - pair_coeff @atom:16_b11_a11_d11_i11 @atom:16_b11_a11_d11_i11 lj/cut/coul/long 0.115 3.8 - pair_coeff @atom:17_b12_a12_d12_i12 @atom:17_b12_a12_d12_i12 lj/cut/coul/long 0.11 3.75 - pair_coeff @atom:18_b13_a13_d13_i13 @atom:18_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:19_b14_a14_d14_i14 @atom:19_b14_a14_d14_i14 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:20_b5_a5_d5_i5 @atom:20_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:21_b7_a7_d7_i7 @atom:21_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:22_b6_a6_d6_i6 @atom:22_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:23_b2_a2_d2_i2 @atom:23_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:24_b15_a15_d15_i15 @atom:24_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7 - pair_coeff @atom:25_b15_a15_d15_i15 @atom:25_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:26_b16_a16_d16_i16 @atom:26_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:27_b16_a16_d16_i16 @atom:27_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:28_b17_a17_d17_i17 @atom:28_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:29_b17_a17_d17_i17 @atom:29_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:30_b6_a6_d6_i6 @atom:30_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:31_b2_a2_d2_i2 @atom:31_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:32_b6_a6_d6_i6 @atom:32_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:33_b2_a2_d2_i2 @atom:33_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:34_b6_a6_d6_i6 @atom:34_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:35_b2_a2_d2_i2 @atom:35_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:36_b18_a18_d18_i18 @atom:36_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:37_b19_a19_d19_i19 @atom:37_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:38_b6_a6_d6_i6 @atom:38_b6_a6_d6_i6 lj/cut/coul/long 0.207 3.775 - pair_coeff @atom:39_b10_a10_d10_i10 @atom:39_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.85 - pair_coeff @atom:40_b13_a13_d13_i13 @atom:40_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:41_b20_a20_d20_i20 @atom:41_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:42_b6_a6_d6_i6 @atom:42_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:43_b2_a2_d2_i2 @atom:43_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:44_b2_a2_d2_i2 @atom:44_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.8 - pair_coeff @atom:45_b21_a21_d21_i21 @atom:45_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:46_b10_a10_d10_i10 @atom:46_b10_a10_d10_i10 lj/cut/coul/long 0.08 3.8 - pair_coeff @atom:47_b21_a21_d21_i21 @atom:47_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.47 - pair_coeff @atom:48_b13_a13_d13_i13 @atom:48_b13_a13_d13_i13 lj/cut/coul/long 0.05 3.8 - pair_coeff @atom:49_b21_a21_d21_i21 @atom:49_b21_a21_d21_i21 lj/cut/coul/long 0.266 3.47 - pair_coeff @atom:50_b22_a22_d22_i22 @atom:50_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:51_b23_a23_d23_i23 @atom:51_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93 - pair_coeff @atom:52_b6_a6_d6_i6 @atom:52_b6_a6_d6_i6 lj/cut/coul/long 0.16 3.81 - pair_coeff @atom:53_b4_a4_d4_i4 @atom:53_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:54_b24_a24_d24_i24 @atom:54_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:55_b3_a3_d3_i3 @atom:55_b3_a3_d3_i3 lj/cut/coul/long 0.115 3.8 - pair_coeff @atom:56_b6_a6_d6_i6 @atom:56_b6_a6_d6_i6 lj/cut/coul/long 0.17 3.8 - pair_coeff @atom:57_b25_a25_d25_i25 @atom:57_b25_a25_d25_i25 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:58_b26_a26_d26_i26 @atom:58_b26_a26_d26_i26 lj/cut/coul/long 0.02 2.556 - pair_coeff @atom:59_b27_a27_d27_i27 @atom:59_b27_a27_d27_i27 lj/cut/coul/long 0.069 2.78 - pair_coeff @atom:60_b28_a28_d28_i28 @atom:60_b28_a28_d28_i28 lj/cut/coul/long 0.2339 3.401 - pair_coeff @atom:61_b29_a29_d29_i29 @atom:61_b29_a29_d29_i29 lj/cut/coul/long 0.317 3.624 - pair_coeff @atom:62_b30_a30_d30_i30 @atom:62_b30_a30_d30_i30 lj/cut/coul/long 0.433 3.935 - pair_coeff @atom:63_b31_a31_d31_i31 @atom:63_b31_a31_d31_i31 lj/cut/coul/long 0.1521 3.15061 - pair_coeff @atom:64_b32_a32_d32_i32 @atom:64_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:65_b31_a31_d31_i31 @atom:65_b31_a31_d31_i31 lj/cut/coul/long 0.155 3.15365 - pair_coeff @atom:66_b32_a32_d32_i32 @atom:66_b32_a32_d32_i32 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:67_b33_a33_d33_i33 @atom:67_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:68_b34_a34_d34_i34 @atom:68_b34_a34_d34_i34 lj/cut/coul/long 0.15 3.176 - pair_coeff @atom:69_b35_a35_d35_i35 @atom:69_b35_a35_d35_i35 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:70_b36_a36_d36_i36 @atom:70_b36_a36_d36_i36 lj/cut/coul/long 0.1 3.27 - pair_coeff @atom:71_b37_a37_d37_i37 @atom:71_b37_a37_d37_i37 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:72_b38_a38_d38_i38 @atom:72_b38_a38_d38_i38 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:73_b39_a39_d39_i39 @atom:73_b39_a39_d39_i39 lj/cut/coul/long 0.16 3.12 - pair_coeff @atom:74_b40_a40_d40_i40 @atom:74_b40_a40_d40_i40 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:75_b41_a41_d41_i41 @atom:75_b41_a41_d41_i41 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:76_b42_a42_d42_i42 @atom:76_b42_a42_d42_i42 lj/cut/coul/long 0.1554 3.16557 - pair_coeff @atom:77_b43_a43_d43_i43 @atom:77_b43_a43_d43_i43 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:78_b44_a44_d44_i44 @atom:78_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.42 - pair_coeff @atom:79_b45_a45_d45_i45 @atom:79_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:80_b13_a13_d13_i13 @atom:80_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:81_b13_a13_d13_i13 @atom:81_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:82_b13_a13_d13_i13 @atom:82_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:83_b13_a13_d13_i13 @atom:83_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:84_b13_a13_d13_i13 @atom:84_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:85_b46_a46_d46_i46 @atom:85_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:86_b47_a47_d47_i47 @atom:86_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:87_b47_a47_d47_i47 @atom:87_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:88_b47_a47_d47_i47 @atom:88_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:89_b46_a46_d46_i46 @atom:89_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:90_b48_a48_d48_i48 @atom:90_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:91_b49_a49_d49_i49 @atom:91_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:92_b48_a48_d48_i48 @atom:92_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:93_b13_a13_d13_i13 @atom:93_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:94_b13_a13_d13_i13 @atom:94_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:95_b50_a50_d50_i50 @atom:95_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:96_b5_a5_d5_i5 @atom:96_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:97_b7_a7_d7_i7 @atom:97_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:98_b46_a46_d46_i46 @atom:98_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:99_b13_a13_d13_i13 @atom:99_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:100_b13_a13_d13_i13 @atom:100_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:101_b13_a13_d13_i13 @atom:101_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:102_b13_a13_d13_i13 @atom:102_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:103_b13_a13_d13_i13 @atom:103_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:104_b5_a5_d5_i5 @atom:104_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:105_b7_a7_d7_i7 @atom:105_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:106_b1_a1_d1_i1 @atom:106_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:107_b46_a46_d46_i46 @atom:107_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:108_b48_a48_d48_i48 @atom:108_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:109_b5_a5_d5_i5 @atom:109_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:110_b7_a7_d7_i7 @atom:110_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:111_b5_a5_d5_i5 @atom:111_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:112_b7_a7_d7_i7 @atom:112_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:113_b5_a5_d5_i5 @atom:113_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:114_b7_a7_d7_i7 @atom:114_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:115_b13_a13_d13_i13 @atom:115_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:116_b13_a13_d13_i13 @atom:116_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:117_b13_a13_d13_i13 @atom:117_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:118_b46_a46_d46_i46 @atom:118_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:119_b20_a20_d20_i20 @atom:119_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:120_b50_a50_d50_i50 @atom:120_b50_a50_d50_i50 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:121_b20_a20_d20_i20 @atom:121_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:122_b20_a20_d20_i20 @atom:122_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:123_b13_a13_d13_i13 @atom:123_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:124_b13_a13_d13_i13 @atom:124_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:125_b13_a13_d13_i13 @atom:125_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:126_b13_a13_d13_i13 @atom:126_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:127_b46_a46_d46_i46 @atom:127_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:128_b20_a20_d20_i20 @atom:128_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:129_b5_a5_d5_i5 @atom:129_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.07 - pair_coeff @atom:130_b7_a7_d7_i7 @atom:130_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:131_b51_a51_d51_i51 @atom:131_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:132_b46_a46_d46_i46 @atom:132_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:133_b51_a51_d51_i51 @atom:133_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:134_b46_a46_d46_i46 @atom:134_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:135_b51_a51_d51_i51 @atom:135_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:136_b46_a46_d46_i46 @atom:136_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:137_b51_a51_d51_i51 @atom:137_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:138_b46_a46_d46_i46 @atom:138_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:139_b51_a51_d51_i51 @atom:139_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:140_b51_a51_d51_i51 @atom:140_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:141_b48_a48_d48_i48 @atom:141_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:142_b15_a15_d15_i15 @atom:142_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:143_b15_a15_d15_i15 @atom:143_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.7 - pair_coeff @atom:144_b16_a16_d16_i16 @atom:144_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:145_b16_a16_d16_i16 @atom:145_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:146_b17_a17_d17_i17 @atom:146_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:147_b17_a17_d17_i17 @atom:147_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:148_b13_a13_d13_i13 @atom:148_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:149_b13_a13_d13_i13 @atom:149_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:150_b13_a13_d13_i13 @atom:150_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:151_b13_a13_d13_i13 @atom:151_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:152_b13_a13_d13_i13 @atom:152_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:153_b13_a13_d13_i13 @atom:153_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:154_b13_a13_d13_i13 @atom:154_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:155_b13_a13_d13_i13 @atom:155_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:156_b13_a13_d13_i13 @atom:156_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:157_b13_a13_d13_i13 @atom:157_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:158_b13_a13_d13_i13 @atom:158_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:159_b13_a13_d13_i13 @atom:159_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:160_b13_a13_d13_i13 @atom:160_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:161_b13_a13_d13_i13 @atom:161_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:162_b13_a13_d13_i13 @atom:162_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:163_b48_a48_d48_i48 @atom:163_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:164_b16_a16_d16_i16 @atom:164_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:165_b13_a13_d13_i13 @atom:165_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:166_b13_a13_d13_i13 @atom:166_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:167_b13_a13_d13_i13 @atom:167_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:168_b21_a21_d21_i21 @atom:168_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:169_b47_a47_d47_i47 @atom:169_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:170_b48_a48_d48_i48 @atom:170_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:171_b13_a13_d13_i13 @atom:171_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:172_b13_a13_d13_i13 @atom:172_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:173_b3_a3_d3_i3 @atom:173_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:174_b3_a3_d3_i3 @atom:174_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:175_b3_a3_d3_i3 @atom:175_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:176_b3_a3_d3_i3 @atom:176_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:177_b3_a3_d3_i3 @atom:177_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:178_b4_a4_d4_i4 @atom:178_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:179_b24_a24_d24_i24 @atom:179_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:180_b24_a24_d24_i24 @atom:180_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:181_b24_a24_d24_i24 @atom:181_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:182_b45_a45_d45_i45 @atom:182_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:183_b45_a45_d45_i45 @atom:183_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:184_b13_a13_d13_i13 @atom:184_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:185_b13_a13_d13_i13 @atom:185_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:186_b13_a13_d13_i13 @atom:186_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:187_b13_a13_d13_i13 @atom:187_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:188_b13_a13_d13_i13 @atom:188_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:189_b3_a3_d3_i3 @atom:189_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:190_b4_a4_d4_i4 @atom:190_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:191_b24_a24_d24_i24 @atom:191_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:192_b45_a45_d45_i45 @atom:192_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:193_b24_a24_d24_i24 @atom:193_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:194_b3_a3_d3_i3 @atom:194_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:195_b4_a4_d4_i4 @atom:195_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:196_b45_a45_d45_i45 @atom:196_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:197_b46_a46_d46_i46 @atom:197_b46_a46_d46_i46 lj/cut/coul/long 0.02 2.5 - pair_coeff @atom:198_b13_a13_d13_i13 @atom:198_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:199_b13_a13_d13_i13 @atom:199_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:200_b13_a13_d13_i13 @atom:200_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:201_b13_a13_d13_i13 @atom:201_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:202_b48_a48_d48_i48 @atom:202_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:203_b19_a19_d19_i19 @atom:203_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:204_b18_a18_d18_i18 @atom:204_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:205_b48_a48_d48_i48 @atom:205_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:206_b21_a21_d21_i21 @atom:206_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:207_b24_a24_d24_i24 @atom:207_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:208_b48_a48_d48_i48 @atom:208_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:209_b3_a3_d3_i3 @atom:209_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:210_b4_a4_d4_i4 @atom:210_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:211_b5_a5_d5_i5 @atom:211_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:212_b7_a7_d7_i7 @atom:212_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:213_b3_a3_d3_i3 @atom:213_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:214_b52_a52_d52_i52 @atom:214_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:215_b13_a13_d13_i13 @atom:215_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:216_b13_a13_d13_i13 @atom:216_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:217_b13_a13_d13_i13 @atom:217_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:218_b13_a13_d13_i13 @atom:218_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:219_b3_a3_d3_i3 @atom:219_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:220_b4_a4_d4_i4 @atom:220_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:221_b46_a46_d46_i46 @atom:221_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:222_b3_a3_d3_i3 @atom:222_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:223_b4_a4_d4_i4 @atom:223_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:224_b46_a46_d46_i46 @atom:224_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:225_b13_a13_d13_i13 @atom:225_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:226_b13_a13_d13_i13 @atom:226_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:227_b13_a13_d13_i13 @atom:227_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:228_b13_a13_d13_i13 @atom:228_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:229_b53_a53_d53_i53 @atom:229_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:230_b53_a53_d53_i53 @atom:230_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:231_b53_a53_d53_i53 @atom:231_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:232_b54_a54_d54_i54 @atom:232_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:233_b54_a54_d54_i54 @atom:233_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:234_b13_a13_d13_i13 @atom:234_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:235_b13_a13_d13_i13 @atom:235_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:236_b13_a13_d13_i13 @atom:236_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:237_b13_a13_d13_i13 @atom:237_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:238_b13_a13_d13_i13 @atom:238_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:239_b13_a13_d13_i13 @atom:239_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:240_b13_a13_d13_i13 @atom:240_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:241_b13_a13_d13_i13 @atom:241_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:242_b13_a13_d13_i13 @atom:242_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:243_b55_a55_d55_i55 @atom:243_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:244_b54_a54_d54_i54 @atom:244_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:245_b48_a48_d48_i48 @atom:245_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:246_b55_a55_d55_i55 @atom:246_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:247_b54_a54_d54_i54 @atom:247_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:248_b13_a13_d13_i13 @atom:248_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:249_b13_a13_d13_i13 @atom:249_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:250_b13_a13_d13_i13 @atom:250_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:251_b13_a13_d13_i13 @atom:251_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:252_b53_a53_d53_i53 @atom:252_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:253_b54_a54_d54_i54 @atom:253_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:254_b56_a56_d56_i56 @atom:254_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:255_b48_a48_d48_i48 @atom:255_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:256_b55_a55_d55_i55 @atom:256_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:257_b45_a45_d45_i45 @atom:257_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:258_b48_a48_d48_i48 @atom:258_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:259_b49_a49_d49_i49 @atom:259_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:260_b48_a48_d48_i48 @atom:260_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:261_b49_a49_d49_i49 @atom:261_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:262_b57_a57_d57_i57 @atom:262_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:263_b3_a3_d3_i3 @atom:263_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:264_b57_a57_d57_i57 @atom:264_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:265_b3_a3_d3_i3 @atom:265_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:266_b47_a47_d47_i47 @atom:266_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:267_b47_a47_d47_i47 @atom:267_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:268_b45_a45_d45_i45 @atom:268_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:269_b4_a4_d4_i4 @atom:269_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:270_b45_a45_d45_i45 @atom:270_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:271_b4_a4_d4_i4 @atom:271_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:272_b46_a46_d46_i46 @atom:272_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:273_b46_a46_d46_i46 @atom:273_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:274_b13_a13_d13_i13 @atom:274_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:275_b46_a46_d46_i46 @atom:275_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:276_b57_a57_d57_i57 @atom:276_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:277_b3_a3_d3_i3 @atom:277_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:278_b56_a56_d56_i56 @atom:278_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:279_b48_a48_d48_i48 @atom:279_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:280_b47_a47_d47_i47 @atom:280_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:281_b47_a47_d47_i47 @atom:281_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:282_b45_a45_d45_i45 @atom:282_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:283_b4_a4_d4_i4 @atom:283_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:284_b55_a55_d55_i55 @atom:284_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:285_b45_a45_d45_i45 @atom:285_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:286_b45_a45_d45_i45 @atom:286_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:287_b46_a46_d46_i46 @atom:287_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:288_b58_a58_d58_i58 @atom:288_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:289_b56_a56_d56_i56 @atom:289_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:290_b59_a59_d59_i59 @atom:290_b59_a59_d59_i59 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:291_b56_a56_d56_i56 @atom:291_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:292_b60_a60_d60_i60 @atom:292_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:293_b60_a60_d60_i60 @atom:293_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:294_b48_a48_d48_i48 @atom:294_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:295_b61_a61_d61_i61 @atom:295_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:296_b62_a62_d62_i62 @atom:296_b62_a62_d62_i62 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:297_b57_a57_d57_i57 @atom:297_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:298_b63_a63_d63_i63 @atom:298_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:299_b55_a55_d55_i55 @atom:299_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:300_b45_a45_d45_i45 @atom:300_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:301_b45_a45_d45_i45 @atom:301_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:302_b63_a63_d63_i63 @atom:302_b63_a63_d63_i63 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:303_b45_a45_d45_i45 @atom:303_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:304_b57_a57_d57_i57 @atom:304_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:305_b48_a48_d48_i48 @atom:305_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:306_b56_a56_d56_i56 @atom:306_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:307_b60_a60_d60_i60 @atom:307_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:308_b60_a60_d60_i60 @atom:308_b60_a60_d60_i60 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:309_b3_a3_d3_i3 @atom:309_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:310_b45_a45_d45_i45 @atom:310_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:311_b55_a55_d55_i55 @atom:311_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:312_b45_a45_d45_i45 @atom:312_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:313_b4_a4_d4_i4 @atom:313_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:314_b13_a13_d13_i13 @atom:314_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:315_b46_a46_d46_i46 @atom:315_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:316_b13_a13_d13_i13 @atom:316_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:317_b46_a46_d46_i46 @atom:317_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:318_b13_a13_d13_i13 @atom:318_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:319_b46_a46_d46_i46 @atom:319_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:320_b57_a57_d57_i57 @atom:320_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:321_b3_a3_d3_i3 @atom:321_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:322_b57_a57_d57_i57 @atom:322_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:323_b48_a48_d48_i48 @atom:323_b48_a48_d48_i48 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:324_b47_a47_d47_i47 @atom:324_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:325_b47_a47_d47_i47 @atom:325_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:326_b45_a45_d45_i45 @atom:326_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:327_b4_a4_d4_i4 @atom:327_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:328_b45_a45_d45_i45 @atom:328_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:329_b55_a55_d55_i55 @atom:329_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:330_b45_a45_d45_i45 @atom:330_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:331_b45_a45_d45_i45 @atom:331_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:332_b49_a49_d49_i49 @atom:332_b49_a49_d49_i49 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:333_b58_a58_d58_i58 @atom:333_b58_a58_d58_i58 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:334_b13_a13_d13_i13 @atom:334_b13_a13_d13_i13 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:335_b46_a46_d46_i46 @atom:335_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:336_b64_a64_d64_i64 @atom:336_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:337_b52_a52_d52_i52 @atom:337_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:338_b20_a20_d20_i20 @atom:338_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:339_b13_a13_d13_i13 @atom:339_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.55 - pair_coeff @atom:340_b47_a47_d47_i47 @atom:340_b47_a47_d47_i47 lj/cut/coul/long 0.08 3.5 - pair_coeff @atom:341_b21_a21_d21_i21 @atom:341_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:342_b47_a47_d47_i47 @atom:342_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:343_b1_a1_d1_i1 @atom:343_b1_a1_d1_i1 lj/cut/coul/long 0.71 3.05 - pair_coeff @atom:344_b21_a21_d21_i21 @atom:344_b21_a21_d21_i21 lj/cut/coul/long 0.71 4.02 - pair_coeff @atom:345_b65_a65_d65_i65 @atom:345_b65_a65_d65_i65 lj/cut/coul/long 0.71 4.28 - pair_coeff @atom:346_b66_a66_d66_i66 @atom:346_b66_a66_d66_i66 lj/cut/coul/long 0.71 4.81 - pair_coeff @atom:347_b67_a67_d67_i67 @atom:347_b67_a67_d67_i67 lj/cut/coul/long 0.0005 5.34 - pair_coeff @atom:348_b68_a68_d68_i68 @atom:348_b68_a68_d68_i68 lj/cut/coul/long 0.0005 2.87 - pair_coeff @atom:349_b69_a69_d69_i69 @atom:349_b69_a69_d69_i69 lj/cut/coul/long 0.0005 4.07 - pair_coeff @atom:350_b70_a70_d70_i70 @atom:350_b70_a70_d70_i70 lj/cut/coul/long 0.0005 5.17 - pair_coeff @atom:351_b71_a71_d71_i71 @atom:351_b71_a71_d71_i71 lj/cut/coul/long 0.0005 5.6 - pair_coeff @atom:352_b72_a72_d72_i72 @atom:352_b72_a72_d72_i72 lj/cut/coul/long 0.0005 6.2 - pair_coeff @atom:353_b73_a73_d73_i73 @atom:353_b73_a73_d73_i73 lj/cut/coul/long 0.875044 1.644471 - pair_coeff @atom:354_b74_a74_d74_i74 @atom:354_b74_a74_d74_i74 lj/cut/coul/long 0.449657 2.412031 - pair_coeff @atom:355_b75_a75_d75_i75 @atom:355_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.102688 - pair_coeff @atom:356_b76_a76_d76_i76 @atom:356_b76_a76_d76_i76 lj/cut/coul/long 0.047096 3.81661 - pair_coeff @atom:357_b6_a6_d6_i6 @atom:357_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:358_b46_a46_d46_i46 @atom:358_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:359_b15_a15_d15_i15 @atom:359_b15_a15_d15_i15 lj/cut/coul/long 0.5 4.25 - pair_coeff @atom:360_b6_a6_d6_i6 @atom:360_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:361_b46_a46_d46_i46 @atom:361_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:362_b5_a5_d5_i5 @atom:362_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.15 - pair_coeff @atom:363_b13_a13_d13_i13 @atom:363_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:364_b46_a46_d46_i46 @atom:364_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:365_b19_a19_d19_i19 @atom:365_b19_a19_d19_i19 lj/cut/coul/long 0.15 3.65 - pair_coeff @atom:366_b18_a18_d18_i18 @atom:366_b18_a18_d18_i18 lj/cut/coul/long 0.25 3.4 - pair_coeff @atom:367_b6_a6_d6_i6 @atom:367_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:368_b46_a46_d46_i46 @atom:368_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:369_b53_a53_d53_i53 @atom:369_b53_a53_d53_i53 lj/cut/coul/long 0.25 3.4 - pair_coeff @atom:370_b45_a45_d45_i45 @atom:370_b45_a45_d45_i45 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:371_b6_a6_d6_i6 @atom:371_b6_a6_d6_i6 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:372_b46_a46_d46_i46 @atom:372_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:373_b13_a13_d13_i13 @atom:373_b13_a13_d13_i13 lj/cut/coul/long 0.3 4.2 - pair_coeff @atom:374_b46_a46_d46_i46 @atom:374_b46_a46_d46_i46 lj/cut/coul/long 0.05 2.5 - pair_coeff @atom:375_b33_a33_d33_i33 @atom:375_b33_a33_d33_i33 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:376_b5_a5_d5_i5 @atom:376_b5_a5_d5_i5 lj/cut/coul/long 0.25 3.2 - pair_coeff @atom:377_b7_a7_d7_i7 @atom:377_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:378_b77_a77_d77_i77 @atom:378_b77_a77_d77_i77 lj/cut/coul/long 0.4 2.81524 - pair_coeff @atom:379_b78_a78_d78_i78 @atom:379_b78_a78_d78_i78 lj/cut/coul/long 0.2 3.11815 - pair_coeff @atom:380_b20_a20_d20_i20 @atom:380_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:381_b64_a64_d64_i64 @atom:381_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:382_b52_a52_d52_i52 @atom:382_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:383_b20_a20_d20_i20 @atom:383_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:384_b13_a13_d13_i13 @atom:384_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:385_b46_a46_d46_i46 @atom:385_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:386_b64_a64_d64_i64 @atom:386_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:387_b52_a52_d52_i52 @atom:387_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:388_b20_a20_d20_i20 @atom:388_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:389_b13_a13_d13_i13 @atom:389_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:390_b46_a46_d46_i46 @atom:390_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:391_b64_a64_d64_i64 @atom:391_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:392_b52_a52_d52_i52 @atom:392_b52_a52_d52_i52 lj/cut/coul/long 0.2 3.15 - pair_coeff @atom:393_b20_a20_d20_i20 @atom:393_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:394_b13_a13_d13_i13 @atom:394_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:395_b46_a46_d46_i46 @atom:395_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:396_b13_a13_d13_i13 @atom:396_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:397_b46_a46_d46_i46 @atom:397_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:398_b48_a48_d48_i48 @atom:398_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:399_b13_a13_d13_i13 @atom:399_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:400_b46_a46_d46_i46 @atom:400_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:401_b48_a48_d48_i48 @atom:401_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:402_b13_a13_d13_i13 @atom:402_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:403_b46_a46_d46_i46 @atom:403_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:404_b48_a48_d48_i48 @atom:404_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:405_b13_a13_d13_i13 @atom:405_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:406_b3_a3_d3_i3 @atom:406_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:407_b4_a4_d4_i4 @atom:407_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:408_b20_a20_d20_i20 @atom:408_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:409_b13_a13_d13_i13 @atom:409_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:410_b46_a46_d46_i46 @atom:410_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:411_b3_a3_d3_i3 @atom:411_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:412_b3_a3_d3_i3 @atom:412_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:413_b48_a48_d48_i48 @atom:413_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:414_b20_a20_d20_i20 @atom:414_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:415_b79_a79_d79_i79 @atom:415_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:416_b23_a23_d23_i23 @atom:416_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:417_b13_a13_d13_i13 @atom:417_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:418_b46_a46_d46_i46 @atom:418_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:419_b24_a24_d24_i24 @atom:419_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:420_b45_a45_d45_i45 @atom:420_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:421_b24_a24_d24_i24 @atom:421_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:422_b45_a45_d45_i45 @atom:422_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:423_b13_a13_d13_i13 @atom:423_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:424_b46_a46_d46_i46 @atom:424_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:425_b13_a13_d13_i13 @atom:425_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:426_b46_a46_d46_i46 @atom:426_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:427_b13_a13_d13_i13 @atom:427_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:428_b46_a46_d46_i46 @atom:428_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:429_b48_a48_d48_i48 @atom:429_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:430_b48_a48_d48_i48 @atom:430_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:431_b13_a13_d13_i13 @atom:431_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:432_b13_a13_d13_i13 @atom:432_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:433_b13_a13_d13_i13 @atom:433_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:434_b79_a79_d79_i79 @atom:434_b79_a79_d79_i79 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:435_b23_a23_d23_i23 @atom:435_b23_a23_d23_i23 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:436_b22_a22_d22_i22 @atom:436_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:437_b22_a22_d22_i22 @atom:437_b22_a22_d22_i22 lj/cut/coul/long 0.395 3.56 - pair_coeff @atom:438_b23_a23_d23_i23 @atom:438_b23_a23_d23_i23 lj/cut/coul/long 0.28 2.93 - pair_coeff @atom:439_b13_a13_d13_i13 @atom:439_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:440_b13_a13_d13_i13 @atom:440_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:441_b80_a80_d80_i80 @atom:441_b80_a80_d80_i80 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:442_b60_a60_d60_i60 @atom:442_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:443_b81_a81_d81_i81 @atom:443_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:444_b57_a57_d57_i57 @atom:444_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:445_b45_a45_d45_i45 @atom:445_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:446_b13_a13_d13_i13 @atom:446_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:447_b82_a82_d82_i82 @atom:447_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:448_b83_a83_d83_i83 @atom:448_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:449_b84_a84_d84_i84 @atom:449_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:450_b82_a82_d82_i82 @atom:450_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:451_b85_a85_d85_i85 @atom:451_b85_a85_d85_i85 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:452_b61_a61_d61_i61 @atom:452_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:453_b57_a57_d57_i57 @atom:453_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:454_b45_a45_d45_i45 @atom:454_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:455_b84_a84_d84_i84 @atom:455_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:456_b13_a13_d13_i13 @atom:456_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:457_b13_a13_d13_i13 @atom:457_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:458_b47_a47_d47_i47 @atom:458_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:459_b47_a47_d47_i47 @atom:459_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:460_b86_a86_d86_i86 @atom:460_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:461_b56_a56_d56_i56 @atom:461_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:462_b48_a48_d48_i48 @atom:462_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:463_b48_a48_d48_i48 @atom:463_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:464_b48_a48_d48_i48 @atom:464_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:465_b49_a49_d49_i49 @atom:465_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:466_b49_a49_d49_i49 @atom:466_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:467_b49_a49_d49_i49 @atom:467_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:468_b56_a56_d56_i56 @atom:468_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:469_b48_a48_d48_i48 @atom:469_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:470_b49_a49_d49_i49 @atom:470_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:471_b56_a56_d56_i56 @atom:471_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:472_b59_a59_d59_i59 @atom:472_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:473_b48_a48_d48_i48 @atom:473_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:474_b48_a48_d48_i48 @atom:474_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:475_b49_a49_d49_i49 @atom:475_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:476_b49_a49_d49_i49 @atom:476_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:477_b49_a49_d49_i49 @atom:477_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:478_b56_a56_d56_i56 @atom:478_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:479_b48_a48_d48_i48 @atom:479_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:480_b48_a48_d48_i48 @atom:480_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:481_b49_a49_d49_i49 @atom:481_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:482_b49_a49_d49_i49 @atom:482_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:483_b57_a57_d57_i57 @atom:483_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:484_b84_a84_d84_i84 @atom:484_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:485_b87_a87_d87_i87 @atom:485_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:486_b45_a45_d45_i45 @atom:486_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:487_b49_a49_d49_i49 @atom:487_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:488_b49_a49_d49_i49 @atom:488_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:489_b57_a57_d57_i57 @atom:489_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:490_b61_a61_d61_i61 @atom:490_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:491_b88_a88_d88_i88 @atom:491_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:492_b87_a87_d87_i87 @atom:492_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:493_b84_a84_d84_i84 @atom:493_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:494_b45_a45_d45_i45 @atom:494_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:495_b49_a49_d49_i49 @atom:495_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:496_b49_a49_d49_i49 @atom:496_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:497_b49_a49_d49_i49 @atom:497_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:498_b57_a57_d57_i57 @atom:498_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:499_b82_a82_d82_i82 @atom:499_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:500_b61_a61_d61_i61 @atom:500_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:501_b83_a83_d83_i83 @atom:501_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:502_b84_a84_d84_i84 @atom:502_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:503_b45_a45_d45_i45 @atom:503_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:504_b49_a49_d49_i49 @atom:504_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:505_b49_a49_d49_i49 @atom:505_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:506_b49_a49_d49_i49 @atom:506_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:507_b20_a20_d20_i20 @atom:507_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:508_b84_a84_d84_i84 @atom:508_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:509_b87_a87_d87_i87 @atom:509_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:510_b49_a49_d49_i49 @atom:510_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:511_b49_a49_d49_i49 @atom:511_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:512_b20_a20_d20_i20 @atom:512_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:513_b82_a82_d82_i82 @atom:513_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:514_b61_a61_d61_i61 @atom:514_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:515_b83_a83_d83_i83 @atom:515_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:516_b84_a84_d84_i84 @atom:516_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:517_b49_a49_d49_i49 @atom:517_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:518_b49_a49_d49_i49 @atom:518_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:519_b49_a49_d49_i49 @atom:519_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:520_b20_a20_d20_i20 @atom:520_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:521_b61_a61_d61_i61 @atom:521_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:522_b88_a88_d88_i88 @atom:522_b88_a88_d88_i88 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:523_b87_a87_d87_i87 @atom:523_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:524_b84_a84_d84_i84 @atom:524_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:525_b49_a49_d49_i49 @atom:525_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:526_b49_a49_d49_i49 @atom:526_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:527_b49_a49_d49_i49 @atom:527_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:528_b57_a57_d57_i57 @atom:528_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:529_b84_a84_d84_i84 @atom:529_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:530_b87_a87_d87_i87 @atom:530_b87_a87_d87_i87 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:531_b48_a48_d48_i48 @atom:531_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:532_b48_a48_d48_i48 @atom:532_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:533_b48_a48_d48_i48 @atom:533_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:534_b48_a48_d48_i48 @atom:534_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:535_b81_a81_d81_i81 @atom:535_b81_a81_d81_i81 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:536_b60_a60_d60_i60 @atom:536_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:537_b45_a45_d45_i45 @atom:537_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:538_b49_a49_d49_i49 @atom:538_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:539_b49_a49_d49_i49 @atom:539_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:540_b49_a49_d49_i49 @atom:540_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:541_b49_a49_d49_i49 @atom:541_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:542_b49_a49_d49_i49 @atom:542_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:543_b49_a49_d49_i49 @atom:543_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:544_b56_a56_d56_i56 @atom:544_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:545_b48_a48_d48_i48 @atom:545_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:546_b48_a48_d48_i48 @atom:546_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:547_b48_a48_d48_i48 @atom:547_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:548_b48_a48_d48_i48 @atom:548_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:549_b48_a48_d48_i48 @atom:549_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:550_b48_a48_d48_i48 @atom:550_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:551_b48_a48_d48_i48 @atom:551_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:552_b48_a48_d48_i48 @atom:552_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:553_b48_a48_d48_i48 @atom:553_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:554_b49_a49_d49_i49 @atom:554_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:555_b49_a49_d49_i49 @atom:555_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:556_b49_a49_d49_i49 @atom:556_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:557_b49_a49_d49_i49 @atom:557_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:558_b49_a49_d49_i49 @atom:558_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:559_b49_a49_d49_i49 @atom:559_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:560_b49_a49_d49_i49 @atom:560_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:561_b56_a56_d56_i56 @atom:561_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:562_b59_a59_d59_i59 @atom:562_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:563_b56_a56_d56_i56 @atom:563_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:564_b60_a60_d60_i60 @atom:564_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:565_b60_a60_d60_i60 @atom:565_b60_a60_d60_i60 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:566_b48_a48_d48_i48 @atom:566_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:567_b61_a61_d61_i61 @atom:567_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:568_b62_a62_d62_i62 @atom:568_b62_a62_d62_i62 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:569_b57_a57_d57_i57 @atom:569_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:570_b49_a49_d49_i49 @atom:570_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:571_b49_a49_d49_i49 @atom:571_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:572_b49_a49_d49_i49 @atom:572_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:573_b45_a45_d45_i45 @atom:573_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:574_b16_a16_d16_i16 @atom:574_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:575_b82_a82_d82_i82 @atom:575_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:576_b61_a61_d61_i61 @atom:576_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:577_b83_a83_d83_i83 @atom:577_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:578_b84_a84_d84_i84 @atom:578_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:579_b49_a49_d49_i49 @atom:579_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:580_b49_a49_d49_i49 @atom:580_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:581_b49_a49_d49_i49 @atom:581_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:582_b56_a56_d56_i56 @atom:582_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:583_b59_a59_d59_i59 @atom:583_b59_a59_d59_i59 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:584_b49_a49_d49_i49 @atom:584_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:585_b48_a48_d48_i48 @atom:585_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:586_b13_a13_d13_i13 @atom:586_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:587_b56_a56_d56_i56 @atom:587_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:588_b48_a48_d48_i48 @atom:588_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:589_b48_a48_d48_i48 @atom:589_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:590_b48_a48_d48_i48 @atom:590_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:591_b48_a48_d48_i48 @atom:591_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:592_b48_a48_d48_i48 @atom:592_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:593_b48_a48_d48_i48 @atom:593_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:594_b49_a49_d49_i49 @atom:594_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:595_b49_a49_d49_i49 @atom:595_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:596_b49_a49_d49_i49 @atom:596_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:597_b49_a49_d49_i49 @atom:597_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:598_b57_a57_d57_i57 @atom:598_b57_a57_d57_i57 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:599_b82_a82_d82_i82 @atom:599_b82_a82_d82_i82 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:600_b61_a61_d61_i61 @atom:600_b61_a61_d61_i61 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:601_b83_a83_d83_i83 @atom:601_b83_a83_d83_i83 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:602_b84_a84_d84_i84 @atom:602_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:603_b13_a13_d13_i13 @atom:603_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:604_b49_a49_d49_i49 @atom:604_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:605_b49_a49_d49_i49 @atom:605_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:606_b49_a49_d49_i49 @atom:606_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:607_b46_a46_d46_i46 @atom:607_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:608_b13_a13_d13_i13 @atom:608_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:609_b13_a13_d13_i13 @atom:609_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:610_b13_a13_d13_i13 @atom:610_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:611_b13_a13_d13_i13 @atom:611_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:612_b13_a13_d13_i13 @atom:612_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:613_b13_a13_d13_i13 @atom:613_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:614_b13_a13_d13_i13 @atom:614_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:615_b13_a13_d13_i13 @atom:615_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:616_b13_a13_d13_i13 @atom:616_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:617_b13_a13_d13_i13 @atom:617_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:618_b13_a13_d13_i13 @atom:618_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:619_b13_a13_d13_i13 @atom:619_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:620_b13_a13_d13_i13 @atom:620_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:621_b13_a13_d13_i13 @atom:621_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:622_b13_a13_d13_i13 @atom:622_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:623_b15_a15_d15_i15 @atom:623_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:624_b17_a17_d17_i17 @atom:624_b17_a17_d17_i17 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:625_b48_a48_d48_i48 @atom:625_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:626_b89_a89_d89_i89 @atom:626_b89_a89_d89_i89 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:627_b90_a90_d90_i90 @atom:627_b90_a90_d90_i90 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:628_b91_a91_d91_i91 @atom:628_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:629_b91_a91_d91_i91 @atom:629_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:630_b13_a13_d13_i13 @atom:630_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:631_b86_a86_d86_i86 @atom:631_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:632_b86_a86_d86_i86 @atom:632_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:633_b86_a86_d86_i86 @atom:633_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:634_b86_a86_d86_i86 @atom:634_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:635_b86_a86_d86_i86 @atom:635_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:636_b86_a86_d86_i86 @atom:636_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:637_b16_a16_d16_i16 @atom:637_b16_a16_d16_i16 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:638_b92_a92_d92_i92 @atom:638_b92_a92_d92_i92 lj/cut/coul/long 0.054 3.473 - pair_coeff @atom:639_b93_a93_d93_i93 @atom:639_b93_a93_d93_i93 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:640_b94_a94_d94_i94 @atom:640_b94_a94_d94_i94 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:641_b95_a95_d95_i95 @atom:641_b95_a95_d95_i95 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:642_b13_a13_d13_i13 @atom:642_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:643_b46_a46_d46_i46 @atom:643_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:644_b96_a96_d96_i96 @atom:644_b96_a96_d96_i96 lj/cut/coul/long 0.06 3.75 - pair_coeff @atom:645_b97_a97_d97_i97 @atom:645_b97_a97_d97_i97 lj/cut/coul/long 0.054 3.473 - pair_coeff @atom:646_b98_a98_d98_i98 @atom:646_b98_a98_d98_i98 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:647_b99_a99_d99_i99 @atom:647_b99_a99_d99_i99 lj/cut/coul/long 0.05 3.3 - pair_coeff @atom:648_b100_a100_d100_i100 @atom:648_b100_a100_d100_i100 lj/cut/coul/long 0.04 2.95 - pair_coeff @atom:649_b47_a47_d47_i47 @atom:649_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:650_b21_a21_d21_i21 @atom:650_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:651_b46_a46_d46_i46 @atom:651_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:652_b91_a91_d91_i91 @atom:652_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:653_b91_a91_d91_i91 @atom:653_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:654_b91_a91_d91_i91 @atom:654_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:655_b48_a48_d48_i48 @atom:655_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:656_b49_a49_d49_i49 @atom:656_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:657_b48_a48_d48_i48 @atom:657_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:658_b49_a49_d49_i49 @atom:658_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:659_b48_a48_d48_i48 @atom:659_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:660_b1_a1_d1_i1 @atom:660_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:661_b48_a48_d48_i48 @atom:661_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:662_b1_a1_d1_i1 @atom:662_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:663_b65_a65_d65_i65 @atom:663_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:664_b2_a2_d2_i2 @atom:664_b2_a2_d2_i2 lj/cut/coul/long 0.118 3.905 - pair_coeff @atom:665_b48_a48_d48_i48 @atom:665_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:666_b13_a13_d13_i13 @atom:666_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:667_b1_a1_d1_i1 @atom:667_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:668_b48_a48_d48_i48 @atom:668_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:669_b1_a1_d1_i1 @atom:669_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.85 - pair_coeff @atom:670_b48_a48_d48_i48 @atom:670_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:671_b65_a65_d65_i65 @atom:671_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:672_b48_a48_d48_i48 @atom:672_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:673_b66_a66_d66_i66 @atom:673_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75 - pair_coeff @atom:674_b91_a91_d91_i91 @atom:674_b91_a91_d91_i91 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:675_b15_a15_d15_i15 @atom:675_b15_a15_d15_i15 lj/cut/coul/long 0.25 3.55 - pair_coeff @atom:676_b48_a48_d48_i48 @atom:676_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:677_b48_a48_d48_i48 @atom:677_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:678_b48_a48_d48_i48 @atom:678_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:679_b48_a48_d48_i48 @atom:679_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:680_b48_a48_d48_i48 @atom:680_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:681_b49_a49_d49_i49 @atom:681_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:682_b49_a49_d49_i49 @atom:682_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:683_b48_a48_d48_i48 @atom:683_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:684_b55_a55_d55_i55 @atom:684_b55_a55_d55_i55 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:685_b45_a45_d45_i45 @atom:685_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:686_b45_a45_d45_i45 @atom:686_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:687_b49_a49_d49_i49 @atom:687_b49_a49_d49_i49 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:688_b13_a13_d13_i13 @atom:688_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:689_b13_a13_d13_i13 @atom:689_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:690_b101_a101_d101_i101 @atom:690_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:691_b56_a56_d56_i56 @atom:691_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:692_b101_a101_d101_i101 @atom:692_b101_a101_d101_i101 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:693_b48_a48_d48_i48 @atom:693_b48_a48_d48_i48 lj/cut/coul/long 0.05 3.55 - pair_coeff @atom:694_b18_a18_d18_i18 @atom:694_b18_a18_d18_i18 lj/cut/coul/long 0.17 3.2 - pair_coeff @atom:695_b19_a19_d19_i19 @atom:695_b19_a19_d19_i19 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:696_b13_a13_d13_i13 @atom:696_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:697_b13_a13_d13_i13 @atom:697_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:698_b13_a13_d13_i13 @atom:698_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:699_b13_a13_d13_i13 @atom:699_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:700_b46_a46_d46_i46 @atom:700_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:701_b102_a102_d102_i102 @atom:701_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25 - pair_coeff @atom:702_b103_a103_d103_i103 @atom:702_b103_a103_d103_i103 lj/cut/coul/long 0.17 2.96 - pair_coeff @atom:703_b13_a13_d13_i13 @atom:703_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:704_b46_a46_d46_i46 @atom:704_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:705_b13_a13_d13_i13 @atom:705_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:706_b13_a13_d13_i13 @atom:706_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:707_b13_a13_d13_i13 @atom:707_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:708_b102_a102_d102_i102 @atom:708_b102_a102_d102_i102 lj/cut/coul/long 0.12 3.25 - pair_coeff @atom:709_b48_a48_d48_i48 @atom:709_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:710_b13_a13_d13_i13 @atom:710_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.3 - pair_coeff @atom:711_b56_a56_d56_i56 @atom:711_b56_a56_d56_i56 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:712_b4_a4_d4_i4 @atom:712_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:713_b3_a3_d3_i3 @atom:713_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:714_b20_a20_d20_i20 @atom:714_b20_a20_d20_i20 lj/cut/coul/long 0.17 3.0 - pair_coeff @atom:715_b13_a13_d13_i13 @atom:715_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:716_b13_a13_d13_i13 @atom:716_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:717_b13_a13_d13_i13 @atom:717_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:718_b46_a46_d46_i46 @atom:718_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:719_b46_a46_d46_i46 @atom:719_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:720_b46_a46_d46_i46 @atom:720_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:721_b20_a20_d20_i20 @atom:721_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:722_b104_a104_d104_i104 @atom:722_b104_a104_d104_i104 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:723_b13_a13_d13_i13 @atom:723_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:724_b13_a13_d13_i13 @atom:724_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:725_b46_a46_d46_i46 @atom:725_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:726_b64_a64_d64_i64 @atom:726_b64_a64_d64_i64 lj/cut/coul/long 0.2 3.74 - pair_coeff @atom:727_b1_a1_d1_i1 @atom:727_b1_a1_d1_i1 lj/cut/coul/long 0.061 3.1181 - pair_coeff @atom:728_b24_a24_d24_i24 @atom:728_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.15 - pair_coeff @atom:729_b4_a4_d4_i4 @atom:729_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.86 - pair_coeff @atom:730_b44_a44_d44_i44 @atom:730_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:731_b44_a44_d44_i44 @atom:731_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:732_b44_a44_d44_i44 @atom:732_b44_a44_d44_i44 lj/cut/coul/long 0.17 3.3 - pair_coeff @atom:733_b13_a13_d13_i13 @atom:733_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:734_b13_a13_d13_i13 @atom:734_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:735_b13_a13_d13_i13 @atom:735_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:736_b13_a13_d13_i13 @atom:736_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:737_b13_a13_d13_i13 @atom:737_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:738_b13_a13_d13_i13 @atom:738_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:739_b45_a45_d45_i45 @atom:739_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:740_b45_a45_d45_i45 @atom:740_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:741_b46_a46_d46_i46 @atom:741_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:742_b13_a13_d13_i13 @atom:742_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:743_b13_a13_d13_i13 @atom:743_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:744_b13_a13_d13_i13 @atom:744_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:745_b13_a13_d13_i13 @atom:745_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:746_b48_a48_d48_i48 @atom:746_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:747_b48_a48_d48_i48 @atom:747_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:748_b48_a48_d48_i48 @atom:748_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:749_b13_a13_d13_i13 @atom:749_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:750_b13_a13_d13_i13 @atom:750_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:751_b13_a13_d13_i13 @atom:751_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:752_b13_a13_d13_i13 @atom:752_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:753_b13_a13_d13_i13 @atom:753_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:754_b13_a13_d13_i13 @atom:754_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:755_b19_a19_d19_i19 @atom:755_b19_a19_d19_i19 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:756_b46_a46_d46_i46 @atom:756_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:757_b19_a19_d19_i19 @atom:757_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3 - pair_coeff @atom:758_b19_a19_d19_i19 @atom:758_b19_a19_d19_i19 lj/cut/coul/long 0.135 3.3 - pair_coeff @atom:759_b19_a19_d19_i19 @atom:759_b19_a19_d19_i19 lj/cut/coul/long 0.1 3.3 - pair_coeff @atom:760_b46_a46_d46_i46 @atom:760_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.5 - pair_coeff @atom:761_b51_a51_d51_i51 @atom:761_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:762_b51_a51_d51_i51 @atom:762_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:763_b51_a51_d51_i51 @atom:763_b51_a51_d51_i51 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:764_b5_a5_d5_i5 @atom:764_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:765_b7_a7_d7_i7 @atom:765_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:766_b105_a105_d105_i105 @atom:766_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:767_b105_a105_d105_i105 @atom:767_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:768_b105_a105_d105_i105 @atom:768_b105_a105_d105_i105 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:769_b19_a19_d19_i19 @atom:769_b19_a19_d19_i19 lj/cut/coul/long 0.21 3.3 - pair_coeff @atom:770_b53_a53_d53_i53 @atom:770_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:771_b54_a54_d54_i54 @atom:771_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:772_b13_a13_d13_i13 @atom:772_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:773_b13_a13_d13_i13 @atom:773_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:774_b13_a13_d13_i13 @atom:774_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:775_b13_a13_d13_i13 @atom:775_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:776_b84_a84_d84_i84 @atom:776_b84_a84_d84_i84 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:777_b87_a87_d87_i87 @atom:777_b87_a87_d87_i87 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:778_b86_a86_d86_i86 @atom:778_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:779_b86_a86_d86_i86 @atom:779_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:780_b46_a46_d46_i46 @atom:780_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:781_b13_a13_d13_i13 @atom:781_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:782_b3_a3_d3_i3 @atom:782_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:783_b53_a53_d53_i53 @atom:783_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:784_b52_a52_d52_i52 @atom:784_b52_a52_d52_i52 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:785_b54_a54_d54_i54 @atom:785_b54_a54_d54_i54 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:786_b1_a1_d1_i1 @atom:786_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:787_b13_a13_d13_i13 @atom:787_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:788_b46_a46_d46_i46 @atom:788_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:789_b13_a13_d13_i13 @atom:789_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:790_b13_a13_d13_i13 @atom:790_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:791_b13_a13_d13_i13 @atom:791_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:792_b13_a13_d13_i13 @atom:792_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:793_b13_a13_d13_i13 @atom:793_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:794_b13_a13_d13_i13 @atom:794_b13_a13_d13_i13 lj/cut/coul/long 0.097 3.5 - pair_coeff @atom:795_b1_a1_d1_i1 @atom:795_b1_a1_d1_i1 lj/cut/coul/long 0.053 2.95 - pair_coeff @atom:796_b13_a13_d13_i13 @atom:796_b13_a13_d13_i13 lj/cut/coul/long 0.062 3.25 - pair_coeff @atom:797_b46_a46_d46_i46 @atom:797_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:798_b13_a13_d13_i13 @atom:798_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:799_b13_a13_d13_i13 @atom:799_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:800_b21_a21_d21_i21 @atom:800_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:801_b13_a13_d13_i13 @atom:801_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:802_b46_a46_d46_i46 @atom:802_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:803_b13_a13_d13_i13 @atom:803_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:804_b13_a13_d13_i13 @atom:804_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:805_b65_a65_d65_i65 @atom:805_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:806_b13_a13_d13_i13 @atom:806_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:807_b46_a46_d46_i46 @atom:807_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:808_b13_a13_d13_i13 @atom:808_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:809_b13_a13_d13_i13 @atom:809_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:810_b1_a1_d1_i1 @atom:810_b1_a1_d1_i1 lj/cut/coul/long 0.061 2.94 - pair_coeff @atom:811_b21_a21_d21_i21 @atom:811_b21_a21_d21_i21 lj/cut/coul/long 0.3 3.4 - pair_coeff @atom:812_b65_a65_d65_i65 @atom:812_b65_a65_d65_i65 lj/cut/coul/long 0.47 3.47 - pair_coeff @atom:813_b48_a48_d48_i48 @atom:813_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:814_b20_a20_d20_i20 @atom:814_b20_a20_d20_i20 lj/cut/coul/long 0.14 2.9 - pair_coeff @atom:815_b13_a13_d13_i13 @atom:815_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:816_b1_a1_d1_i1 @atom:816_b1_a1_d1_i1 lj/cut/coul/long 0.06 2.9 - pair_coeff @atom:817_b24_a24_d24_i24 @atom:817_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:818_b48_a48_d48_i48 @atom:818_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:819_b13_a13_d13_i13 @atom:819_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:820_b3_a3_d3_i3 @atom:820_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:821_b3_a3_d3_i3 @atom:821_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:822_b4_a4_d4_i4 @atom:822_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:823_b24_a24_d24_i24 @atom:823_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:824_b45_a45_d45_i45 @atom:824_b45_a45_d45_i45 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:825_b5_a5_d5_i5 @atom:825_b5_a5_d5_i5 lj/cut/coul/long 0.17 3.12 - pair_coeff @atom:826_b7_a7_d7_i7 @atom:826_b7_a7_d7_i7 lj/cut/coul/long 0.0 0.0 - pair_coeff @atom:827_b13_a13_d13_i13 @atom:827_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:828_b13_a13_d13_i13 @atom:828_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:829_b86_a86_d86_i86 @atom:829_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:830_b86_a86_d86_i86 @atom:830_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:831_b86_a86_d86_i86 @atom:831_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:832_b86_a86_d86_i86 @atom:832_b86_a86_d86_i86 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:833_b48_a48_d48_i48 @atom:833_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:834_b106_a106_d106_i106 @atom:834_b106_a106_d106_i106 lj/cut/coul/long 0.0125 1.96 - pair_coeff @atom:835_b13_a13_d13_i13 @atom:835_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:836_b13_a13_d13_i13 @atom:836_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:837_b13_a13_d13_i13 @atom:837_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:838_b66_a66_d66_i66 @atom:838_b66_a66_d66_i66 lj/cut/coul/long 0.6 3.75 - pair_coeff @atom:839_b46_a46_d46_i46 @atom:839_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:840_b24_a24_d24_i24 @atom:840_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:841_b48_a48_d48_i48 @atom:841_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:842_b48_a48_d48_i48 @atom:842_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:843_b24_a24_d24_i24 @atom:843_b24_a24_d24_i24 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:844_b48_a48_d48_i48 @atom:844_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:845_b3_a3_d3_i3 @atom:845_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:846_b4_a4_d4_i4 @atom:846_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:848_b13_a13_d13_i13 @atom:848_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:849_b13_a13_d13_i13 @atom:849_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:850_b13_a13_d13_i13 @atom:850_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:851_b13_a13_d13_i13 @atom:851_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:852_b46_a46_d46_i46 @atom:852_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:853_b3_a3_d3_i3 @atom:853_b3_a3_d3_i3 lj/cut/coul/long 0.105 3.75 - pair_coeff @atom:854_b4_a4_d4_i4 @atom:854_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:855_b46_a46_d46_i46 @atom:855_b46_a46_d46_i46 lj/cut/coul/long 0.015 2.42 - pair_coeff @atom:856_b13_a13_d13_i13 @atom:856_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:857_b13_a13_d13_i13 @atom:857_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:858_b13_a13_d13_i13 @atom:858_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:859_b13_a13_d13_i13 @atom:859_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:860_b13_a13_d13_i13 @atom:860_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:861_b13_a13_d13_i13 @atom:861_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:862_b13_a13_d13_i13 @atom:862_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:863_b13_a13_d13_i13 @atom:863_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:864_b13_a13_d13_i13 @atom:864_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:865_b13_a13_d13_i13 @atom:865_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 lj/cut/coul/long 0.1 4.0 - pair_coeff @atom:870_b45_a45_d45_i45 @atom:870_b45_a45_d45_i45 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:871_b13_a13_d13_i13 @atom:871_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:872_b13_a13_d13_i13 @atom:872_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:873_b13_a13_d13_i13 @atom:873_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:874_b13_a13_d13_i13 @atom:874_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:875_b1_a1_d1_i1 @atom:875_b1_a1_d1_i1 lj/cut/coul/long 0.72 3.08 - pair_coeff @atom:876_b21_a21_d21_i21 @atom:876_b21_a21_d21_i21 lj/cut/coul/long 0.11779 4.18 - pair_coeff @atom:877_b65_a65_d65_i65 @atom:877_b65_a65_d65_i65 lj/cut/coul/long 0.09 4.51 - pair_coeff @atom:878_b66_a66_d66_i66 @atom:878_b66_a66_d66_i66 lj/cut/coul/long 0.07 5.15 - pair_coeff @atom:879_b68_a68_d68_i68 @atom:879_b68_a68_d68_i68 lj/cut/coul/long 0.018279 2.7 - pair_coeff @atom:880_b69_a69_d69_i69 @atom:880_b69_a69_d69_i69 lj/cut/coul/long 0.002772 3.35 - pair_coeff @atom:881_b70_a70_d70_i70 @atom:881_b70_a70_d70_i70 lj/cut/coul/long 0.000328 4.06 - pair_coeff @atom:882_b71_a71_d71_i71 @atom:882_b71_a71_d71_i71 lj/cut/coul/long 0.000171 4.32 - pair_coeff @atom:883_b72_a72_d72_i72 @atom:883_b72_a72_d72_i72 lj/cut/coul/long 8.1e-05 4.82 - pair_coeff @atom:884_b73_a73_d73_i73 @atom:884_b73_a73_d73_i73 lj/cut/coul/long 0.875044 2.91 - pair_coeff @atom:885_b74_a74_d74_i74 @atom:885_b74_a74_d74_i74 lj/cut/coul/long 0.449657 3.47 - pair_coeff @atom:886_b75_a75_d75_i75 @atom:886_b75_a75_d75_i75 lj/cut/coul/long 0.118226 3.82 - pair_coeff @atom:887_b76_a76_d76_i76 @atom:887_b76_a76_d76_i76 lj/cut/coul/long 0.047096 4.18 - pair_coeff @atom:888_b13_a13_d13_i13 @atom:888_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:889_b13_a13_d13_i13 @atom:889_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:890_b13_a13_d13_i13 @atom:890_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:891_b13_a13_d13_i13 @atom:891_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:892_b46_a46_d46_i46 @atom:892_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:893_b53_a53_d53_i53 @atom:893_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:894_b48_a48_d48_i48 @atom:894_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:895_b53_a53_d53_i53 @atom:895_b53_a53_d53_i53 lj/cut/coul/long 0.17 3.25 - pair_coeff @atom:896_b48_a48_d48_i48 @atom:896_b48_a48_d48_i48 lj/cut/coul/long 0.07 3.55 - pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:899_b46_a46_d46_i46 @atom:899_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - pair_coeff @atom:900_b47_a47_d47_i47 @atom:900_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:901_b47_a47_d47_i47 @atom:901_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:902_b47_a47_d47_i47 @atom:902_b47_a47_d47_i47 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 lj/cut/coul/long 0.086 3.3 - pair_coeff @atom:905_b4_a4_d4_i4 @atom:905_b4_a4_d4_i4 lj/cut/coul/long 0.21 2.96 - pair_coeff @atom:906_b13_a13_d13_i13 @atom:906_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 + pair_coeff @atom:1_b001_a001_d001_i001 @atom:1_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:2_b002_a002_d002_i002 @atom:2_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:3_b003_a003_d003_i003 @atom:3_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:4_b004_a004_d004_i004 @atom:4_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:5_b005_a005_d005_i005 @atom:5_b005_a005_d005_i005 0.17 3.0 + pair_coeff @atom:6_b006_a006_d006_i006 @atom:6_b006_a006_d006_i006 0.16 3.91 + pair_coeff @atom:7_b007_a007_d007_i007 @atom:7_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:8_b008_a008_d008_i008 @atom:8_b008_a008_d008_i008 0.294 3.73 + pair_coeff @atom:9_b006_a006_d006_i006 @atom:9_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:10_b006_a006_d006_i006 @atom:10_b006_a006_d006_i006 0.175 3.905 + pair_coeff @atom:11_b006_a006_d006_i006 @atom:11_b006_a006_d006_i006 0.16 3.91 + pair_coeff @atom:12_b006_a006_d006_i006 @atom:12_b006_a006_d006_i006 0.145 3.96 + pair_coeff @atom:13_b002_a002_d002_i002 @atom:13_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:14_b009_a009_d009_i009 @atom:14_b009_a009_d009_i009 0.14 3.85 + pair_coeff @atom:15_b010_a010_d010_i010 @atom:15_b010_a010_d010_i010 0.08 3.85 + pair_coeff @atom:16_b011_a011_d011_i011 @atom:16_b011_a011_d011_i011 0.115 3.8 + pair_coeff @atom:17_b012_a012_d012_i012 @atom:17_b012_a012_d012_i012 0.11 3.75 + pair_coeff @atom:18_b013_a013_d013_i013 @atom:18_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:19_b014_a014_d014_i014 @atom:19_b014_a014_d014_i014 0.105 3.75 + pair_coeff @atom:20_b005_a005_d005_i005 @atom:20_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:21_b007_a007_d007_i007 @atom:21_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:22_b006_a006_d006_i006 @atom:22_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:23_b002_a002_d002_i002 @atom:23_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:24_b015_a015_d015_i015 @atom:24_b015_a015_d015_i015 0.25 3.7 + pair_coeff @atom:25_b015_a015_d015_i015 @atom:25_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:26_b016_a016_d016_i016 @atom:26_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:27_b016_a016_d016_i016 @atom:27_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:28_b017_a017_d017_i017 @atom:28_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:29_b017_a017_d017_i017 @atom:29_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:30_b006_a006_d006_i006 @atom:30_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:31_b002_a002_d002_i002 @atom:31_b002_a002_d002_i002 0.118 3.905 + pair_coeff @atom:32_b006_a006_d006_i006 @atom:32_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:33_b002_a002_d002_i002 @atom:33_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:34_b006_a006_d006_i006 @atom:34_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:35_b002_a002_d002_i002 @atom:35_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:36_b018_a018_d018_i018 @atom:36_b018_a018_d018_i018 0.17 3.2 + pair_coeff @atom:37_b019_a019_d019_i019 @atom:37_b019_a019_d019_i019 0.15 3.65 + pair_coeff @atom:38_b006_a006_d006_i006 @atom:38_b006_a006_d006_i006 0.207 3.775 + pair_coeff @atom:39_b010_a010_d010_i010 @atom:39_b010_a010_d010_i010 0.08 3.85 + pair_coeff @atom:40_b013_a013_d013_i013 @atom:40_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:41_b020_a020_d020_i020 @atom:41_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:42_b006_a006_d006_i006 @atom:42_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:43_b002_a002_d002_i002 @atom:43_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:44_b002_a002_d002_i002 @atom:44_b002_a002_d002_i002 0.118 3.8 + pair_coeff @atom:45_b021_a021_d021_i021 @atom:45_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:46_b010_a010_d010_i010 @atom:46_b010_a010_d010_i010 0.08 3.8 + pair_coeff @atom:47_b021_a021_d021_i021 @atom:47_b021_a021_d021_i021 0.3 3.47 + pair_coeff @atom:48_b013_a013_d013_i013 @atom:48_b013_a013_d013_i013 0.05 3.8 + pair_coeff @atom:49_b021_a021_d021_i021 @atom:49_b021_a021_d021_i021 0.266 3.47 + pair_coeff @atom:50_b022_a022_d022_i022 @atom:50_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:51_b023_a023_d023_i023 @atom:51_b023_a023_d023_i023 0.28 2.93 + pair_coeff @atom:52_b006_a006_d006_i006 @atom:52_b006_a006_d006_i006 0.16 3.81 + pair_coeff @atom:53_b004_a004_d004_i004 @atom:53_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:54_b024_a024_d024_i024 @atom:54_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:55_b003_a003_d003_i003 @atom:55_b003_a003_d003_i003 0.115 3.8 + pair_coeff @atom:56_b006_a006_d006_i006 @atom:56_b006_a006_d006_i006 0.17 3.8 + pair_coeff @atom:57_b025_a025_d025_i025 @atom:57_b025_a025_d025_i025 0.0 0.0 + pair_coeff @atom:58_b026_a026_d026_i026 @atom:58_b026_a026_d026_i026 0.02 2.556 + pair_coeff @atom:59_b027_a027_d027_i027 @atom:59_b027_a027_d027_i027 0.069 2.78 + pair_coeff @atom:60_b028_a028_d028_i028 @atom:60_b028_a028_d028_i028 0.2339 3.401 + pair_coeff @atom:61_b029_a029_d029_i029 @atom:61_b029_a029_d029_i029 0.317 3.624 + pair_coeff @atom:62_b030_a030_d030_i030 @atom:62_b030_a030_d030_i030 0.433 3.935 + pair_coeff @atom:63_b031_a031_d031_i031 @atom:63_b031_a031_d031_i031 0.1521 3.15061 + pair_coeff @atom:64_b032_a032_d032_i032 @atom:64_b032_a032_d032_i032 0.0 0.0 + pair_coeff @atom:65_b031_a031_d031_i031 @atom:65_b031_a031_d031_i031 0.155 3.15365 + pair_coeff @atom:66_b032_a032_d032_i032 @atom:66_b032_a032_d032_i032 0.0 0.0 + pair_coeff @atom:67_b033_a033_d033_i033 @atom:67_b033_a033_d033_i033 0.0 0.0 + pair_coeff @atom:68_b034_a034_d034_i034 @atom:68_b034_a034_d034_i034 0.15 3.176 + pair_coeff @atom:69_b035_a035_d035_i035 @atom:69_b035_a035_d035_i035 0.0 0.0 + pair_coeff @atom:70_b036_a036_d036_i036 @atom:70_b036_a036_d036_i036 0.1 3.27 + pair_coeff @atom:71_b037_a037_d037_i037 @atom:71_b037_a037_d037_i037 0.0 0.0 + pair_coeff @atom:72_b038_a038_d038_i038 @atom:72_b038_a038_d038_i038 0.0 0.0 + pair_coeff @atom:73_b039_a039_d039_i039 @atom:73_b039_a039_d039_i039 0.16 3.12 + pair_coeff @atom:74_b040_a040_d040_i040 @atom:74_b040_a040_d040_i040 0.0 0.0 + pair_coeff @atom:75_b041_a041_d041_i041 @atom:75_b041_a041_d041_i041 0.0 0.0 + pair_coeff @atom:76_b042_a042_d042_i042 @atom:76_b042_a042_d042_i042 0.1554 3.16557 + pair_coeff @atom:77_b043_a043_d043_i043 @atom:77_b043_a043_d043_i043 0.0 0.0 + pair_coeff @atom:78_b044_a044_d044_i044 @atom:78_b044_a044_d044_i044 0.17 3.42 + pair_coeff @atom:79_b045_a045_d045_i045 @atom:79_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:80_b013_a013_d013_i013 @atom:80_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:81_b013_a013_d013_i013 @atom:81_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:82_b013_a013_d013_i013 @atom:82_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:83_b013_a013_d013_i013 @atom:83_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:84_b013_a013_d013_i013 @atom:84_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:85_b046_a046_d046_i046 @atom:85_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:86_b047_a047_d047_i047 @atom:86_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:87_b047_a047_d047_i047 @atom:87_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:88_b047_a047_d047_i047 @atom:88_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:89_b046_a046_d046_i046 @atom:89_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:90_b048_a048_d048_i048 @atom:90_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:91_b049_a049_d049_i049 @atom:91_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:92_b048_a048_d048_i048 @atom:92_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:93_b013_a013_d013_i013 @atom:93_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:94_b013_a013_d013_i013 @atom:94_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:95_b050_a050_d050_i050 @atom:95_b050_a050_d050_i050 0.076 3.55 + pair_coeff @atom:96_b005_a005_d005_i005 @atom:96_b005_a005_d005_i005 0.17 3.12 + pair_coeff @atom:97_b007_a007_d007_i007 @atom:97_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:98_b046_a046_d046_i046 @atom:98_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:99_b013_a013_d013_i013 @atom:99_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:100_b013_a013_d013_i013 @atom:100_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:101_b013_a013_d013_i013 @atom:101_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:102_b013_a013_d013_i013 @atom:102_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:103_b013_a013_d013_i013 @atom:103_b013_a013_d013_i013 0.062 3.25 + pair_coeff @atom:104_b005_a005_d005_i005 @atom:104_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:105_b007_a007_d007_i007 @atom:105_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:106_b001_a001_d001_i001 @atom:106_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:107_b046_a046_d046_i046 @atom:107_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:108_b048_a048_d048_i048 @atom:108_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:109_b005_a005_d005_i005 @atom:109_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:110_b007_a007_d007_i007 @atom:110_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:111_b005_a005_d005_i005 @atom:111_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:112_b007_a007_d007_i007 @atom:112_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:113_b005_a005_d005_i005 @atom:113_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:114_b007_a007_d007_i007 @atom:114_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:115_b013_a013_d013_i013 @atom:115_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:116_b013_a013_d013_i013 @atom:116_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:117_b013_a013_d013_i013 @atom:117_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:118_b046_a046_d046_i046 @atom:118_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:119_b020_a020_d020_i020 @atom:119_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:120_b050_a050_d050_i050 @atom:120_b050_a050_d050_i050 0.076 3.55 + pair_coeff @atom:121_b020_a020_d020_i020 @atom:121_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:122_b020_a020_d020_i020 @atom:122_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:123_b013_a013_d013_i013 @atom:123_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:124_b013_a013_d013_i013 @atom:124_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:125_b013_a013_d013_i013 @atom:125_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:126_b013_a013_d013_i013 @atom:126_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:127_b046_a046_d046_i046 @atom:127_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:128_b020_a020_d020_i020 @atom:128_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:129_b005_a005_d005_i005 @atom:129_b005_a005_d005_i005 0.17 3.07 + pair_coeff @atom:130_b007_a007_d007_i007 @atom:130_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:131_b051_a051_d051_i051 @atom:131_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:132_b046_a046_d046_i046 @atom:132_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:133_b051_a051_d051_i051 @atom:133_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:134_b046_a046_d046_i046 @atom:134_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:135_b051_a051_d051_i051 @atom:135_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:136_b046_a046_d046_i046 @atom:136_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:137_b051_a051_d051_i051 @atom:137_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:138_b046_a046_d046_i046 @atom:138_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:139_b051_a051_d051_i051 @atom:139_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:140_b051_a051_d051_i051 @atom:140_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:141_b048_a048_d048_i048 @atom:141_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:142_b015_a015_d015_i015 @atom:142_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:143_b015_a015_d015_i015 @atom:143_b015_a015_d015_i015 0.25 3.7 + pair_coeff @atom:144_b016_a016_d016_i016 @atom:144_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:145_b016_a016_d016_i016 @atom:145_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:146_b017_a017_d017_i017 @atom:146_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:147_b017_a017_d017_i017 @atom:147_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:148_b013_a013_d013_i013 @atom:148_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:149_b013_a013_d013_i013 @atom:149_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:150_b013_a013_d013_i013 @atom:150_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:151_b013_a013_d013_i013 @atom:151_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:152_b013_a013_d013_i013 @atom:152_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:153_b013_a013_d013_i013 @atom:153_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:154_b013_a013_d013_i013 @atom:154_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:155_b013_a013_d013_i013 @atom:155_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:156_b013_a013_d013_i013 @atom:156_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:157_b013_a013_d013_i013 @atom:157_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:158_b013_a013_d013_i013 @atom:158_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:159_b013_a013_d013_i013 @atom:159_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:160_b013_a013_d013_i013 @atom:160_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:161_b013_a013_d013_i013 @atom:161_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:162_b013_a013_d013_i013 @atom:162_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:163_b048_a048_d048_i048 @atom:163_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:164_b016_a016_d016_i016 @atom:164_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:165_b013_a013_d013_i013 @atom:165_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:166_b013_a013_d013_i013 @atom:166_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:167_b013_a013_d013_i013 @atom:167_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:168_b021_a021_d021_i021 @atom:168_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:169_b047_a047_d047_i047 @atom:169_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:170_b048_a048_d048_i048 @atom:170_b048_a048_d048_i048 0.07 3.55 + pair_coeff 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@atom:303_b045_a045_d045_i045 @atom:303_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:304_b057_a057_d057_i057 @atom:304_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:305_b048_a048_d048_i048 @atom:305_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:306_b056_a056_d056_i056 @atom:306_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:307_b060_a060_d060_i060 @atom:307_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:308_b060_a060_d060_i060 @atom:308_b060_a060_d060_i060 0.08 3.5 + pair_coeff @atom:309_b003_a003_d003_i003 @atom:309_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:310_b045_a045_d045_i045 @atom:310_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:311_b055_a055_d055_i055 @atom:311_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:312_b045_a045_d045_i045 @atom:312_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:313_b004_a004_d004_i004 @atom:313_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:314_b013_a013_d013_i013 @atom:314_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:315_b046_a046_d046_i046 @atom:315_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:316_b013_a013_d013_i013 @atom:316_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:317_b046_a046_d046_i046 @atom:317_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:318_b013_a013_d013_i013 @atom:318_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:319_b046_a046_d046_i046 @atom:319_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:320_b057_a057_d057_i057 @atom:320_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:321_b003_a003_d003_i003 @atom:321_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:322_b057_a057_d057_i057 @atom:322_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:323_b048_a048_d048_i048 @atom:323_b048_a048_d048_i048 0.08 3.5 + pair_coeff @atom:324_b047_a047_d047_i047 @atom:324_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:325_b047_a047_d047_i047 @atom:325_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:326_b045_a045_d045_i045 @atom:326_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:327_b004_a004_d004_i004 @atom:327_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:328_b045_a045_d045_i045 @atom:328_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:329_b055_a055_d055_i055 @atom:329_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:330_b045_a045_d045_i045 @atom:330_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:331_b045_a045_d045_i045 @atom:331_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:332_b049_a049_d049_i049 @atom:332_b049_a049_d049_i049 0.05 2.5 + pair_coeff @atom:333_b058_a058_d058_i058 @atom:333_b058_a058_d058_i058 0.05 2.5 + pair_coeff @atom:334_b013_a013_d013_i013 @atom:334_b013_a013_d013_i013 0.08 3.5 + pair_coeff @atom:335_b046_a046_d046_i046 @atom:335_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:336_b064_a064_d064_i064 @atom:336_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:337_b052_a052_d052_i052 @atom:337_b052_a052_d052_i052 0.21 2.96 + pair_coeff @atom:338_b020_a020_d020_i020 @atom:338_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:339_b013_a013_d013_i013 @atom:339_b013_a013_d013_i013 0.066 3.55 + pair_coeff @atom:340_b047_a047_d047_i047 @atom:340_b047_a047_d047_i047 0.08 3.5 + pair_coeff @atom:341_b021_a021_d021_i021 @atom:341_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:342_b047_a047_d047_i047 @atom:342_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:343_b001_a001_d001_i001 @atom:343_b001_a001_d001_i001 0.71 3.05 + pair_coeff @atom:344_b021_a021_d021_i021 @atom:344_b021_a021_d021_i021 0.71 4.02 + pair_coeff @atom:345_b065_a065_d065_i065 @atom:345_b065_a065_d065_i065 0.71 4.28 + pair_coeff @atom:346_b066_a066_d066_i066 @atom:346_b066_a066_d066_i066 0.71 4.81 + pair_coeff @atom:347_b067_a067_d067_i067 @atom:347_b067_a067_d067_i067 0.0005 5.34 + pair_coeff @atom:348_b068_a068_d068_i068 @atom:348_b068_a068_d068_i068 0.0005 2.87 + pair_coeff @atom:349_b069_a069_d069_i069 @atom:349_b069_a069_d069_i069 0.0005 4.07 + pair_coeff @atom:350_b070_a070_d070_i070 @atom:350_b070_a070_d070_i070 0.0005 5.17 + pair_coeff @atom:351_b071_a071_d071_i071 @atom:351_b071_a071_d071_i071 0.0005 5.6 + pair_coeff @atom:352_b072_a072_d072_i072 @atom:352_b072_a072_d072_i072 0.0005 6.2 + pair_coeff @atom:353_b073_a073_d073_i073 @atom:353_b073_a073_d073_i073 0.875044 1.644471 + pair_coeff @atom:354_b074_a074_d074_i074 @atom:354_b074_a074_d074_i074 0.449657 2.412031 + pair_coeff @atom:355_b075_a075_d075_i075 @atom:355_b075_a075_d075_i075 0.118226 3.102688 + pair_coeff @atom:356_b076_a076_d076_i076 @atom:356_b076_a076_d076_i076 0.047096 3.81661 + pair_coeff @atom:357_b006_a006_d006_i006 @atom:357_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:358_b046_a046_d046_i046 @atom:358_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:359_b015_a015_d015_i015 @atom:359_b015_a015_d015_i015 0.5 4.25 + pair_coeff @atom:360_b006_a006_d006_i006 @atom:360_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:361_b046_a046_d046_i046 @atom:361_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:362_b005_a005_d005_i005 @atom:362_b005_a005_d005_i005 0.25 3.15 + pair_coeff @atom:363_b013_a013_d013_i013 @atom:363_b013_a013_d013_i013 0.3 4.2 + pair_coeff @atom:364_b046_a046_d046_i046 @atom:364_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:365_b019_a019_d019_i019 @atom:365_b019_a019_d019_i019 0.15 3.65 + pair_coeff @atom:366_b018_a018_d018_i018 @atom:366_b018_a018_d018_i018 0.25 3.4 + pair_coeff @atom:367_b006_a006_d006_i006 @atom:367_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:368_b046_a046_d046_i046 @atom:368_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:369_b053_a053_d053_i053 @atom:369_b053_a053_d053_i053 0.25 3.4 + pair_coeff @atom:370_b045_a045_d045_i045 @atom:370_b045_a045_d045_i045 0.05 2.5 + pair_coeff @atom:371_b006_a006_d006_i006 @atom:371_b006_a006_d006_i006 0.3 4.2 + pair_coeff @atom:372_b046_a046_d046_i046 @atom:372_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:373_b013_a013_d013_i013 @atom:373_b013_a013_d013_i013 0.3 4.2 + pair_coeff @atom:374_b046_a046_d046_i046 @atom:374_b046_a046_d046_i046 0.05 2.5 + pair_coeff @atom:375_b033_a033_d033_i033 @atom:375_b033_a033_d033_i033 0.0 0.0 + pair_coeff @atom:376_b005_a005_d005_i005 @atom:376_b005_a005_d005_i005 0.25 3.2 + pair_coeff @atom:377_b007_a007_d007_i007 @atom:377_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:378_b077_a077_d077_i077 @atom:378_b077_a077_d077_i077 0.4 2.81524 + pair_coeff @atom:379_b078_a078_d078_i078 @atom:379_b078_a078_d078_i078 0.2 3.11815 + pair_coeff @atom:380_b020_a020_d020_i020 @atom:380_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:381_b064_a064_d064_i064 @atom:381_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:382_b052_a052_d052_i052 @atom:382_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:383_b020_a020_d020_i020 @atom:383_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:384_b013_a013_d013_i013 @atom:384_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:385_b046_a046_d046_i046 @atom:385_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:386_b064_a064_d064_i064 @atom:386_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:387_b052_a052_d052_i052 @atom:387_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:388_b020_a020_d020_i020 @atom:388_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:389_b013_a013_d013_i013 @atom:389_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:390_b046_a046_d046_i046 @atom:390_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:391_b064_a064_d064_i064 @atom:391_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:392_b052_a052_d052_i052 @atom:392_b052_a052_d052_i052 0.2 3.15 + pair_coeff @atom:393_b020_a020_d020_i020 @atom:393_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:394_b013_a013_d013_i013 @atom:394_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:395_b046_a046_d046_i046 @atom:395_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:396_b013_a013_d013_i013 @atom:396_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:397_b046_a046_d046_i046 @atom:397_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:398_b048_a048_d048_i048 @atom:398_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:399_b013_a013_d013_i013 @atom:399_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:400_b046_a046_d046_i046 @atom:400_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:401_b048_a048_d048_i048 @atom:401_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:402_b013_a013_d013_i013 @atom:402_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:403_b046_a046_d046_i046 @atom:403_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:404_b048_a048_d048_i048 @atom:404_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:405_b013_a013_d013_i013 @atom:405_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:406_b003_a003_d003_i003 @atom:406_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:407_b004_a004_d004_i004 @atom:407_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:408_b020_a020_d020_i020 @atom:408_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:409_b013_a013_d013_i013 @atom:409_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:410_b046_a046_d046_i046 @atom:410_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:411_b003_a003_d003_i003 @atom:411_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:412_b003_a003_d003_i003 @atom:412_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:413_b048_a048_d048_i048 @atom:413_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:414_b020_a020_d020_i020 @atom:414_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:415_b079_a079_d079_i079 @atom:415_b079_a079_d079_i079 0.25 3.55 + pair_coeff @atom:416_b023_a023_d023_i023 @atom:416_b023_a023_d023_i023 0.17 2.96 + pair_coeff @atom:417_b013_a013_d013_i013 @atom:417_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:418_b046_a046_d046_i046 @atom:418_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:419_b024_a024_d024_i024 @atom:419_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:420_b045_a045_d045_i045 @atom:420_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:421_b024_a024_d024_i024 @atom:421_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:422_b045_a045_d045_i045 @atom:422_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:423_b013_a013_d013_i013 @atom:423_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:424_b046_a046_d046_i046 @atom:424_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:425_b013_a013_d013_i013 @atom:425_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:426_b046_a046_d046_i046 @atom:426_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:427_b013_a013_d013_i013 @atom:427_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:428_b046_a046_d046_i046 @atom:428_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:429_b048_a048_d048_i048 @atom:429_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:430_b048_a048_d048_i048 @atom:430_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:431_b013_a013_d013_i013 @atom:431_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:432_b013_a013_d013_i013 @atom:432_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:433_b013_a013_d013_i013 @atom:433_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:434_b079_a079_d079_i079 @atom:434_b079_a079_d079_i079 0.25 3.55 + pair_coeff @atom:435_b023_a023_d023_i023 @atom:435_b023_a023_d023_i023 0.17 2.96 + pair_coeff @atom:436_b022_a022_d022_i022 @atom:436_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:437_b022_a022_d022_i022 @atom:437_b022_a022_d022_i022 0.395 3.56 + pair_coeff @atom:438_b023_a023_d023_i023 @atom:438_b023_a023_d023_i023 0.28 2.93 + pair_coeff @atom:439_b013_a013_d013_i013 @atom:439_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:440_b013_a013_d013_i013 @atom:440_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:441_b080_a080_d080_i080 @atom:441_b080_a080_d080_i080 0.07 3.55 + pair_coeff @atom:442_b060_a060_d060_i060 @atom:442_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:443_b081_a081_d081_i081 @atom:443_b081_a081_d081_i081 0.07 3.55 + pair_coeff @atom:444_b057_a057_d057_i057 @atom:444_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:445_b045_a045_d045_i045 @atom:445_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:446_b013_a013_d013_i013 @atom:446_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:447_b082_a082_d082_i082 @atom:447_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:448_b083_a083_d083_i083 @atom:448_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:449_b084_a084_d084_i084 @atom:449_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:450_b082_a082_d082_i082 @atom:450_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:451_b085_a085_d085_i085 @atom:451_b085_a085_d085_i085 0.07 3.55 + pair_coeff @atom:452_b061_a061_d061_i061 @atom:452_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:453_b057_a057_d057_i057 @atom:453_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:454_b045_a045_d045_i045 @atom:454_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:455_b084_a084_d084_i084 @atom:455_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:456_b013_a013_d013_i013 @atom:456_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:457_b013_a013_d013_i013 @atom:457_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:458_b047_a047_d047_i047 @atom:458_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:459_b047_a047_d047_i047 @atom:459_b047_a047_d047_i047 0.076 3.55 + pair_coeff @atom:460_b086_a086_d086_i086 @atom:460_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:461_b056_a056_d056_i056 @atom:461_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:462_b048_a048_d048_i048 @atom:462_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:463_b048_a048_d048_i048 @atom:463_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:464_b048_a048_d048_i048 @atom:464_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:465_b049_a049_d049_i049 @atom:465_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:466_b049_a049_d049_i049 @atom:466_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:467_b049_a049_d049_i049 @atom:467_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:468_b056_a056_d056_i056 @atom:468_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:469_b048_a048_d048_i048 @atom:469_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:470_b049_a049_d049_i049 @atom:470_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:471_b056_a056_d056_i056 @atom:471_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:472_b059_a059_d059_i059 @atom:472_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:473_b048_a048_d048_i048 @atom:473_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:474_b048_a048_d048_i048 @atom:474_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:475_b049_a049_d049_i049 @atom:475_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:476_b049_a049_d049_i049 @atom:476_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:477_b049_a049_d049_i049 @atom:477_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:478_b056_a056_d056_i056 @atom:478_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:479_b048_a048_d048_i048 @atom:479_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:480_b048_a048_d048_i048 @atom:480_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:481_b049_a049_d049_i049 @atom:481_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:482_b049_a049_d049_i049 @atom:482_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:483_b057_a057_d057_i057 @atom:483_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:484_b084_a084_d084_i084 @atom:484_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:485_b087_a087_d087_i087 @atom:485_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:486_b045_a045_d045_i045 @atom:486_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:487_b049_a049_d049_i049 @atom:487_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:488_b049_a049_d049_i049 @atom:488_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:489_b057_a057_d057_i057 @atom:489_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:490_b061_a061_d061_i061 @atom:490_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:491_b088_a088_d088_i088 @atom:491_b088_a088_d088_i088 0.07 3.55 + pair_coeff @atom:492_b087_a087_d087_i087 @atom:492_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:493_b084_a084_d084_i084 @atom:493_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:494_b045_a045_d045_i045 @atom:494_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:495_b049_a049_d049_i049 @atom:495_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:496_b049_a049_d049_i049 @atom:496_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:497_b049_a049_d049_i049 @atom:497_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:498_b057_a057_d057_i057 @atom:498_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:499_b082_a082_d082_i082 @atom:499_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:500_b061_a061_d061_i061 @atom:500_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:501_b083_a083_d083_i083 @atom:501_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:502_b084_a084_d084_i084 @atom:502_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:503_b045_a045_d045_i045 @atom:503_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:504_b049_a049_d049_i049 @atom:504_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:505_b049_a049_d049_i049 @atom:505_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:506_b049_a049_d049_i049 @atom:506_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:507_b020_a020_d020_i020 @atom:507_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:508_b084_a084_d084_i084 @atom:508_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:509_b087_a087_d087_i087 @atom:509_b087_a087_d087_i087 0.076 3.55 + pair_coeff @atom:510_b049_a049_d049_i049 @atom:510_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:511_b049_a049_d049_i049 @atom:511_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:512_b020_a020_d020_i020 @atom:512_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:513_b082_a082_d082_i082 @atom:513_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:514_b061_a061_d061_i061 @atom:514_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:515_b083_a083_d083_i083 @atom:515_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:516_b084_a084_d084_i084 @atom:516_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:517_b049_a049_d049_i049 @atom:517_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:518_b049_a049_d049_i049 @atom:518_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:519_b049_a049_d049_i049 @atom:519_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:520_b020_a020_d020_i020 @atom:520_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:521_b061_a061_d061_i061 @atom:521_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:522_b088_a088_d088_i088 @atom:522_b088_a088_d088_i088 0.07 3.55 + pair_coeff @atom:523_b087_a087_d087_i087 @atom:523_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:524_b084_a084_d084_i084 @atom:524_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:525_b049_a049_d049_i049 @atom:525_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:526_b049_a049_d049_i049 @atom:526_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:527_b049_a049_d049_i049 @atom:527_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:528_b057_a057_d057_i057 @atom:528_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:529_b084_a084_d084_i084 @atom:529_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:530_b087_a087_d087_i087 @atom:530_b087_a087_d087_i087 0.07 3.55 + pair_coeff @atom:531_b048_a048_d048_i048 @atom:531_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:532_b048_a048_d048_i048 @atom:532_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:533_b048_a048_d048_i048 @atom:533_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:534_b048_a048_d048_i048 @atom:534_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:535_b081_a081_d081_i081 @atom:535_b081_a081_d081_i081 0.07 3.55 + pair_coeff @atom:536_b060_a060_d060_i060 @atom:536_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:537_b045_a045_d045_i045 @atom:537_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:538_b049_a049_d049_i049 @atom:538_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:539_b049_a049_d049_i049 @atom:539_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:540_b049_a049_d049_i049 @atom:540_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:541_b049_a049_d049_i049 @atom:541_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:542_b049_a049_d049_i049 @atom:542_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:543_b049_a049_d049_i049 @atom:543_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:544_b056_a056_d056_i056 @atom:544_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:545_b048_a048_d048_i048 @atom:545_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:546_b048_a048_d048_i048 @atom:546_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:547_b048_a048_d048_i048 @atom:547_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:548_b048_a048_d048_i048 @atom:548_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:549_b048_a048_d048_i048 @atom:549_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:550_b048_a048_d048_i048 @atom:550_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:551_b048_a048_d048_i048 @atom:551_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:552_b048_a048_d048_i048 @atom:552_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:553_b048_a048_d048_i048 @atom:553_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:554_b049_a049_d049_i049 @atom:554_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:555_b049_a049_d049_i049 @atom:555_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:556_b049_a049_d049_i049 @atom:556_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:557_b049_a049_d049_i049 @atom:557_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:558_b049_a049_d049_i049 @atom:558_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:559_b049_a049_d049_i049 @atom:559_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:560_b049_a049_d049_i049 @atom:560_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:561_b056_a056_d056_i056 @atom:561_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:562_b059_a059_d059_i059 @atom:562_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:563_b056_a056_d056_i056 @atom:563_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:564_b060_a060_d060_i060 @atom:564_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:565_b060_a060_d060_i060 @atom:565_b060_a060_d060_i060 0.07 3.55 + pair_coeff @atom:566_b048_a048_d048_i048 @atom:566_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:567_b061_a061_d061_i061 @atom:567_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:568_b062_a062_d062_i062 @atom:568_b062_a062_d062_i062 0.07 3.55 + pair_coeff @atom:569_b057_a057_d057_i057 @atom:569_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:570_b049_a049_d049_i049 @atom:570_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:571_b049_a049_d049_i049 @atom:571_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:572_b049_a049_d049_i049 @atom:572_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:573_b045_a045_d045_i045 @atom:573_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:574_b016_a016_d016_i016 @atom:574_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:575_b082_a082_d082_i082 @atom:575_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:576_b061_a061_d061_i061 @atom:576_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:577_b083_a083_d083_i083 @atom:577_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:578_b084_a084_d084_i084 @atom:578_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:579_b049_a049_d049_i049 @atom:579_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:580_b049_a049_d049_i049 @atom:580_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:581_b049_a049_d049_i049 @atom:581_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:582_b056_a056_d056_i056 @atom:582_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:583_b059_a059_d059_i059 @atom:583_b059_a059_d059_i059 0.07 3.55 + pair_coeff @atom:584_b049_a049_d049_i049 @atom:584_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:585_b048_a048_d048_i048 @atom:585_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:586_b013_a013_d013_i013 @atom:586_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:587_b056_a056_d056_i056 @atom:587_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:588_b048_a048_d048_i048 @atom:588_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:589_b048_a048_d048_i048 @atom:589_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:590_b048_a048_d048_i048 @atom:590_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:591_b048_a048_d048_i048 @atom:591_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:592_b048_a048_d048_i048 @atom:592_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:593_b048_a048_d048_i048 @atom:593_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:594_b049_a049_d049_i049 @atom:594_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:595_b049_a049_d049_i049 @atom:595_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:596_b049_a049_d049_i049 @atom:596_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:597_b049_a049_d049_i049 @atom:597_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:598_b057_a057_d057_i057 @atom:598_b057_a057_d057_i057 0.17 3.25 + pair_coeff @atom:599_b082_a082_d082_i082 @atom:599_b082_a082_d082_i082 0.07 3.55 + pair_coeff @atom:600_b061_a061_d061_i061 @atom:600_b061_a061_d061_i061 0.17 3.25 + pair_coeff @atom:601_b083_a083_d083_i083 @atom:601_b083_a083_d083_i083 0.07 3.55 + pair_coeff @atom:602_b084_a084_d084_i084 @atom:602_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:603_b013_a013_d013_i013 @atom:603_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:604_b049_a049_d049_i049 @atom:604_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:605_b049_a049_d049_i049 @atom:605_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:606_b049_a049_d049_i049 @atom:606_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:607_b046_a046_d046_i046 @atom:607_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:608_b013_a013_d013_i013 @atom:608_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:609_b013_a013_d013_i013 @atom:609_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:610_b013_a013_d013_i013 @atom:610_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:611_b013_a013_d013_i013 @atom:611_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:612_b013_a013_d013_i013 @atom:612_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:613_b013_a013_d013_i013 @atom:613_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:614_b013_a013_d013_i013 @atom:614_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:615_b013_a013_d013_i013 @atom:615_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:616_b013_a013_d013_i013 @atom:616_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:617_b013_a013_d013_i013 @atom:617_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:618_b013_a013_d013_i013 @atom:618_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:619_b013_a013_d013_i013 @atom:619_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:620_b013_a013_d013_i013 @atom:620_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:621_b013_a013_d013_i013 @atom:621_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:622_b013_a013_d013_i013 @atom:622_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:623_b015_a015_d015_i015 @atom:623_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:624_b017_a017_d017_i017 @atom:624_b017_a017_d017_i017 0.0 0.0 + pair_coeff @atom:625_b048_a048_d048_i048 @atom:625_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:626_b089_a089_d089_i089 @atom:626_b089_a089_d089_i089 0.105 3.75 + pair_coeff @atom:627_b090_a090_d090_i090 @atom:627_b090_a090_d090_i090 0.17 3.25 + pair_coeff @atom:628_b091_a091_d091_i091 @atom:628_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:629_b091_a091_d091_i091 @atom:629_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:630_b013_a013_d013_i013 @atom:630_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:631_b086_a086_d086_i086 @atom:631_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:632_b086_a086_d086_i086 @atom:632_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:633_b086_a086_d086_i086 @atom:633_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:634_b086_a086_d086_i086 @atom:634_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:635_b086_a086_d086_i086 @atom:635_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:636_b086_a086_d086_i086 @atom:636_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:637_b016_a016_d016_i016 @atom:637_b016_a016_d016_i016 0.25 3.55 + pair_coeff @atom:638_b092_a092_d092_i092 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@atom:674_b091_a091_d091_i091 0.066 3.5 + pair_coeff @atom:675_b015_a015_d015_i015 @atom:675_b015_a015_d015_i015 0.25 3.55 + pair_coeff @atom:676_b048_a048_d048_i048 @atom:676_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:677_b048_a048_d048_i048 @atom:677_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:678_b048_a048_d048_i048 @atom:678_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:679_b048_a048_d048_i048 @atom:679_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:680_b048_a048_d048_i048 @atom:680_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:681_b049_a049_d049_i049 @atom:681_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:682_b049_a049_d049_i049 @atom:682_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:683_b048_a048_d048_i048 @atom:683_b048_a048_d048_i048 0.05 3.55 + pair_coeff @atom:684_b055_a055_d055_i055 @atom:684_b055_a055_d055_i055 0.17 3.25 + pair_coeff @atom:685_b045_a045_d045_i045 @atom:685_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:686_b045_a045_d045_i045 @atom:686_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:687_b049_a049_d049_i049 @atom:687_b049_a049_d049_i049 0.03 2.42 + pair_coeff @atom:688_b013_a013_d013_i013 @atom:688_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:689_b013_a013_d013_i013 @atom:689_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:690_b101_a101_d101_i101 @atom:690_b101_a101_d101_i101 0.17 3.25 + pair_coeff @atom:691_b056_a056_d056_i056 @atom:691_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:692_b101_a101_d101_i101 @atom:692_b101_a101_d101_i101 0.17 3.25 + pair_coeff @atom:693_b048_a048_d048_i048 @atom:693_b048_a048_d048_i048 0.05 3.55 + pair_coeff @atom:694_b018_a018_d018_i018 @atom:694_b018_a018_d018_i018 0.17 3.2 + pair_coeff @atom:695_b019_a019_d019_i019 @atom:695_b019_a019_d019_i019 0.066 3.3 + pair_coeff @atom:696_b013_a013_d013_i013 @atom:696_b013_a013_d013_i013 0.066 3.3 + pair_coeff @atom:697_b013_a013_d013_i013 @atom:697_b013_a013_d013_i013 0.066 3.3 + pair_coeff @atom:698_b013_a013_d013_i013 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@atom:710_b013_a013_d013_i013 0.066 3.3 + pair_coeff @atom:711_b056_a056_d056_i056 @atom:711_b056_a056_d056_i056 0.17 3.25 + pair_coeff @atom:712_b004_a004_d004_i004 @atom:712_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:713_b003_a003_d003_i003 @atom:713_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:714_b020_a020_d020_i020 @atom:714_b020_a020_d020_i020 0.17 3.0 + pair_coeff @atom:715_b013_a013_d013_i013 @atom:715_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:716_b013_a013_d013_i013 @atom:716_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:717_b013_a013_d013_i013 @atom:717_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:718_b046_a046_d046_i046 @atom:718_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:719_b046_a046_d046_i046 @atom:719_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:720_b046_a046_d046_i046 @atom:720_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:721_b020_a020_d020_i020 @atom:721_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:722_b104_a104_d104_i104 @atom:722_b104_a104_d104_i104 0.2 3.74 + pair_coeff @atom:723_b013_a013_d013_i013 @atom:723_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:724_b013_a013_d013_i013 @atom:724_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:725_b046_a046_d046_i046 @atom:725_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:726_b064_a064_d064_i064 @atom:726_b064_a064_d064_i064 0.2 3.74 + pair_coeff @atom:727_b001_a001_d001_i001 @atom:727_b001_a001_d001_i001 0.061 3.1181 + pair_coeff @atom:728_b024_a024_d024_i024 @atom:728_b024_a024_d024_i024 0.17 3.15 + pair_coeff @atom:729_b004_a004_d004_i004 @atom:729_b004_a004_d004_i004 0.21 2.86 + pair_coeff @atom:730_b044_a044_d044_i044 @atom:730_b044_a044_d044_i044 0.17 3.3 + pair_coeff @atom:731_b044_a044_d044_i044 @atom:731_b044_a044_d044_i044 0.17 3.3 + pair_coeff @atom:732_b044_a044_d044_i044 @atom:732_b044_a044_d044_i044 0.17 3.3 + pair_coeff @atom:733_b013_a013_d013_i013 @atom:733_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:734_b013_a013_d013_i013 @atom:734_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:735_b013_a013_d013_i013 @atom:735_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:736_b013_a013_d013_i013 @atom:736_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:737_b013_a013_d013_i013 @atom:737_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:738_b013_a013_d013_i013 @atom:738_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:739_b045_a045_d045_i045 @atom:739_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:740_b045_a045_d045_i045 @atom:740_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:741_b046_a046_d046_i046 @atom:741_b046_a046_d046_i046 0.015 2.5 + pair_coeff @atom:742_b013_a013_d013_i013 @atom:742_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:743_b013_a013_d013_i013 @atom:743_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:744_b013_a013_d013_i013 @atom:744_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:745_b013_a013_d013_i013 @atom:745_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:746_b048_a048_d048_i048 @atom:746_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:747_b048_a048_d048_i048 @atom:747_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:748_b048_a048_d048_i048 @atom:748_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:749_b013_a013_d013_i013 @atom:749_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:750_b013_a013_d013_i013 @atom:750_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:751_b013_a013_d013_i013 @atom:751_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:752_b013_a013_d013_i013 @atom:752_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:753_b013_a013_d013_i013 @atom:753_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:754_b013_a013_d013_i013 @atom:754_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:755_b019_a019_d019_i019 @atom:755_b019_a019_d019_i019 0.086 3.3 + pair_coeff @atom:756_b046_a046_d046_i046 @atom:756_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:757_b019_a019_d019_i019 @atom:757_b019_a019_d019_i019 0.21 3.3 + pair_coeff @atom:758_b019_a019_d019_i019 @atom:758_b019_a019_d019_i019 0.135 3.3 + pair_coeff @atom:759_b019_a019_d019_i019 @atom:759_b019_a019_d019_i019 0.1 3.3 + pair_coeff @atom:760_b046_a046_d046_i046 @atom:760_b046_a046_d046_i046 0.015 2.5 + pair_coeff @atom:761_b051_a051_d051_i051 @atom:761_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:762_b051_a051_d051_i051 @atom:762_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:763_b051_a051_d051_i051 @atom:763_b051_a051_d051_i051 0.066 3.5 + pair_coeff @atom:764_b005_a005_d005_i005 @atom:764_b005_a005_d005_i005 0.17 3.12 + pair_coeff @atom:765_b007_a007_d007_i007 @atom:765_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:766_b105_a105_d105_i105 @atom:766_b105_a105_d105_i105 0.17 3.25 + pair_coeff @atom:767_b105_a105_d105_i105 @atom:767_b105_a105_d105_i105 0.17 3.25 + pair_coeff @atom:768_b105_a105_d105_i105 @atom:768_b105_a105_d105_i105 0.17 3.25 + pair_coeff @atom:769_b019_a019_d019_i019 @atom:769_b019_a019_d019_i019 0.21 3.3 + pair_coeff @atom:770_b053_a053_d053_i053 @atom:770_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:771_b054_a054_d054_i054 @atom:771_b054_a054_d054_i054 0.0 0.0 + pair_coeff @atom:772_b013_a013_d013_i013 @atom:772_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:773_b013_a013_d013_i013 @atom:773_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:774_b013_a013_d013_i013 @atom:774_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:775_b013_a013_d013_i013 @atom:775_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:776_b084_a084_d084_i084 @atom:776_b084_a084_d084_i084 0.07 3.55 + pair_coeff @atom:777_b087_a087_d087_i087 @atom:777_b087_a087_d087_i087 0.076 3.55 + pair_coeff @atom:778_b086_a086_d086_i086 @atom:778_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:779_b086_a086_d086_i086 @atom:779_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:780_b046_a046_d046_i046 @atom:780_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:781_b013_a013_d013_i013 @atom:781_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:782_b003_a003_d003_i003 @atom:782_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:783_b053_a053_d053_i053 @atom:783_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:784_b052_a052_d052_i052 @atom:784_b052_a052_d052_i052 0.21 2.96 + pair_coeff @atom:785_b054_a054_d054_i054 @atom:785_b054_a054_d054_i054 0.0 0.0 + pair_coeff @atom:786_b001_a001_d001_i001 @atom:786_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:787_b013_a013_d013_i013 @atom:787_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:788_b046_a046_d046_i046 @atom:788_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:789_b013_a013_d013_i013 @atom:789_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:790_b013_a013_d013_i013 @atom:790_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:791_b013_a013_d013_i013 @atom:791_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:792_b013_a013_d013_i013 @atom:792_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:793_b013_a013_d013_i013 @atom:793_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:794_b013_a013_d013_i013 @atom:794_b013_a013_d013_i013 0.097 3.5 + pair_coeff @atom:795_b001_a001_d001_i001 @atom:795_b001_a001_d001_i001 0.053 2.95 + pair_coeff @atom:796_b013_a013_d013_i013 @atom:796_b013_a013_d013_i013 0.062 3.25 + pair_coeff @atom:797_b046_a046_d046_i046 @atom:797_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:798_b013_a013_d013_i013 @atom:798_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:799_b013_a013_d013_i013 @atom:799_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:800_b021_a021_d021_i021 @atom:800_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:801_b013_a013_d013_i013 @atom:801_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:802_b046_a046_d046_i046 @atom:802_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:803_b013_a013_d013_i013 @atom:803_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:804_b013_a013_d013_i013 @atom:804_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:805_b065_a065_d065_i065 @atom:805_b065_a065_d065_i065 0.47 3.47 + pair_coeff @atom:806_b013_a013_d013_i013 @atom:806_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:807_b046_a046_d046_i046 @atom:807_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:808_b013_a013_d013_i013 @atom:808_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:809_b013_a013_d013_i013 @atom:809_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:810_b001_a001_d001_i001 @atom:810_b001_a001_d001_i001 0.061 2.94 + pair_coeff @atom:811_b021_a021_d021_i021 @atom:811_b021_a021_d021_i021 0.3 3.4 + pair_coeff @atom:812_b065_a065_d065_i065 @atom:812_b065_a065_d065_i065 0.47 3.47 + pair_coeff @atom:813_b048_a048_d048_i048 @atom:813_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:814_b020_a020_d020_i020 @atom:814_b020_a020_d020_i020 0.14 2.9 + pair_coeff @atom:815_b013_a013_d013_i013 @atom:815_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:816_b001_a001_d001_i001 @atom:816_b001_a001_d001_i001 0.06 2.9 + pair_coeff @atom:817_b024_a024_d024_i024 @atom:817_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:818_b048_a048_d048_i048 @atom:818_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:819_b013_a013_d013_i013 @atom:819_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:820_b003_a003_d003_i003 @atom:820_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:821_b003_a003_d003_i003 @atom:821_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:822_b004_a004_d004_i004 @atom:822_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:823_b024_a024_d024_i024 @atom:823_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:824_b045_a045_d045_i045 @atom:824_b045_a045_d045_i045 0.0 0.0 + pair_coeff @atom:825_b005_a005_d005_i005 @atom:825_b005_a005_d005_i005 0.17 3.12 + pair_coeff @atom:826_b007_a007_d007_i007 @atom:826_b007_a007_d007_i007 0.0 0.0 + pair_coeff @atom:827_b013_a013_d013_i013 @atom:827_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:828_b013_a013_d013_i013 @atom:828_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:829_b086_a086_d086_i086 @atom:829_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:830_b086_a086_d086_i086 @atom:830_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:831_b086_a086_d086_i086 @atom:831_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:832_b086_a086_d086_i086 @atom:832_b086_a086_d086_i086 0.07 3.55 + pair_coeff @atom:833_b048_a048_d048_i048 @atom:833_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:834_b106_a106_d106_i106 @atom:834_b106_a106_d106_i106 0.0125 1.96 + pair_coeff @atom:835_b013_a013_d013_i013 @atom:835_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:836_b013_a013_d013_i013 @atom:836_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:837_b013_a013_d013_i013 @atom:837_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:838_b066_a066_d066_i066 @atom:838_b066_a066_d066_i066 0.6 3.75 + pair_coeff @atom:839_b046_a046_d046_i046 @atom:839_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:840_b024_a024_d024_i024 @atom:840_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:841_b048_a048_d048_i048 @atom:841_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:842_b048_a048_d048_i048 @atom:842_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:843_b024_a024_d024_i024 @atom:843_b024_a024_d024_i024 0.17 3.25 + pair_coeff @atom:844_b048_a048_d048_i048 @atom:844_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:845_b003_a003_d003_i003 @atom:845_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:846_b004_a004_d004_i004 @atom:846_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 0.17 3.25 + pair_coeff @atom:848_b013_a013_d013_i013 @atom:848_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:849_b013_a013_d013_i013 @atom:849_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:850_b013_a013_d013_i013 @atom:850_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:851_b013_a013_d013_i013 @atom:851_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:852_b046_a046_d046_i046 @atom:852_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:853_b003_a003_d003_i003 @atom:853_b003_a003_d003_i003 0.105 3.75 + pair_coeff @atom:854_b004_a004_d004_i004 @atom:854_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:855_b046_a046_d046_i046 @atom:855_b046_a046_d046_i046 0.015 2.42 + pair_coeff @atom:856_b013_a013_d013_i013 @atom:856_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:857_b013_a013_d013_i013 @atom:857_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:858_b013_a013_d013_i013 @atom:858_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:859_b013_a013_d013_i013 @atom:859_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:860_b013_a013_d013_i013 @atom:860_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:861_b013_a013_d013_i013 @atom:861_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:862_b013_a013_d013_i013 @atom:862_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:863_b013_a013_d013_i013 @atom:863_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:864_b013_a013_d013_i013 @atom:864_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:865_b013_a013_d013_i013 @atom:865_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 0.1 4.0 + pair_coeff @atom:870_b045_a045_d045_i045 @atom:870_b045_a045_d045_i045 0.03 2.5 + pair_coeff @atom:871_b013_a013_d013_i013 @atom:871_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:872_b013_a013_d013_i013 @atom:872_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:873_b013_a013_d013_i013 @atom:873_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:874_b013_a013_d013_i013 @atom:874_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:875_b001_a001_d001_i001 @atom:875_b001_a001_d001_i001 0.72 3.08 + pair_coeff @atom:876_b021_a021_d021_i021 @atom:876_b021_a021_d021_i021 0.11779 4.18 + pair_coeff @atom:877_b065_a065_d065_i065 @atom:877_b065_a065_d065_i065 0.09 4.51 + pair_coeff @atom:878_b066_a066_d066_i066 @atom:878_b066_a066_d066_i066 0.07 5.15 + pair_coeff @atom:879_b068_a068_d068_i068 @atom:879_b068_a068_d068_i068 0.018279 2.7 + pair_coeff @atom:880_b069_a069_d069_i069 @atom:880_b069_a069_d069_i069 0.002772 3.35 + pair_coeff @atom:881_b070_a070_d070_i070 @atom:881_b070_a070_d070_i070 0.000328 4.06 + pair_coeff @atom:882_b071_a071_d071_i071 @atom:882_b071_a071_d071_i071 0.000171 4.32 + pair_coeff @atom:883_b072_a072_d072_i072 @atom:883_b072_a072_d072_i072 8.1e-05 4.82 + pair_coeff @atom:884_b073_a073_d073_i073 @atom:884_b073_a073_d073_i073 0.875044 2.91 + pair_coeff @atom:885_b074_a074_d074_i074 @atom:885_b074_a074_d074_i074 0.449657 3.47 + pair_coeff @atom:886_b075_a075_d075_i075 @atom:886_b075_a075_d075_i075 0.118226 3.82 + pair_coeff @atom:887_b076_a076_d076_i076 @atom:887_b076_a076_d076_i076 0.047096 4.18 + pair_coeff @atom:888_b013_a013_d013_i013 @atom:888_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:889_b013_a013_d013_i013 @atom:889_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:890_b013_a013_d013_i013 @atom:890_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:891_b013_a013_d013_i013 @atom:891_b013_a013_d013_i013 0.066 3.5 + pair_coeff @atom:892_b046_a046_d046_i046 @atom:892_b046_a046_d046_i046 0.03 2.5 + pair_coeff @atom:893_b053_a053_d053_i053 @atom:893_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:894_b048_a048_d048_i048 @atom:894_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:895_b053_a053_d053_i053 @atom:895_b053_a053_d053_i053 0.17 3.25 + pair_coeff @atom:896_b048_a048_d048_i048 @atom:896_b048_a048_d048_i048 0.07 3.55 + pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 0.076 3.55 + pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 0.076 3.55 + pair_coeff @atom:899_b046_a046_d046_i046 @atom:899_b046_a046_d046_i046 0.03 2.42 + pair_coeff @atom:900_b047_a047_d047_i047 @atom:900_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:901_b047_a047_d047_i047 @atom:901_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:902_b047_a047_d047_i047 @atom:902_b047_a047_d047_i047 0.086 3.3 + pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 0.086 3.3 + pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 0.086 3.3 + pair_coeff @atom:905_b004_a004_d004_i004 @atom:905_b004_a004_d004_i004 0.21 2.96 + pair_coeff @atom:906_b013_a013_d013_i013 @atom:906_b013_a013_d013_i013 0.066 3.5 } #(end of pair_coeffs) @@ -3689,388 +3702,388 @@ OPLSAA { # ------- Bonded Interactions: ------- # http://lammps.sandia.gov/doc/bond_harmonic.html # Syntax: - # bond_coeff BondTypeName BondStyle parameters... + # bond_coeff BondTypeName parameters... write_once("In Settings") { - bond_coeff @bond:1-2 harmonic 367.0 1.38 - bond_coeff @bond:1-3 harmonic 420.0 1.357 - bond_coeff @bond:1-13 harmonic 367.0 1.36 - bond_coeff @bond:1-19 harmonic 450.0 1.279 - bond_coeff @bond:1-25 harmonic 300.0 0.3 - bond_coeff @bond:1-47 harmonic 420.0 1.34 - bond_coeff @bond:1-48 harmonic 420.0 1.354 - bond_coeff @bond:1-82 harmonic 420.0 1.354 - bond_coeff @bond:1-83 harmonic 420.0 1.354 - bond_coeff @bond:1-84 harmonic 420.0 1.354 - bond_coeff @bond:1-87 harmonic 420.0 1.354 - bond_coeff @bond:1-88 harmonic 420.0 1.354 - bond_coeff @bond:1-108 harmonic 461.0 1.57 - bond_coeff @bond:2-2 harmonic 260.0 1.526 - bond_coeff @bond:2-3 harmonic 317.0 1.522 - bond_coeff @bond:2-5 harmonic 386.0 1.425 - bond_coeff @bond:2-6 harmonic 260.0 1.526 - bond_coeff @bond:2-10 harmonic 260.0 1.526 - bond_coeff @bond:2-11 harmonic 317.0 1.5 - bond_coeff @bond:2-12 harmonic 317.0 1.51 - bond_coeff @bond:2-13 harmonic 260.0 1.526 - bond_coeff @bond:2-14 harmonic 317.0 1.5 - bond_coeff @bond:2-15 harmonic 222.0 1.81 - bond_coeff @bond:2-16 harmonic 222.0 1.81 - bond_coeff @bond:2-20 harmonic 320.0 1.425 - bond_coeff @bond:2-24 harmonic 337.0 1.449 - bond_coeff @bond:2-44 harmonic 382.0 1.448 - bond_coeff @bond:2-48 harmonic 317.0 1.51 - bond_coeff @bond:2-51 harmonic 260.0 1.526 - bond_coeff @bond:2-53 harmonic 367.0 1.471 - bond_coeff @bond:2-55 harmonic 337.0 1.463 - bond_coeff @bond:2-80 harmonic 317.0 1.495 - bond_coeff @bond:3-3 harmonic 350.0 1.51 - bond_coeff @bond:3-4 harmonic 570.0 1.229 - bond_coeff @bond:3-5 harmonic 450.0 1.364 - bond_coeff @bond:3-6 harmonic 317.0 1.522 - bond_coeff @bond:3-10 harmonic 317.0 1.522 - bond_coeff @bond:3-12 harmonic 469.0 1.4 - bond_coeff @bond:3-13 harmonic 317.0 1.522 - bond_coeff @bond:3-19 harmonic 400.0 1.444 - bond_coeff @bond:3-20 harmonic 214.0 1.327 - bond_coeff @bond:3-21 harmonic 300.0 1.79 - bond_coeff @bond:3-24 harmonic 490.0 1.335 - bond_coeff @bond:3-44 harmonic 317.0 1.522 - bond_coeff @bond:3-46 harmonic 340.0 1.09 - bond_coeff @bond:3-47 harmonic 410.0 1.444 - bond_coeff @bond:3-48 harmonic 400.0 1.49 - bond_coeff @bond:3-50 harmonic 385.0 1.46 - bond_coeff @bond:3-52 harmonic 656.0 1.25 - bond_coeff @bond:3-56 harmonic 457.0 1.358 - bond_coeff @bond:3-57 harmonic 418.0 1.388 - bond_coeff @bond:3-60 harmonic 447.0 1.419 - bond_coeff @bond:3-65 harmonic 300.0 1.98 - bond_coeff @bond:3-84 harmonic 400.0 1.49 - bond_coeff @bond:3-86 harmonic 385.0 1.46 - bond_coeff @bond:3-105 harmonic 424.0 1.383 - bond_coeff @bond:3-107 harmonic 490.0 1.335 - bond_coeff @bond:4-25 harmonic 553.0 0.3 - bond_coeff @bond:4-64 harmonic 525.0 1.48 - bond_coeff @bond:4-89 harmonic 570.0 1.229 - bond_coeff @bond:4-110 harmonic 700.0 1.171 - bond_coeff @bond:5-6 harmonic 386.0 1.425 - bond_coeff @bond:5-7 harmonic 553.0 0.945 - bond_coeff @bond:5-10 harmonic 386.0 1.425 - bond_coeff @bond:5-13 harmonic 320.0 1.41 - bond_coeff @bond:5-20 harmonic 250.0 1.47 - bond_coeff @bond:5-24 harmonic 400.0 1.38 - bond_coeff @bond:5-25 harmonic 340.0 0.3 - bond_coeff @bond:5-44 harmonic 320.0 1.45 - bond_coeff @bond:5-47 harmonic 450.0 1.37 - bond_coeff @bond:5-48 harmonic 450.0 1.364 - bond_coeff @bond:5-51 harmonic 320.0 1.38 - bond_coeff @bond:5-64 harmonic 230.0 1.61 - bond_coeff @bond:5-79 harmonic 450.0 1.67 - bond_coeff @bond:5-106 harmonic 94.0 1.8 - bond_coeff @bond:5-108 harmonic 374.0 1.64 - bond_coeff @bond:6-6 harmonic 260.0 1.526 - bond_coeff @bond:6-10 harmonic 260.0 1.526 - bond_coeff @bond:6-11 harmonic 317.0 1.5 - bond_coeff @bond:6-13 harmonic 260.0 1.526 - bond_coeff @bond:6-14 harmonic 317.0 1.5 - bond_coeff @bond:6-15 harmonic 222.0 1.81 - bond_coeff @bond:6-16 harmonic 222.0 1.81 - bond_coeff @bond:6-20 harmonic 320.0 1.425 - bond_coeff @bond:6-24 harmonic 337.0 1.449 - bond_coeff @bond:6-44 harmonic 382.0 1.448 - bond_coeff @bond:6-47 harmonic 317.0 1.51 - bond_coeff @bond:6-51 harmonic 260.0 1.526 - bond_coeff @bond:6-53 harmonic 367.0 1.471 - bond_coeff @bond:6-55 harmonic 337.0 1.463 - bond_coeff @bond:6-79 harmonic 222.0 1.81 - bond_coeff @bond:6-105 harmonic 337.0 1.475 - bond_coeff @bond:7-20 harmonic 553.0 0.945 - bond_coeff @bond:7-25 harmonic 340.0 0.1 - bond_coeff @bond:9-9 harmonic 530.0 1.34 - bond_coeff @bond:9-11 harmonic 530.0 1.34 - bond_coeff @bond:9-14 harmonic 530.0 1.34 - bond_coeff @bond:10-10 harmonic 260.0 1.526 - bond_coeff @bond:10-11 harmonic 317.0 1.5 - bond_coeff @bond:10-14 harmonic 317.0 1.5 - bond_coeff @bond:10-20 harmonic 320.0 1.425 - bond_coeff @bond:10-24 harmonic 337.0 1.449 - bond_coeff @bond:10-44 harmonic 382.0 1.448 - bond_coeff @bond:10-105 harmonic 337.0 1.475 - bond_coeff @bond:11-11 harmonic 530.0 1.34 - bond_coeff @bond:11-13 harmonic 317.0 1.5 - bond_coeff @bond:11-14 harmonic 530.0 1.34 - bond_coeff @bond:11-79 harmonic 222.0 1.76 - bond_coeff @bond:12-12 harmonic 469.0 1.4 - bond_coeff @bond:12-48 harmonic 469.0 1.4 - bond_coeff @bond:12-60 harmonic 469.0 1.4 - bond_coeff @bond:12-81 harmonic 469.0 1.4 - bond_coeff @bond:13-13 harmonic 268.0 1.529 - bond_coeff @bond:13-14 harmonic 317.0 1.5 - bond_coeff @bond:13-15 harmonic 222.0 1.81 - bond_coeff @bond:13-16 harmonic 222.0 1.81 - bond_coeff @bond:13-18 harmonic 390.0 1.43 - bond_coeff @bond:13-19 harmonic 390.0 1.47 - bond_coeff @bond:13-20 harmonic 320.0 1.41 - bond_coeff @bond:13-21 harmonic 245.0 1.781 - bond_coeff @bond:13-22 harmonic 340.0 1.79 - bond_coeff @bond:13-24 harmonic 337.0 1.449 - bond_coeff @bond:13-25 harmonic 340.0 0.3 - bond_coeff @bond:13-44 harmonic 382.0 1.448 - bond_coeff @bond:13-46 harmonic 340.0 1.09 - bond_coeff @bond:13-47 harmonic 317.0 1.51 - bond_coeff @bond:13-48 harmonic 317.0 1.51 - bond_coeff @bond:13-50 harmonic 317.0 1.51 - bond_coeff @bond:13-51 harmonic 268.0 1.529 - bond_coeff @bond:13-53 harmonic 367.0 1.471 - bond_coeff @bond:13-55 harmonic 337.0 1.463 - bond_coeff @bond:13-56 harmonic 337.0 1.449 - bond_coeff @bond:13-57 harmonic 337.0 1.475 - bond_coeff @bond:13-60 harmonic 317.0 1.51 - bond_coeff @bond:13-64 harmonic 212.0 1.843 - bond_coeff @bond:13-65 harmonic 245.0 1.945 - bond_coeff @bond:13-66 harmonic 200.0 2.19 - bond_coeff @bond:13-79 harmonic 340.0 1.77 - bond_coeff @bond:13-80 harmonic 317.0 1.495 - bond_coeff @bond:13-83 harmonic 317.0 1.504 - bond_coeff @bond:13-84 harmonic 317.0 1.504 - bond_coeff @bond:13-85 harmonic 317.0 1.504 - bond_coeff @bond:13-87 harmonic 317.0 1.495 - bond_coeff @bond:13-90 harmonic 337.0 1.449 - bond_coeff @bond:13-91 harmonic 280.0 1.51 - bond_coeff @bond:13-95 harmonic 532.8 1.46 - bond_coeff @bond:13-101 harmonic 382.0 1.448 - bond_coeff @bond:13-102 harmonic 375.0 1.49 - bond_coeff @bond:13-104 harmonic 212.0 1.82 - bond_coeff @bond:13-105 harmonic 337.0 1.475 - bond_coeff @bond:13-107 harmonic 337.0 1.449 - bond_coeff @bond:13-108 harmonic 187.0 1.86 - bond_coeff @bond:13-109 harmonic 317.0 1.51 - bond_coeff @bond:14-14 harmonic 530.0 1.34 - bond_coeff @bond:15-17 harmonic 274.0 1.336 - bond_coeff @bond:15-48 harmonic 250.0 1.74 - bond_coeff @bond:16-16 harmonic 166.0 2.038 - bond_coeff @bond:16-19 harmonic 300.0 1.685 - bond_coeff @bond:16-24 harmonic 250.0 1.73 - bond_coeff @bond:16-25 harmonic 340.0 0.5 - bond_coeff @bond:16-47 harmonic 250.0 1.76 - bond_coeff @bond:16-48 harmonic 250.0 1.76 - bond_coeff @bond:16-61 harmonic 250.0 1.73 - bond_coeff @bond:16-82 harmonic 250.0 1.76 - bond_coeff @bond:16-84 harmonic 250.0 1.74 - bond_coeff @bond:16-91 harmonic 222.0 1.81 - bond_coeff @bond:16-108 harmonic 144.0 2.15 - bond_coeff @bond:17-25 harmonic 340.0 0.1 - bond_coeff @bond:18-18 harmonic 550.0 1.12 - bond_coeff @bond:18-19 harmonic 650.0 1.157 - bond_coeff @bond:18-48 harmonic 400.0 1.41 - bond_coeff @bond:18-56 harmonic 550.0 1.24 - bond_coeff @bond:19-19 harmonic 1150.0 1.21 - bond_coeff @bond:19-21 harmonic 330.0 1.637 - bond_coeff @bond:19-46 harmonic 420.0 1.08 - bond_coeff @bond:19-47 harmonic 400.0 1.426 - bond_coeff @bond:19-48 harmonic 400.0 1.451 - bond_coeff @bond:19-50 harmonic 400.0 1.426 - bond_coeff @bond:19-65 harmonic 330.0 1.784 - bond_coeff @bond:19-88 harmonic 400.0 1.451 - bond_coeff @bond:19-91 harmonic 400.0 1.451 - bond_coeff @bond:20-20 harmonic 250.0 1.47 - bond_coeff @bond:20-21 harmonic 200.0 1.69 - bond_coeff @bond:20-24 harmonic 320.0 1.45 - bond_coeff @bond:20-25 harmonic 340.0 0.3 - bond_coeff @bond:20-44 harmonic 320.0 1.45 - bond_coeff @bond:20-47 harmonic 450.0 1.37 - bond_coeff @bond:20-48 harmonic 450.0 1.364 - bond_coeff @bond:20-51 harmonic 320.0 1.38 - bond_coeff @bond:20-60 harmonic 340.0 1.36 - bond_coeff @bond:20-61 harmonic 462.0 1.399 - bond_coeff @bond:20-64 harmonic 230.0 1.61 - bond_coeff @bond:20-82 harmonic 462.0 1.357 - bond_coeff @bond:20-84 harmonic 340.0 1.36 - bond_coeff @bond:20-108 harmonic 374.0 1.64 - bond_coeff @bond:21-25 harmonic 300.0 0.3 - bond_coeff @bond:21-47 harmonic 300.0 1.725 - bond_coeff @bond:21-48 harmonic 300.0 1.725 - bond_coeff @bond:21-82 harmonic 300.0 1.725 - bond_coeff @bond:21-83 harmonic 300.0 1.725 - bond_coeff @bond:21-84 harmonic 300.0 1.725 - bond_coeff @bond:21-87 harmonic 300.0 1.725 - bond_coeff @bond:21-88 harmonic 300.0 1.725 - bond_coeff @bond:21-108 harmonic 223.0 2.02 - bond_coeff @bond:22-23 harmonic 700.0 1.53 - bond_coeff @bond:22-25 harmonic 340.0 0.5 - bond_coeff @bond:23-25 harmonic 340.0 0.3 - bond_coeff @bond:23-79 harmonic 700.0 1.44 - bond_coeff @bond:24-25 harmonic 367.0 0.3 - bond_coeff @bond:24-45 harmonic 434.0 1.01 - bond_coeff @bond:24-48 harmonic 427.0 1.381 - bond_coeff @bond:24-59 harmonic 427.0 1.381 - bond_coeff @bond:24-79 harmonic 434.0 1.67 - bond_coeff @bond:24-84 harmonic 427.0 1.381 - bond_coeff @bond:24-88 harmonic 427.0 1.381 - bond_coeff @bond:24-91 harmonic 337.0 1.449 - bond_coeff @bond:24-103 harmonic 500.0 1.27 - bond_coeff @bond:24-106 harmonic 40.0 2.05 - bond_coeff @bond:25-25 harmonic 340.0 0.3 - bond_coeff @bond:25-44 harmonic 340.0 0.3 - bond_coeff @bond:25-45 harmonic 340.0 0.1 - bond_coeff @bond:25-46 harmonic 340.0 0.3 - bond_coeff @bond:25-47 harmonic 340.0 0.3 - bond_coeff @bond:25-48 harmonic 367.0 0.3 - bond_coeff @bond:25-49 harmonic 340.0 0.3 - bond_coeff @bond:25-53 harmonic 340.0 0.3 - bond_coeff @bond:25-56 harmonic 367.0 0.3 - bond_coeff @bond:25-61 harmonic 367.0 0.3 - bond_coeff @bond:25-65 harmonic 300.0 0.3 - bond_coeff @bond:25-103 harmonic 340.0 0.1 - bond_coeff @bond:31-32 harmonic 600.0 0.9572 - bond_coeff @bond:31-33 harmonic 900.0 0.15 - bond_coeff @bond:31-106 harmonic 40.0 2.05 - bond_coeff @bond:34-35 harmonic 529.6 0.9572 - bond_coeff @bond:36-37 harmonic 600.0 0.9572 - bond_coeff @bond:36-38 harmonic 900.0 0.175 - bond_coeff @bond:39-40 harmonic 600.0 0.9572 - bond_coeff @bond:39-41 harmonic 900.0 0.7 - bond_coeff @bond:42-43 harmonic 600.0 1.0 - bond_coeff @bond:44-44 harmonic 350.0 1.445 - bond_coeff @bond:44-45 harmonic 434.0 1.01 - bond_coeff @bond:44-48 harmonic 481.0 1.34 - bond_coeff @bond:44-79 harmonic 340.0 1.77 - bond_coeff @bond:44-91 harmonic 382.0 1.448 - bond_coeff @bond:44-108 harmonic 266.0 1.74 - bond_coeff @bond:45-53 harmonic 434.0 1.01 - bond_coeff @bond:45-55 harmonic 434.0 1.01 - bond_coeff @bond:45-56 harmonic 434.0 1.01 - bond_coeff @bond:45-57 harmonic 434.0 1.01 - bond_coeff @bond:45-101 harmonic 434.0 1.01 - bond_coeff @bond:45-105 harmonic 434.0 1.01 - bond_coeff @bond:45-108 harmonic 166.0 1.48 - bond_coeff @bond:46-47 harmonic 340.0 1.08 - bond_coeff @bond:46-50 harmonic 340.0 1.08 - bond_coeff @bond:46-51 harmonic 340.0 1.09 - bond_coeff @bond:46-80 harmonic 340.0 1.08 - bond_coeff @bond:46-91 harmonic 340.0 1.088 - bond_coeff @bond:46-95 harmonic 532.8 1.084 - bond_coeff @bond:46-108 harmonic 166.0 1.48 - bond_coeff @bond:46-109 harmonic 340.0 1.08 - bond_coeff @bond:47-47 harmonic 549.0 1.34 - bond_coeff @bond:47-48 harmonic 427.0 1.433 - bond_coeff @bond:47-50 harmonic 549.0 1.34 - bond_coeff @bond:47-57 harmonic 448.0 1.365 - bond_coeff @bond:47-58 harmonic 367.0 1.08 - bond_coeff @bond:47-65 harmonic 300.0 1.9 - bond_coeff @bond:47-66 harmonic 250.0 2.08 - bond_coeff @bond:47-86 harmonic 385.0 1.46 - bond_coeff @bond:47-91 harmonic 317.0 1.51 - bond_coeff @bond:47-105 harmonic 448.0 1.365 - bond_coeff @bond:47-110 harmonic 700.0 1.305 - bond_coeff @bond:48-48 harmonic 469.0 1.4 - bond_coeff @bond:48-49 harmonic 367.0 1.08 - bond_coeff @bond:48-50 harmonic 427.0 1.433 - bond_coeff @bond:48-53 harmonic 400.0 1.45 - bond_coeff @bond:48-55 harmonic 481.0 1.34 - bond_coeff @bond:48-56 harmonic 483.0 1.339 - bond_coeff @bond:48-57 harmonic 427.0 1.381 - bond_coeff @bond:48-60 harmonic 469.0 1.404 - bond_coeff @bond:48-61 harmonic 414.0 1.391 - bond_coeff @bond:48-64 harmonic 220.0 1.78 - bond_coeff @bond:48-65 harmonic 300.0 1.87 - bond_coeff @bond:48-66 harmonic 250.0 2.08 - bond_coeff @bond:48-79 harmonic 340.0 1.77 - bond_coeff @bond:48-81 harmonic 469.0 1.4 - bond_coeff @bond:48-84 harmonic 546.0 1.367 - bond_coeff @bond:48-86 harmonic 469.0 1.4 - bond_coeff @bond:48-88 harmonic 469.0 1.421 - bond_coeff @bond:48-91 harmonic 317.0 1.49 - bond_coeff @bond:48-101 harmonic 382.0 1.385 - bond_coeff @bond:48-102 harmonic 400.0 1.46 - bond_coeff @bond:48-109 harmonic 427.0 1.433 - bond_coeff @bond:49-59 harmonic 367.0 1.08 - bond_coeff @bond:49-62 harmonic 340.0 1.08 - bond_coeff @bond:49-82 harmonic 367.0 1.08 - bond_coeff @bond:49-83 harmonic 367.0 1.08 - bond_coeff @bond:49-84 harmonic 367.0 1.08 - bond_coeff @bond:49-85 harmonic 367.0 1.08 - bond_coeff @bond:49-87 harmonic 367.0 1.08 - bond_coeff @bond:49-88 harmonic 367.0 1.08 - bond_coeff @bond:50-50 harmonic 385.0 1.46 - bond_coeff @bond:50-56 harmonic 457.0 1.29 - bond_coeff @bond:50-84 harmonic 549.0 1.365 - bond_coeff @bond:50-109 harmonic 385.0 1.46 - bond_coeff @bond:51-105 harmonic 337.0 1.475 - bond_coeff @bond:52-64 harmonic 525.0 1.48 - bond_coeff @bond:53-54 harmonic 434.0 1.01 - bond_coeff @bond:54-55 harmonic 434.0 1.01 - bond_coeff @bond:55-59 harmonic 481.0 1.34 - bond_coeff @bond:55-82 harmonic 481.0 1.34 - bond_coeff @bond:56-56 harmonic 500.0 1.32 - bond_coeff @bond:56-59 harmonic 502.0 1.324 - bond_coeff @bond:56-60 harmonic 461.0 1.354 - bond_coeff @bond:56-82 harmonic 461.0 1.354 - bond_coeff @bond:56-86 harmonic 483.0 1.339 - bond_coeff @bond:56-103 harmonic 550.0 1.21 - bond_coeff @bond:56-109 harmonic 457.0 1.29 - bond_coeff @bond:57-60 harmonic 436.0 1.374 - bond_coeff @bond:57-61 harmonic 400.0 1.349 - bond_coeff @bond:57-62 harmonic 440.0 1.371 - bond_coeff @bond:57-81 harmonic 428.0 1.38 - bond_coeff @bond:57-82 harmonic 477.0 1.343 - bond_coeff @bond:57-84 harmonic 427.0 1.381 - bond_coeff @bond:57-85 harmonic 427.0 1.381 - bond_coeff @bond:57-86 harmonic 385.0 1.44 - bond_coeff @bond:58-83 harmonic 367.0 1.08 - bond_coeff @bond:58-84 harmonic 367.0 1.08 - bond_coeff @bond:59-63 harmonic 367.0 1.08 - bond_coeff @bond:60-60 harmonic 520.0 1.37 - bond_coeff @bond:60-61 harmonic 414.0 1.391 - bond_coeff @bond:60-80 harmonic 388.0 1.459 - bond_coeff @bond:60-81 harmonic 447.0 1.419 - bond_coeff @bond:60-87 harmonic 469.0 1.424 - bond_coeff @bond:60-105 harmonic 436.0 1.374 - bond_coeff @bond:61-61 harmonic 400.0 1.28 - bond_coeff @bond:61-62 harmonic 529.0 1.304 - bond_coeff @bond:61-82 harmonic 488.0 1.335 - bond_coeff @bond:61-83 harmonic 410.0 1.394 - bond_coeff @bond:61-84 harmonic 410.0 1.394 - bond_coeff @bond:61-88 harmonic 410.0 1.32 - bond_coeff @bond:62-63 harmonic 367.0 1.08 - bond_coeff @bond:62-105 harmonic 440.0 1.371 - bond_coeff @bond:63-82 harmonic 367.0 1.08 - bond_coeff @bond:64-108 harmonic 108.0 2.25 - bond_coeff @bond:65-82 harmonic 300.0 1.87 - bond_coeff @bond:65-83 harmonic 300.0 1.87 - bond_coeff @bond:65-84 harmonic 300.0 1.87 - bond_coeff @bond:65-87 harmonic 300.0 1.87 - bond_coeff @bond:65-88 harmonic 300.0 1.87 - bond_coeff @bond:65-108 harmonic 151.0 2.19 - bond_coeff @bond:66-82 harmonic 250.0 2.08 - bond_coeff @bond:66-83 harmonic 250.0 2.08 - bond_coeff @bond:66-84 harmonic 250.0 2.08 - bond_coeff @bond:66-87 harmonic 250.0 2.08 - bond_coeff @bond:66-88 harmonic 250.0 2.08 - bond_coeff @bond:66-108 harmonic 108.0 2.44 - bond_coeff @bond:77-78 harmonic 500.0 1.8 - bond_coeff @bond:80-84 harmonic 546.0 1.352 - bond_coeff @bond:82-86 harmonic 385.0 1.46 - bond_coeff @bond:82-87 harmonic 520.0 1.37 - bond_coeff @bond:83-84 harmonic 520.0 1.37 - bond_coeff @bond:83-86 harmonic 385.0 1.46 - bond_coeff @bond:84-84 harmonic 512.0 1.375 - bond_coeff @bond:84-86 harmonic 385.0 1.46 - bond_coeff @bond:84-87 harmonic 546.0 1.367 - bond_coeff @bond:84-88 harmonic 520.0 1.37 - bond_coeff @bond:85-85 harmonic 520.0 1.37 - bond_coeff @bond:86-86 harmonic 385.0 1.46 - bond_coeff @bond:86-87 harmonic 385.0 1.46 - bond_coeff @bond:86-88 harmonic 385.0 1.46 - bond_coeff @bond:87-87 harmonic 469.0 1.424 - bond_coeff @bond:87-88 harmonic 469.0 1.424 - bond_coeff @bond:89-90 harmonic 490.0 1.335 - bond_coeff @bond:89-91 harmonic 317.0 1.522 - bond_coeff @bond:90-91 harmonic 337.0 1.449 - bond_coeff @bond:91-91 harmonic 260.0 1.52 - bond_coeff @bond:102-103 harmonic 550.0 1.225 - bond_coeff @bond:108-108 harmonic 94.0 2.32 - bond_coeff @bond:109-109 harmonic 549.0 1.345 + bond_coeff @bond:001_002 367.0 1.38 + bond_coeff @bond:001_003 420.0 1.357 + bond_coeff @bond:001_013 367.0 1.36 + bond_coeff @bond:001_019 450.0 1.279 + bond_coeff @bond:001_025 300.0 0.3 + bond_coeff @bond:001_047 420.0 1.34 + bond_coeff @bond:001_048 420.0 1.354 + bond_coeff @bond:001_082 420.0 1.354 + bond_coeff @bond:001_083 420.0 1.354 + bond_coeff @bond:001_084 420.0 1.354 + bond_coeff @bond:001_087 420.0 1.354 + bond_coeff @bond:001_088 420.0 1.354 + bond_coeff @bond:001_108 461.0 1.57 + bond_coeff @bond:002_002 260.0 1.526 + bond_coeff @bond:002_003 317.0 1.522 + bond_coeff @bond:002_005 386.0 1.425 + bond_coeff @bond:002_006 260.0 1.526 + bond_coeff @bond:002_010 260.0 1.526 + bond_coeff @bond:002_011 317.0 1.5 + bond_coeff @bond:002_012 317.0 1.51 + bond_coeff @bond:002_013 260.0 1.526 + bond_coeff @bond:002_014 317.0 1.5 + bond_coeff @bond:002_015 222.0 1.81 + bond_coeff @bond:002_016 222.0 1.81 + bond_coeff @bond:002_020 320.0 1.425 + bond_coeff @bond:002_024 337.0 1.449 + bond_coeff @bond:002_044 382.0 1.448 + bond_coeff @bond:002_048 317.0 1.51 + bond_coeff @bond:002_051 260.0 1.526 + bond_coeff @bond:002_053 367.0 1.471 + bond_coeff @bond:002_055 337.0 1.463 + bond_coeff @bond:002_080 317.0 1.495 + bond_coeff @bond:003_003 350.0 1.51 + bond_coeff @bond:003_004 570.0 1.229 + bond_coeff @bond:003_005 450.0 1.364 + bond_coeff @bond:003_006 317.0 1.522 + bond_coeff @bond:003_010 317.0 1.522 + bond_coeff @bond:003_012 469.0 1.4 + bond_coeff @bond:003_013 317.0 1.522 + bond_coeff @bond:003_019 400.0 1.444 + bond_coeff @bond:003_020 214.0 1.327 + bond_coeff @bond:003_021 300.0 1.79 + bond_coeff @bond:003_024 490.0 1.335 + bond_coeff @bond:003_044 317.0 1.522 + bond_coeff @bond:003_046 340.0 1.09 + bond_coeff @bond:003_047 410.0 1.444 + bond_coeff @bond:003_048 400.0 1.49 + bond_coeff @bond:003_050 385.0 1.46 + bond_coeff @bond:003_052 656.0 1.25 + bond_coeff @bond:003_056 457.0 1.358 + bond_coeff @bond:003_057 418.0 1.388 + bond_coeff @bond:003_060 447.0 1.419 + bond_coeff @bond:003_065 300.0 1.98 + bond_coeff @bond:003_084 400.0 1.49 + bond_coeff @bond:003_086 385.0 1.46 + bond_coeff @bond:003_105 424.0 1.383 + bond_coeff @bond:003_107 490.0 1.335 + bond_coeff @bond:004_025 553.0 0.3 + bond_coeff @bond:004_064 525.0 1.48 + bond_coeff @bond:004_089 570.0 1.229 + bond_coeff @bond:004_110 700.0 1.171 + bond_coeff @bond:005_006 386.0 1.425 + bond_coeff @bond:005_007 553.0 0.945 + bond_coeff @bond:005_010 386.0 1.425 + bond_coeff @bond:005_013 320.0 1.41 + bond_coeff @bond:005_020 250.0 1.47 + bond_coeff @bond:005_024 400.0 1.38 + bond_coeff @bond:005_025 340.0 0.3 + bond_coeff @bond:005_044 320.0 1.45 + bond_coeff @bond:005_047 450.0 1.37 + bond_coeff @bond:005_048 450.0 1.364 + bond_coeff @bond:005_051 320.0 1.38 + bond_coeff @bond:005_064 230.0 1.61 + bond_coeff @bond:005_079 450.0 1.67 + bond_coeff @bond:005_106 94.0 1.8 + bond_coeff @bond:005_108 374.0 1.64 + bond_coeff @bond:006_006 260.0 1.526 + bond_coeff @bond:006_010 260.0 1.526 + bond_coeff @bond:006_011 317.0 1.5 + bond_coeff @bond:006_013 260.0 1.526 + bond_coeff @bond:006_014 317.0 1.5 + bond_coeff @bond:006_015 222.0 1.81 + bond_coeff @bond:006_016 222.0 1.81 + bond_coeff @bond:006_020 320.0 1.425 + bond_coeff @bond:006_024 337.0 1.449 + bond_coeff @bond:006_044 382.0 1.448 + bond_coeff @bond:006_047 317.0 1.51 + bond_coeff @bond:006_051 260.0 1.526 + bond_coeff @bond:006_053 367.0 1.471 + bond_coeff @bond:006_055 337.0 1.463 + bond_coeff @bond:006_079 222.0 1.81 + bond_coeff @bond:006_105 337.0 1.475 + bond_coeff @bond:007_020 553.0 0.945 + bond_coeff @bond:007_025 340.0 0.1 + bond_coeff @bond:009_009 530.0 1.34 + bond_coeff @bond:009_011 530.0 1.34 + bond_coeff @bond:009_014 530.0 1.34 + bond_coeff @bond:010_010 260.0 1.526 + bond_coeff @bond:010_011 317.0 1.5 + bond_coeff @bond:010_014 317.0 1.5 + bond_coeff @bond:010_020 320.0 1.425 + bond_coeff @bond:010_024 337.0 1.449 + bond_coeff @bond:010_044 382.0 1.448 + bond_coeff @bond:010_105 337.0 1.475 + bond_coeff @bond:011_011 530.0 1.34 + bond_coeff @bond:011_013 317.0 1.5 + bond_coeff @bond:011_014 530.0 1.34 + bond_coeff @bond:011_079 222.0 1.76 + bond_coeff @bond:012_012 469.0 1.4 + bond_coeff @bond:012_048 469.0 1.4 + bond_coeff @bond:012_060 469.0 1.4 + bond_coeff @bond:012_081 469.0 1.4 + bond_coeff @bond:013_013 268.0 1.529 + bond_coeff @bond:013_014 317.0 1.5 + bond_coeff @bond:013_015 222.0 1.81 + bond_coeff @bond:013_016 222.0 1.81 + bond_coeff @bond:013_018 390.0 1.43 + bond_coeff @bond:013_019 390.0 1.47 + bond_coeff @bond:013_020 320.0 1.41 + bond_coeff @bond:013_021 245.0 1.781 + bond_coeff @bond:013_022 340.0 1.79 + bond_coeff @bond:013_024 337.0 1.449 + bond_coeff @bond:013_025 340.0 0.3 + bond_coeff @bond:013_044 382.0 1.448 + bond_coeff @bond:013_046 340.0 1.09 + bond_coeff @bond:013_047 317.0 1.51 + bond_coeff @bond:013_048 317.0 1.51 + bond_coeff @bond:013_050 317.0 1.51 + bond_coeff @bond:013_051 268.0 1.529 + bond_coeff @bond:013_053 367.0 1.471 + bond_coeff @bond:013_055 337.0 1.463 + bond_coeff @bond:013_056 337.0 1.449 + bond_coeff @bond:013_057 337.0 1.475 + bond_coeff @bond:013_060 317.0 1.51 + bond_coeff @bond:013_064 212.0 1.843 + bond_coeff @bond:013_065 245.0 1.945 + bond_coeff @bond:013_066 200.0 2.19 + bond_coeff @bond:013_079 340.0 1.77 + bond_coeff @bond:013_080 317.0 1.495 + bond_coeff @bond:013_083 317.0 1.504 + bond_coeff @bond:013_084 317.0 1.504 + bond_coeff @bond:013_085 317.0 1.504 + bond_coeff @bond:013_087 317.0 1.495 + bond_coeff @bond:013_090 337.0 1.449 + bond_coeff @bond:013_091 280.0 1.51 + bond_coeff @bond:013_095 532.8 1.46 + bond_coeff @bond:013_101 382.0 1.448 + bond_coeff @bond:013_102 375.0 1.49 + bond_coeff @bond:013_104 212.0 1.82 + bond_coeff @bond:013_105 337.0 1.475 + bond_coeff @bond:013_107 337.0 1.449 + bond_coeff @bond:013_108 187.0 1.86 + bond_coeff @bond:013_109 317.0 1.51 + bond_coeff @bond:014_014 530.0 1.34 + bond_coeff @bond:015_017 274.0 1.336 + bond_coeff @bond:015_048 250.0 1.74 + bond_coeff @bond:016_016 166.0 2.038 + bond_coeff @bond:016_019 300.0 1.685 + bond_coeff @bond:016_024 250.0 1.73 + bond_coeff @bond:016_025 340.0 0.5 + bond_coeff @bond:016_047 250.0 1.76 + bond_coeff @bond:016_048 250.0 1.76 + bond_coeff @bond:016_061 250.0 1.73 + bond_coeff @bond:016_082 250.0 1.76 + bond_coeff @bond:016_084 250.0 1.74 + bond_coeff @bond:016_091 222.0 1.81 + bond_coeff @bond:016_108 144.0 2.15 + bond_coeff @bond:017_025 340.0 0.1 + bond_coeff @bond:018_018 550.0 1.12 + bond_coeff @bond:018_019 650.0 1.157 + bond_coeff @bond:018_048 400.0 1.41 + bond_coeff @bond:018_056 550.0 1.24 + bond_coeff @bond:019_019 1150.0 1.21 + bond_coeff @bond:019_021 330.0 1.637 + bond_coeff @bond:019_046 420.0 1.08 + bond_coeff @bond:019_047 400.0 1.426 + bond_coeff @bond:019_048 400.0 1.451 + bond_coeff @bond:019_050 400.0 1.426 + bond_coeff @bond:019_065 330.0 1.784 + bond_coeff @bond:019_088 400.0 1.451 + bond_coeff @bond:019_091 400.0 1.451 + bond_coeff @bond:020_020 250.0 1.47 + bond_coeff @bond:020_021 200.0 1.69 + bond_coeff @bond:020_024 320.0 1.45 + bond_coeff @bond:020_025 340.0 0.3 + bond_coeff @bond:020_044 320.0 1.45 + bond_coeff @bond:020_047 450.0 1.37 + bond_coeff @bond:020_048 450.0 1.364 + bond_coeff @bond:020_051 320.0 1.38 + bond_coeff @bond:020_060 340.0 1.36 + bond_coeff @bond:020_061 462.0 1.399 + bond_coeff @bond:020_064 230.0 1.61 + bond_coeff @bond:020_082 462.0 1.357 + bond_coeff @bond:020_084 340.0 1.36 + bond_coeff @bond:020_108 374.0 1.64 + bond_coeff @bond:021_025 300.0 0.3 + bond_coeff @bond:021_047 300.0 1.725 + bond_coeff @bond:021_048 300.0 1.725 + bond_coeff @bond:021_082 300.0 1.725 + bond_coeff @bond:021_083 300.0 1.725 + bond_coeff @bond:021_084 300.0 1.725 + bond_coeff @bond:021_087 300.0 1.725 + bond_coeff @bond:021_088 300.0 1.725 + bond_coeff @bond:021_108 223.0 2.02 + bond_coeff @bond:022_023 700.0 1.53 + bond_coeff @bond:022_025 340.0 0.5 + bond_coeff @bond:023_025 340.0 0.3 + bond_coeff @bond:023_079 700.0 1.44 + bond_coeff @bond:024_025 367.0 0.3 + bond_coeff @bond:024_045 434.0 1.01 + bond_coeff @bond:024_048 427.0 1.381 + bond_coeff @bond:024_059 427.0 1.381 + bond_coeff @bond:024_079 434.0 1.67 + bond_coeff @bond:024_084 427.0 1.381 + bond_coeff @bond:024_088 427.0 1.381 + bond_coeff @bond:024_091 337.0 1.449 + bond_coeff @bond:024_103 500.0 1.27 + bond_coeff @bond:024_106 40.0 2.05 + bond_coeff @bond:025_025 340.0 0.3 + bond_coeff @bond:025_044 340.0 0.3 + bond_coeff @bond:025_045 340.0 0.1 + bond_coeff @bond:025_046 340.0 0.3 + bond_coeff @bond:025_047 340.0 0.3 + bond_coeff @bond:025_048 367.0 0.3 + bond_coeff @bond:025_049 340.0 0.3 + bond_coeff @bond:025_053 340.0 0.3 + bond_coeff @bond:025_056 367.0 0.3 + bond_coeff @bond:025_061 367.0 0.3 + bond_coeff @bond:025_065 300.0 0.3 + bond_coeff @bond:025_103 340.0 0.1 + bond_coeff @bond:031_032 600.0 0.9572 + bond_coeff @bond:031_033 900.0 0.15 + bond_coeff @bond:031_106 40.0 2.05 + bond_coeff @bond:034_035 529.6 0.9572 + bond_coeff @bond:036_037 600.0 0.9572 + bond_coeff @bond:036_038 900.0 0.175 + bond_coeff @bond:039_040 600.0 0.9572 + bond_coeff @bond:039_041 900.0 0.7 + bond_coeff @bond:042_043 600.0 1.0 + bond_coeff @bond:044_044 350.0 1.445 + bond_coeff @bond:044_045 434.0 1.01 + bond_coeff @bond:044_048 481.0 1.34 + bond_coeff @bond:044_079 340.0 1.77 + bond_coeff @bond:044_091 382.0 1.448 + bond_coeff @bond:044_108 266.0 1.74 + bond_coeff @bond:045_053 434.0 1.01 + bond_coeff @bond:045_055 434.0 1.01 + bond_coeff @bond:045_056 434.0 1.01 + bond_coeff @bond:045_057 434.0 1.01 + bond_coeff @bond:045_101 434.0 1.01 + bond_coeff @bond:045_105 434.0 1.01 + bond_coeff @bond:045_108 166.0 1.48 + bond_coeff @bond:046_047 340.0 1.08 + bond_coeff @bond:046_050 340.0 1.08 + bond_coeff @bond:046_051 340.0 1.09 + bond_coeff @bond:046_080 340.0 1.08 + bond_coeff @bond:046_091 340.0 1.088 + bond_coeff @bond:046_095 532.8 1.084 + bond_coeff @bond:046_108 166.0 1.48 + bond_coeff @bond:046_109 340.0 1.08 + bond_coeff @bond:047_047 549.0 1.34 + bond_coeff @bond:047_048 427.0 1.433 + bond_coeff @bond:047_050 549.0 1.34 + bond_coeff @bond:047_057 448.0 1.365 + bond_coeff @bond:047_058 367.0 1.08 + bond_coeff @bond:047_065 300.0 1.9 + bond_coeff @bond:047_066 250.0 2.08 + bond_coeff @bond:047_086 385.0 1.46 + bond_coeff @bond:047_091 317.0 1.51 + bond_coeff @bond:047_105 448.0 1.365 + bond_coeff @bond:047_110 700.0 1.305 + bond_coeff @bond:048_048 469.0 1.4 + bond_coeff @bond:048_049 367.0 1.08 + bond_coeff @bond:048_050 427.0 1.433 + bond_coeff @bond:048_053 400.0 1.45 + bond_coeff @bond:048_055 481.0 1.34 + bond_coeff @bond:048_056 483.0 1.339 + bond_coeff @bond:048_057 427.0 1.381 + bond_coeff @bond:048_060 469.0 1.404 + bond_coeff @bond:048_061 414.0 1.391 + bond_coeff @bond:048_064 220.0 1.78 + bond_coeff @bond:048_065 300.0 1.87 + bond_coeff @bond:048_066 250.0 2.08 + bond_coeff @bond:048_079 340.0 1.77 + bond_coeff @bond:048_081 469.0 1.4 + bond_coeff @bond:048_084 546.0 1.367 + bond_coeff @bond:048_086 469.0 1.4 + bond_coeff @bond:048_088 469.0 1.421 + bond_coeff @bond:048_091 317.0 1.49 + bond_coeff @bond:048_101 382.0 1.385 + bond_coeff @bond:048_102 400.0 1.46 + bond_coeff @bond:048_109 427.0 1.433 + bond_coeff @bond:049_059 367.0 1.08 + bond_coeff @bond:049_062 340.0 1.08 + bond_coeff @bond:049_082 367.0 1.08 + bond_coeff @bond:049_083 367.0 1.08 + bond_coeff @bond:049_084 367.0 1.08 + bond_coeff @bond:049_085 367.0 1.08 + bond_coeff @bond:049_087 367.0 1.08 + bond_coeff @bond:049_088 367.0 1.08 + bond_coeff @bond:050_050 385.0 1.46 + bond_coeff @bond:050_056 457.0 1.29 + bond_coeff @bond:050_084 549.0 1.365 + bond_coeff @bond:050_109 385.0 1.46 + bond_coeff @bond:051_105 337.0 1.475 + bond_coeff @bond:052_064 525.0 1.48 + bond_coeff @bond:053_054 434.0 1.01 + bond_coeff @bond:054_055 434.0 1.01 + bond_coeff @bond:055_059 481.0 1.34 + bond_coeff @bond:055_082 481.0 1.34 + bond_coeff @bond:056_056 500.0 1.32 + bond_coeff @bond:056_059 502.0 1.324 + bond_coeff @bond:056_060 461.0 1.354 + bond_coeff @bond:056_082 461.0 1.354 + bond_coeff @bond:056_086 483.0 1.339 + bond_coeff @bond:056_103 550.0 1.21 + bond_coeff @bond:056_109 457.0 1.29 + bond_coeff @bond:057_060 436.0 1.374 + bond_coeff @bond:057_061 400.0 1.349 + bond_coeff @bond:057_062 440.0 1.371 + bond_coeff @bond:057_081 428.0 1.38 + bond_coeff @bond:057_082 477.0 1.343 + bond_coeff @bond:057_084 427.0 1.381 + bond_coeff @bond:057_085 427.0 1.381 + bond_coeff @bond:057_086 385.0 1.44 + bond_coeff @bond:058_083 367.0 1.08 + bond_coeff @bond:058_084 367.0 1.08 + bond_coeff @bond:059_063 367.0 1.08 + bond_coeff @bond:060_060 520.0 1.37 + bond_coeff @bond:060_061 414.0 1.391 + bond_coeff @bond:060_080 388.0 1.459 + bond_coeff @bond:060_081 447.0 1.419 + bond_coeff @bond:060_087 469.0 1.424 + bond_coeff @bond:060_105 436.0 1.374 + bond_coeff @bond:061_061 400.0 1.28 + bond_coeff @bond:061_062 529.0 1.304 + bond_coeff @bond:061_082 488.0 1.335 + bond_coeff @bond:061_083 410.0 1.394 + bond_coeff @bond:061_084 410.0 1.394 + bond_coeff @bond:061_088 410.0 1.32 + bond_coeff @bond:062_063 367.0 1.08 + bond_coeff @bond:062_105 440.0 1.371 + bond_coeff @bond:063_082 367.0 1.08 + bond_coeff @bond:064_108 108.0 2.25 + bond_coeff @bond:065_082 300.0 1.87 + bond_coeff @bond:065_083 300.0 1.87 + bond_coeff @bond:065_084 300.0 1.87 + bond_coeff @bond:065_087 300.0 1.87 + bond_coeff @bond:065_088 300.0 1.87 + bond_coeff @bond:065_108 151.0 2.19 + bond_coeff @bond:066_082 250.0 2.08 + bond_coeff @bond:066_083 250.0 2.08 + bond_coeff @bond:066_084 250.0 2.08 + bond_coeff @bond:066_087 250.0 2.08 + bond_coeff @bond:066_088 250.0 2.08 + bond_coeff @bond:066_108 108.0 2.44 + bond_coeff @bond:077_078 500.0 1.8 + bond_coeff @bond:080_084 546.0 1.352 + bond_coeff @bond:082_086 385.0 1.46 + bond_coeff @bond:082_087 520.0 1.37 + bond_coeff @bond:083_084 520.0 1.37 + bond_coeff @bond:083_086 385.0 1.46 + bond_coeff @bond:084_084 512.0 1.375 + bond_coeff @bond:084_086 385.0 1.46 + bond_coeff @bond:084_087 546.0 1.367 + bond_coeff @bond:084_088 520.0 1.37 + bond_coeff @bond:085_085 520.0 1.37 + bond_coeff @bond:086_086 385.0 1.46 + bond_coeff @bond:086_087 385.0 1.46 + bond_coeff @bond:086_088 385.0 1.46 + bond_coeff @bond:087_087 469.0 1.424 + bond_coeff @bond:087_088 469.0 1.424 + bond_coeff @bond:089_090 490.0 1.335 + bond_coeff @bond:089_091 317.0 1.522 + bond_coeff @bond:090_091 337.0 1.449 + bond_coeff @bond:091_091 260.0 1.52 + bond_coeff @bond:102_103 550.0 1.225 + bond_coeff @bond:108_108 94.0 2.32 + bond_coeff @bond:109_109 549.0 1.345 } #(end of bond_coeffs) # Rules for assigning bond types by atom type: @@ -4078,385 +4091,385 @@ OPLSAA { # (* = wildcard) write_once("Data Bonds By Type") { - @bond:1-2 @atom:*_b1_a*_d*_i* @atom:*_b2_a*_d*_i* - @bond:1-3 @atom:*_b1_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:1-13 @atom:*_b1_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:1-19 @atom:*_b1_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:1-25 @atom:*_b1_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:1-47 @atom:*_b1_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:1-48 @atom:*_b1_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:1-82 @atom:*_b1_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:1-83 @atom:*_b1_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:1-84 @atom:*_b1_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:1-87 @atom:*_b1_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:1-88 @atom:*_b1_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:1-108 @atom:*_b1_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:2-2 @atom:*_b2_a*_d*_i* @atom:*_b2_a*_d*_i* - @bond:2-3 @atom:*_b2_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:2-5 @atom:*_b2_a*_d*_i* @atom:*_b5_a*_d*_i* - @bond:2-6 @atom:*_b2_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:2-10 @atom:*_b2_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:2-11 @atom:*_b2_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:2-12 @atom:*_b2_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:2-13 @atom:*_b2_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:2-14 @atom:*_b2_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:2-15 @atom:*_b2_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:2-16 @atom:*_b2_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:2-20 @atom:*_b2_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:2-24 @atom:*_b2_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:2-44 @atom:*_b2_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:2-48 @atom:*_b2_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:2-51 @atom:*_b2_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:2-53 @atom:*_b2_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:2-55 @atom:*_b2_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:2-80 @atom:*_b2_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:3-3 @atom:*_b3_a*_d*_i* @atom:*_b3_a*_d*_i* - @bond:3-4 @atom:*_b3_a*_d*_i* @atom:*_b4_a*_d*_i* - @bond:3-5 @atom:*_b3_a*_d*_i* @atom:*_b5_a*_d*_i* - @bond:3-6 @atom:*_b3_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:3-10 @atom:*_b3_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:3-12 @atom:*_b3_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:3-13 @atom:*_b3_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:3-19 @atom:*_b3_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:3-20 @atom:*_b3_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:3-21 @atom:*_b3_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:3-24 @atom:*_b3_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:3-44 @atom:*_b3_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:3-46 @atom:*_b3_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:3-47 @atom:*_b3_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:3-48 @atom:*_b3_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:3-50 @atom:*_b3_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:3-52 @atom:*_b3_a*_d*_i* @atom:*_b52_a*_d*_i* - @bond:3-56 @atom:*_b3_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:3-57 @atom:*_b3_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:3-60 @atom:*_b3_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:3-65 @atom:*_b3_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:3-84 @atom:*_b3_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:3-86 @atom:*_b3_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:3-105 @atom:*_b3_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:3-107 @atom:*_b3_a*_d*_i* @atom:*_b107_a*_d*_i* - @bond:4-25 @atom:*_b4_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:4-64 @atom:*_b4_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:4-89 @atom:*_b4_a*_d*_i* @atom:*_b89_a*_d*_i* - @bond:4-110 @atom:*_b4_a*_d*_i* @atom:*_b110_a*_d*_i* - @bond:5-6 @atom:*_b5_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:5-7 @atom:*_b5_a*_d*_i* @atom:*_b7_a*_d*_i* - @bond:5-10 @atom:*_b5_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:5-13 @atom:*_b5_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:5-20 @atom:*_b5_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:5-24 @atom:*_b5_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:5-25 @atom:*_b5_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:5-44 @atom:*_b5_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:5-47 @atom:*_b5_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:5-48 @atom:*_b5_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:5-51 @atom:*_b5_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:5-64 @atom:*_b5_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:5-79 @atom:*_b5_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:5-106 @atom:*_b5_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:5-108 @atom:*_b5_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:6-6 @atom:*_b6_a*_d*_i* @atom:*_b6_a*_d*_i* - @bond:6-10 @atom:*_b6_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:6-11 @atom:*_b6_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:6-13 @atom:*_b6_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:6-14 @atom:*_b6_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:6-15 @atom:*_b6_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:6-16 @atom:*_b6_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:6-20 @atom:*_b6_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:6-24 @atom:*_b6_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:6-44 @atom:*_b6_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:6-47 @atom:*_b6_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:6-51 @atom:*_b6_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:6-53 @atom:*_b6_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:6-55 @atom:*_b6_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:6-79 @atom:*_b6_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:6-105 @atom:*_b6_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:7-20 @atom:*_b7_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:7-25 @atom:*_b7_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:9-9 @atom:*_b9_a*_d*_i* @atom:*_b9_a*_d*_i* - @bond:9-11 @atom:*_b9_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:9-14 @atom:*_b9_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:10-10 @atom:*_b10_a*_d*_i* @atom:*_b10_a*_d*_i* - @bond:10-11 @atom:*_b10_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:10-14 @atom:*_b10_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:10-20 @atom:*_b10_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:10-24 @atom:*_b10_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:10-44 @atom:*_b10_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:10-105 @atom:*_b10_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:11-11 @atom:*_b11_a*_d*_i* @atom:*_b11_a*_d*_i* - @bond:11-13 @atom:*_b11_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:11-14 @atom:*_b11_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:11-79 @atom:*_b11_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:12-12 @atom:*_b12_a*_d*_i* @atom:*_b12_a*_d*_i* - @bond:12-48 @atom:*_b12_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:12-60 @atom:*_b12_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:12-81 @atom:*_b12_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:13-13 @atom:*_b13_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:13-14 @atom:*_b13_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:13-15 @atom:*_b13_a*_d*_i* @atom:*_b15_a*_d*_i* - @bond:13-16 @atom:*_b13_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:13-18 @atom:*_b13_a*_d*_i* @atom:*_b18_a*_d*_i* - @bond:13-19 @atom:*_b13_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:13-20 @atom:*_b13_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:13-21 @atom:*_b13_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:13-22 @atom:*_b13_a*_d*_i* @atom:*_b22_a*_d*_i* - @bond:13-24 @atom:*_b13_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:13-25 @atom:*_b13_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:13-44 @atom:*_b13_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:13-46 @atom:*_b13_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:13-47 @atom:*_b13_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:13-48 @atom:*_b13_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:13-50 @atom:*_b13_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:13-51 @atom:*_b13_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:13-53 @atom:*_b13_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:13-55 @atom:*_b13_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:13-56 @atom:*_b13_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:13-57 @atom:*_b13_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:13-60 @atom:*_b13_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:13-64 @atom:*_b13_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:13-65 @atom:*_b13_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:13-66 @atom:*_b13_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:13-79 @atom:*_b13_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:13-80 @atom:*_b13_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:13-83 @atom:*_b13_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:13-84 @atom:*_b13_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:13-85 @atom:*_b13_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:13-87 @atom:*_b13_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:13-90 @atom:*_b13_a*_d*_i* @atom:*_b90_a*_d*_i* - @bond:13-91 @atom:*_b13_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:13-95 @atom:*_b13_a*_d*_i* @atom:*_b95_a*_d*_i* - @bond:13-101 @atom:*_b13_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:13-102 @atom:*_b13_a*_d*_i* @atom:*_b102_a*_d*_i* - @bond:13-104 @atom:*_b13_a*_d*_i* @atom:*_b104_a*_d*_i* - @bond:13-105 @atom:*_b13_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:13-107 @atom:*_b13_a*_d*_i* @atom:*_b107_a*_d*_i* - @bond:13-108 @atom:*_b13_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:13-109 @atom:*_b13_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:14-14 @atom:*_b14_a*_d*_i* @atom:*_b14_a*_d*_i* - @bond:15-17 @atom:*_b15_a*_d*_i* @atom:*_b17_a*_d*_i* - @bond:15-48 @atom:*_b15_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:16-16 @atom:*_b16_a*_d*_i* @atom:*_b16_a*_d*_i* - @bond:16-19 @atom:*_b16_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:16-24 @atom:*_b16_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:16-25 @atom:*_b16_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:16-47 @atom:*_b16_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:16-48 @atom:*_b16_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:16-61 @atom:*_b16_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:16-82 @atom:*_b16_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:16-84 @atom:*_b16_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:16-91 @atom:*_b16_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:16-108 @atom:*_b16_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:17-25 @atom:*_b17_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:18-18 @atom:*_b18_a*_d*_i* @atom:*_b18_a*_d*_i* - @bond:18-19 @atom:*_b18_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:18-48 @atom:*_b18_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:18-56 @atom:*_b18_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:19-19 @atom:*_b19_a*_d*_i* @atom:*_b19_a*_d*_i* - @bond:19-21 @atom:*_b19_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:19-46 @atom:*_b19_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:19-47 @atom:*_b19_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:19-48 @atom:*_b19_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:19-50 @atom:*_b19_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:19-65 @atom:*_b19_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:19-88 @atom:*_b19_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:19-91 @atom:*_b19_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:20-20 @atom:*_b20_a*_d*_i* @atom:*_b20_a*_d*_i* - @bond:20-21 @atom:*_b20_a*_d*_i* @atom:*_b21_a*_d*_i* - @bond:20-24 @atom:*_b20_a*_d*_i* @atom:*_b24_a*_d*_i* - @bond:20-25 @atom:*_b20_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:20-44 @atom:*_b20_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:20-47 @atom:*_b20_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:20-48 @atom:*_b20_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:20-51 @atom:*_b20_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:20-60 @atom:*_b20_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:20-61 @atom:*_b20_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:20-64 @atom:*_b20_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:20-82 @atom:*_b20_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:20-84 @atom:*_b20_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:20-108 @atom:*_b20_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:21-25 @atom:*_b21_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:21-47 @atom:*_b21_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:21-48 @atom:*_b21_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:21-82 @atom:*_b21_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:21-83 @atom:*_b21_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:21-84 @atom:*_b21_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:21-87 @atom:*_b21_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:21-88 @atom:*_b21_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:21-108 @atom:*_b21_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:22-23 @atom:*_b22_a*_d*_i* @atom:*_b23_a*_d*_i* - @bond:22-25 @atom:*_b22_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:23-25 @atom:*_b23_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:23-79 @atom:*_b23_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:24-25 @atom:*_b24_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:24-45 @atom:*_b24_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:24-48 @atom:*_b24_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:24-59 @atom:*_b24_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:24-79 @atom:*_b24_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:24-84 @atom:*_b24_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:24-88 @atom:*_b24_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:24-91 @atom:*_b24_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:24-103 @atom:*_b24_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:24-106 @atom:*_b24_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:25-25 @atom:*_b25_a*_d*_i* @atom:*_b25_a*_d*_i* - @bond:25-44 @atom:*_b25_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:25-45 @atom:*_b25_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:25-46 @atom:*_b25_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:25-47 @atom:*_b25_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:25-48 @atom:*_b25_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:25-49 @atom:*_b25_a*_d*_i* @atom:*_b49_a*_d*_i* - @bond:25-53 @atom:*_b25_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:25-56 @atom:*_b25_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:25-61 @atom:*_b25_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:25-65 @atom:*_b25_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:25-103 @atom:*_b25_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:31-32 @atom:*_b31_a*_d*_i* @atom:*_b32_a*_d*_i* - @bond:31-33 @atom:*_b31_a*_d*_i* @atom:*_b33_a*_d*_i* - @bond:31-106 @atom:*_b31_a*_d*_i* @atom:*_b106_a*_d*_i* - @bond:34-35 @atom:*_b34_a*_d*_i* @atom:*_b35_a*_d*_i* - @bond:36-37 @atom:*_b36_a*_d*_i* @atom:*_b37_a*_d*_i* - @bond:36-38 @atom:*_b36_a*_d*_i* @atom:*_b38_a*_d*_i* - @bond:39-40 @atom:*_b39_a*_d*_i* @atom:*_b40_a*_d*_i* - @bond:39-41 @atom:*_b39_a*_d*_i* @atom:*_b41_a*_d*_i* - @bond:42-43 @atom:*_b42_a*_d*_i* @atom:*_b43_a*_d*_i* - @bond:44-44 @atom:*_b44_a*_d*_i* @atom:*_b44_a*_d*_i* - @bond:44-45 @atom:*_b44_a*_d*_i* @atom:*_b45_a*_d*_i* - @bond:44-48 @atom:*_b44_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:44-79 @atom:*_b44_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:44-91 @atom:*_b44_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:44-108 @atom:*_b44_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:45-53 @atom:*_b45_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:45-55 @atom:*_b45_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:45-56 @atom:*_b45_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:45-57 @atom:*_b45_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:45-101 @atom:*_b45_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:45-105 @atom:*_b45_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:45-108 @atom:*_b45_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:46-47 @atom:*_b46_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:46-50 @atom:*_b46_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:46-51 @atom:*_b46_a*_d*_i* @atom:*_b51_a*_d*_i* - @bond:46-80 @atom:*_b46_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:46-91 @atom:*_b46_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:46-95 @atom:*_b46_a*_d*_i* @atom:*_b95_a*_d*_i* - @bond:46-108 @atom:*_b46_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:46-109 @atom:*_b46_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:47-47 @atom:*_b47_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:47-48 @atom:*_b47_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:47-50 @atom:*_b47_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:47-57 @atom:*_b47_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:47-58 @atom:*_b47_a*_d*_i* @atom:*_b58_a*_d*_i* - @bond:47-65 @atom:*_b47_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:47-66 @atom:*_b47_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:47-86 @atom:*_b47_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:47-91 @atom:*_b47_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:47-105 @atom:*_b47_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:47-110 @atom:*_b47_a*_d*_i* @atom:*_b110_a*_d*_i* - @bond:48-48 @atom:*_b48_a*_d*_i* @atom:*_b48_a*_d*_i* - @bond:48-49 @atom:*_b48_a*_d*_i* @atom:*_b49_a*_d*_i* - @bond:48-50 @atom:*_b48_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:48-53 @atom:*_b48_a*_d*_i* @atom:*_b53_a*_d*_i* - @bond:48-55 @atom:*_b48_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:48-56 @atom:*_b48_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:48-57 @atom:*_b48_a*_d*_i* @atom:*_b57_a*_d*_i* - @bond:48-60 @atom:*_b48_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:48-61 @atom:*_b48_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:48-64 @atom:*_b48_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:48-65 @atom:*_b48_a*_d*_i* @atom:*_b65_a*_d*_i* - @bond:48-66 @atom:*_b48_a*_d*_i* @atom:*_b66_a*_d*_i* - @bond:48-79 @atom:*_b48_a*_d*_i* @atom:*_b79_a*_d*_i* - @bond:48-81 @atom:*_b48_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:48-84 @atom:*_b48_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:48-86 @atom:*_b48_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:48-88 @atom:*_b48_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:48-91 @atom:*_b48_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:48-101 @atom:*_b48_a*_d*_i* @atom:*_b101_a*_d*_i* - @bond:48-102 @atom:*_b48_a*_d*_i* @atom:*_b102_a*_d*_i* - @bond:48-109 @atom:*_b48_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:49-59 @atom:*_b49_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:49-62 @atom:*_b49_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:49-82 @atom:*_b49_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:49-83 @atom:*_b49_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:49-84 @atom:*_b49_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:49-85 @atom:*_b49_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:49-87 @atom:*_b49_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:49-88 @atom:*_b49_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:50-50 @atom:*_b50_a*_d*_i* @atom:*_b50_a*_d*_i* - @bond:50-56 @atom:*_b50_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:50-84 @atom:*_b50_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:50-109 @atom:*_b50_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:51-105 @atom:*_b51_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:52-64 @atom:*_b52_a*_d*_i* @atom:*_b64_a*_d*_i* - @bond:53-54 @atom:*_b53_a*_d*_i* @atom:*_b54_a*_d*_i* - @bond:54-55 @atom:*_b54_a*_d*_i* @atom:*_b55_a*_d*_i* - @bond:55-59 @atom:*_b55_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:55-82 @atom:*_b55_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:56-56 @atom:*_b56_a*_d*_i* @atom:*_b56_a*_d*_i* - @bond:56-59 @atom:*_b56_a*_d*_i* @atom:*_b59_a*_d*_i* - @bond:56-60 @atom:*_b56_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:56-82 @atom:*_b56_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:56-86 @atom:*_b56_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:56-103 @atom:*_b56_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:56-109 @atom:*_b56_a*_d*_i* @atom:*_b109_a*_d*_i* - @bond:57-60 @atom:*_b57_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:57-61 @atom:*_b57_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:57-62 @atom:*_b57_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:57-81 @atom:*_b57_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:57-82 @atom:*_b57_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:57-84 @atom:*_b57_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:57-85 @atom:*_b57_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:57-86 @atom:*_b57_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:58-83 @atom:*_b58_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:58-84 @atom:*_b58_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:59-63 @atom:*_b59_a*_d*_i* @atom:*_b63_a*_d*_i* - @bond:60-60 @atom:*_b60_a*_d*_i* @atom:*_b60_a*_d*_i* - @bond:60-61 @atom:*_b60_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:60-80 @atom:*_b60_a*_d*_i* @atom:*_b80_a*_d*_i* - @bond:60-81 @atom:*_b60_a*_d*_i* @atom:*_b81_a*_d*_i* - @bond:60-87 @atom:*_b60_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:60-105 @atom:*_b60_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:61-61 @atom:*_b61_a*_d*_i* @atom:*_b61_a*_d*_i* - @bond:61-62 @atom:*_b61_a*_d*_i* @atom:*_b62_a*_d*_i* - @bond:61-82 @atom:*_b61_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:61-83 @atom:*_b61_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:61-84 @atom:*_b61_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:61-88 @atom:*_b61_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:62-63 @atom:*_b62_a*_d*_i* @atom:*_b63_a*_d*_i* - @bond:62-105 @atom:*_b62_a*_d*_i* @atom:*_b105_a*_d*_i* - @bond:63-82 @atom:*_b63_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:64-108 @atom:*_b64_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:65-82 @atom:*_b65_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:65-83 @atom:*_b65_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:65-84 @atom:*_b65_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:65-87 @atom:*_b65_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:65-88 @atom:*_b65_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:65-108 @atom:*_b65_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:66-82 @atom:*_b66_a*_d*_i* @atom:*_b82_a*_d*_i* - @bond:66-83 @atom:*_b66_a*_d*_i* @atom:*_b83_a*_d*_i* - @bond:66-84 @atom:*_b66_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:66-87 @atom:*_b66_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:66-88 @atom:*_b66_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:66-108 @atom:*_b66_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:77-78 @atom:*_b77_a*_d*_i* @atom:*_b78_a*_d*_i* - @bond:80-84 @atom:*_b80_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:82-86 @atom:*_b82_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:82-87 @atom:*_b82_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:83-84 @atom:*_b83_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:83-86 @atom:*_b83_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:84-84 @atom:*_b84_a*_d*_i* @atom:*_b84_a*_d*_i* - @bond:84-86 @atom:*_b84_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:84-87 @atom:*_b84_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:84-88 @atom:*_b84_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:85-85 @atom:*_b85_a*_d*_i* @atom:*_b85_a*_d*_i* - @bond:86-86 @atom:*_b86_a*_d*_i* @atom:*_b86_a*_d*_i* - @bond:86-87 @atom:*_b86_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:86-88 @atom:*_b86_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:87-87 @atom:*_b87_a*_d*_i* @atom:*_b87_a*_d*_i* - @bond:87-88 @atom:*_b87_a*_d*_i* @atom:*_b88_a*_d*_i* - @bond:89-90 @atom:*_b89_a*_d*_i* @atom:*_b90_a*_d*_i* - @bond:89-91 @atom:*_b89_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:90-91 @atom:*_b90_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:91-91 @atom:*_b91_a*_d*_i* @atom:*_b91_a*_d*_i* - @bond:102-103 @atom:*_b102_a*_d*_i* @atom:*_b103_a*_d*_i* - @bond:108-108 @atom:*_b108_a*_d*_i* @atom:*_b108_a*_d*_i* - @bond:109-109 @atom:*_b109_a*_d*_i* @atom:*_b109_a*_d*_i* + @bond:001_002 @atom:*_b001*_a*_d*_i* @atom:*_b002*_a*_d*_i* + @bond:001_003 @atom:*_b001*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:001_013 @atom:*_b001*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:001_019 @atom:*_b001*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:001_025 @atom:*_b001*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:001_047 @atom:*_b001*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:001_048 @atom:*_b001*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:001_082 @atom:*_b001*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:001_083 @atom:*_b001*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:001_084 @atom:*_b001*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:001_087 @atom:*_b001*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:001_088 @atom:*_b001*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:001_108 @atom:*_b001*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:002_002 @atom:*_b002*_a*_d*_i* @atom:*_b002*_a*_d*_i* + @bond:002_003 @atom:*_b002*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:002_005 @atom:*_b002*_a*_d*_i* @atom:*_b005*_a*_d*_i* + @bond:002_006 @atom:*_b002*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:002_010 @atom:*_b002*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:002_011 @atom:*_b002*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:002_012 @atom:*_b002*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:002_013 @atom:*_b002*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:002_014 @atom:*_b002*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:002_015 @atom:*_b002*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:002_016 @atom:*_b002*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:002_020 @atom:*_b002*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:002_024 @atom:*_b002*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:002_044 @atom:*_b002*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:002_048 @atom:*_b002*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:002_051 @atom:*_b002*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:002_053 @atom:*_b002*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:002_055 @atom:*_b002*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:002_080 @atom:*_b002*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:003_003 @atom:*_b003*_a*_d*_i* @atom:*_b003*_a*_d*_i* + @bond:003_004 @atom:*_b003*_a*_d*_i* @atom:*_b004*_a*_d*_i* + @bond:003_005 @atom:*_b003*_a*_d*_i* @atom:*_b005*_a*_d*_i* + @bond:003_006 @atom:*_b003*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:003_010 @atom:*_b003*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:003_012 @atom:*_b003*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:003_013 @atom:*_b003*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:003_019 @atom:*_b003*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:003_020 @atom:*_b003*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:003_021 @atom:*_b003*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:003_024 @atom:*_b003*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:003_044 @atom:*_b003*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:003_046 @atom:*_b003*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:003_047 @atom:*_b003*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:003_048 @atom:*_b003*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:003_050 @atom:*_b003*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:003_052 @atom:*_b003*_a*_d*_i* @atom:*_b052*_a*_d*_i* + @bond:003_056 @atom:*_b003*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:003_057 @atom:*_b003*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:003_060 @atom:*_b003*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:003_065 @atom:*_b003*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:003_084 @atom:*_b003*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:003_086 @atom:*_b003*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:003_105 @atom:*_b003*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:003_107 @atom:*_b003*_a*_d*_i* @atom:*_b107*_a*_d*_i* + @bond:004_025 @atom:*_b004*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:004_064 @atom:*_b004*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:004_089 @atom:*_b004*_a*_d*_i* @atom:*_b089*_a*_d*_i* + @bond:004_110 @atom:*_b004*_a*_d*_i* @atom:*_b110*_a*_d*_i* + @bond:005_006 @atom:*_b005*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:005_007 @atom:*_b005*_a*_d*_i* @atom:*_b007*_a*_d*_i* + @bond:005_010 @atom:*_b005*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:005_013 @atom:*_b005*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:005_020 @atom:*_b005*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:005_024 @atom:*_b005*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:005_025 @atom:*_b005*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:005_044 @atom:*_b005*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:005_047 @atom:*_b005*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:005_048 @atom:*_b005*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:005_051 @atom:*_b005*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:005_064 @atom:*_b005*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:005_079 @atom:*_b005*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:005_106 @atom:*_b005*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:005_108 @atom:*_b005*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:006_006 @atom:*_b006*_a*_d*_i* @atom:*_b006*_a*_d*_i* + @bond:006_010 @atom:*_b006*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:006_011 @atom:*_b006*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:006_013 @atom:*_b006*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:006_014 @atom:*_b006*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:006_015 @atom:*_b006*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:006_016 @atom:*_b006*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:006_020 @atom:*_b006*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:006_024 @atom:*_b006*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:006_044 @atom:*_b006*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:006_047 @atom:*_b006*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:006_051 @atom:*_b006*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:006_053 @atom:*_b006*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:006_055 @atom:*_b006*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:006_079 @atom:*_b006*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:006_105 @atom:*_b006*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:007_020 @atom:*_b007*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:007_025 @atom:*_b007*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:009_009 @atom:*_b009*_a*_d*_i* @atom:*_b009*_a*_d*_i* + @bond:009_011 @atom:*_b009*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:009_014 @atom:*_b009*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:010_010 @atom:*_b010*_a*_d*_i* @atom:*_b010*_a*_d*_i* + @bond:010_011 @atom:*_b010*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:010_014 @atom:*_b010*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:010_020 @atom:*_b010*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:010_024 @atom:*_b010*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:010_044 @atom:*_b010*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:010_105 @atom:*_b010*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:011_011 @atom:*_b011*_a*_d*_i* @atom:*_b011*_a*_d*_i* + @bond:011_013 @atom:*_b011*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:011_014 @atom:*_b011*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:011_079 @atom:*_b011*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:012_012 @atom:*_b012*_a*_d*_i* @atom:*_b012*_a*_d*_i* + @bond:012_048 @atom:*_b012*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:012_060 @atom:*_b012*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:012_081 @atom:*_b012*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:013_013 @atom:*_b013*_a*_d*_i* @atom:*_b013*_a*_d*_i* + @bond:013_014 @atom:*_b013*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:013_015 @atom:*_b013*_a*_d*_i* @atom:*_b015*_a*_d*_i* + @bond:013_016 @atom:*_b013*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:013_018 @atom:*_b013*_a*_d*_i* @atom:*_b018*_a*_d*_i* + @bond:013_019 @atom:*_b013*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:013_020 @atom:*_b013*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:013_021 @atom:*_b013*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:013_022 @atom:*_b013*_a*_d*_i* @atom:*_b022*_a*_d*_i* + @bond:013_024 @atom:*_b013*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:013_025 @atom:*_b013*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:013_044 @atom:*_b013*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:013_046 @atom:*_b013*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:013_047 @atom:*_b013*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:013_048 @atom:*_b013*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:013_050 @atom:*_b013*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:013_051 @atom:*_b013*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:013_053 @atom:*_b013*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:013_055 @atom:*_b013*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:013_056 @atom:*_b013*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:013_057 @atom:*_b013*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:013_060 @atom:*_b013*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:013_064 @atom:*_b013*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:013_065 @atom:*_b013*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:013_066 @atom:*_b013*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:013_079 @atom:*_b013*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:013_080 @atom:*_b013*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:013_083 @atom:*_b013*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:013_084 @atom:*_b013*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:013_085 @atom:*_b013*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:013_087 @atom:*_b013*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:013_090 @atom:*_b013*_a*_d*_i* @atom:*_b090*_a*_d*_i* + @bond:013_091 @atom:*_b013*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:013_095 @atom:*_b013*_a*_d*_i* @atom:*_b095*_a*_d*_i* + @bond:013_101 @atom:*_b013*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:013_102 @atom:*_b013*_a*_d*_i* @atom:*_b102*_a*_d*_i* + @bond:013_104 @atom:*_b013*_a*_d*_i* @atom:*_b104*_a*_d*_i* + @bond:013_105 @atom:*_b013*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:013_107 @atom:*_b013*_a*_d*_i* @atom:*_b107*_a*_d*_i* + @bond:013_108 @atom:*_b013*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:013_109 @atom:*_b013*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:014_014 @atom:*_b014*_a*_d*_i* @atom:*_b014*_a*_d*_i* + @bond:015_017 @atom:*_b015*_a*_d*_i* @atom:*_b017*_a*_d*_i* + @bond:015_048 @atom:*_b015*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:016_016 @atom:*_b016*_a*_d*_i* @atom:*_b016*_a*_d*_i* + @bond:016_019 @atom:*_b016*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:016_024 @atom:*_b016*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:016_025 @atom:*_b016*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:016_047 @atom:*_b016*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:016_048 @atom:*_b016*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:016_061 @atom:*_b016*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:016_082 @atom:*_b016*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:016_084 @atom:*_b016*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:016_091 @atom:*_b016*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:016_108 @atom:*_b016*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:017_025 @atom:*_b017*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:018_018 @atom:*_b018*_a*_d*_i* @atom:*_b018*_a*_d*_i* + @bond:018_019 @atom:*_b018*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:018_048 @atom:*_b018*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:018_056 @atom:*_b018*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:019_019 @atom:*_b019*_a*_d*_i* @atom:*_b019*_a*_d*_i* + @bond:019_021 @atom:*_b019*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:019_046 @atom:*_b019*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:019_047 @atom:*_b019*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:019_048 @atom:*_b019*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:019_050 @atom:*_b019*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:019_065 @atom:*_b019*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:019_088 @atom:*_b019*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:019_091 @atom:*_b019*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:020_020 @atom:*_b020*_a*_d*_i* @atom:*_b020*_a*_d*_i* + @bond:020_021 @atom:*_b020*_a*_d*_i* @atom:*_b021*_a*_d*_i* + @bond:020_024 @atom:*_b020*_a*_d*_i* @atom:*_b024*_a*_d*_i* + @bond:020_025 @atom:*_b020*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:020_044 @atom:*_b020*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:020_047 @atom:*_b020*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:020_048 @atom:*_b020*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:020_051 @atom:*_b020*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:020_060 @atom:*_b020*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:020_061 @atom:*_b020*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:020_064 @atom:*_b020*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:020_082 @atom:*_b020*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:020_084 @atom:*_b020*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:020_108 @atom:*_b020*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:021_025 @atom:*_b021*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:021_047 @atom:*_b021*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:021_048 @atom:*_b021*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:021_082 @atom:*_b021*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:021_083 @atom:*_b021*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:021_084 @atom:*_b021*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:021_087 @atom:*_b021*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:021_088 @atom:*_b021*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:021_108 @atom:*_b021*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:022_023 @atom:*_b022*_a*_d*_i* @atom:*_b023*_a*_d*_i* + @bond:022_025 @atom:*_b022*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:023_025 @atom:*_b023*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:023_079 @atom:*_b023*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:024_025 @atom:*_b024*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:024_045 @atom:*_b024*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:024_048 @atom:*_b024*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:024_059 @atom:*_b024*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:024_079 @atom:*_b024*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:024_084 @atom:*_b024*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:024_088 @atom:*_b024*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:024_091 @atom:*_b024*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:024_103 @atom:*_b024*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:024_106 @atom:*_b024*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:025_025 @atom:*_b025*_a*_d*_i* @atom:*_b025*_a*_d*_i* + @bond:025_044 @atom:*_b025*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:025_045 @atom:*_b025*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:025_046 @atom:*_b025*_a*_d*_i* @atom:*_b046*_a*_d*_i* + @bond:025_047 @atom:*_b025*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:025_048 @atom:*_b025*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:025_049 @atom:*_b025*_a*_d*_i* @atom:*_b049*_a*_d*_i* + @bond:025_053 @atom:*_b025*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:025_056 @atom:*_b025*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:025_061 @atom:*_b025*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:025_065 @atom:*_b025*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:025_103 @atom:*_b025*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:031_032 @atom:*_b031*_a*_d*_i* @atom:*_b032*_a*_d*_i* + @bond:031_033 @atom:*_b031*_a*_d*_i* @atom:*_b033*_a*_d*_i* + @bond:031_106 @atom:*_b031*_a*_d*_i* @atom:*_b106*_a*_d*_i* + @bond:034_035 @atom:*_b034*_a*_d*_i* @atom:*_b035*_a*_d*_i* + @bond:036_037 @atom:*_b036*_a*_d*_i* @atom:*_b037*_a*_d*_i* + @bond:036_038 @atom:*_b036*_a*_d*_i* @atom:*_b038*_a*_d*_i* + @bond:039_040 @atom:*_b039*_a*_d*_i* @atom:*_b040*_a*_d*_i* + @bond:039_041 @atom:*_b039*_a*_d*_i* @atom:*_b041*_a*_d*_i* + @bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i* + @bond:044_044 @atom:*_b044*_a*_d*_i* @atom:*_b044*_a*_d*_i* + @bond:044_045 @atom:*_b044*_a*_d*_i* @atom:*_b045*_a*_d*_i* + @bond:044_048 @atom:*_b044*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:044_079 @atom:*_b044*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:044_091 @atom:*_b044*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:044_108 @atom:*_b044*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:045_053 @atom:*_b045*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:045_055 @atom:*_b045*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:045_056 @atom:*_b045*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:045_057 @atom:*_b045*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:045_101 @atom:*_b045*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:045_105 @atom:*_b045*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:045_108 @atom:*_b045*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:046_047 @atom:*_b046*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:046_050 @atom:*_b046*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:046_051 @atom:*_b046*_a*_d*_i* @atom:*_b051*_a*_d*_i* + @bond:046_080 @atom:*_b046*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:046_091 @atom:*_b046*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:046_095 @atom:*_b046*_a*_d*_i* @atom:*_b095*_a*_d*_i* + @bond:046_108 @atom:*_b046*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:046_109 @atom:*_b046*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:047_047 @atom:*_b047*_a*_d*_i* @atom:*_b047*_a*_d*_i* + @bond:047_048 @atom:*_b047*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:047_050 @atom:*_b047*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:047_057 @atom:*_b047*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:047_058 @atom:*_b047*_a*_d*_i* @atom:*_b058*_a*_d*_i* + @bond:047_065 @atom:*_b047*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:047_066 @atom:*_b047*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:047_086 @atom:*_b047*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:047_091 @atom:*_b047*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:047_105 @atom:*_b047*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:047_110 @atom:*_b047*_a*_d*_i* @atom:*_b110*_a*_d*_i* + @bond:048_048 @atom:*_b048*_a*_d*_i* @atom:*_b048*_a*_d*_i* + @bond:048_049 @atom:*_b048*_a*_d*_i* @atom:*_b049*_a*_d*_i* + @bond:048_050 @atom:*_b048*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:048_053 @atom:*_b048*_a*_d*_i* @atom:*_b053*_a*_d*_i* + @bond:048_055 @atom:*_b048*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:048_056 @atom:*_b048*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:048_057 @atom:*_b048*_a*_d*_i* @atom:*_b057*_a*_d*_i* + @bond:048_060 @atom:*_b048*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:048_061 @atom:*_b048*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:048_064 @atom:*_b048*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:048_065 @atom:*_b048*_a*_d*_i* @atom:*_b065*_a*_d*_i* + @bond:048_066 @atom:*_b048*_a*_d*_i* @atom:*_b066*_a*_d*_i* + @bond:048_079 @atom:*_b048*_a*_d*_i* @atom:*_b079*_a*_d*_i* + @bond:048_081 @atom:*_b048*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:048_084 @atom:*_b048*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:048_086 @atom:*_b048*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:048_088 @atom:*_b048*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:048_091 @atom:*_b048*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:048_101 @atom:*_b048*_a*_d*_i* @atom:*_b101*_a*_d*_i* + @bond:048_102 @atom:*_b048*_a*_d*_i* @atom:*_b102*_a*_d*_i* + @bond:048_109 @atom:*_b048*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:049_059 @atom:*_b049*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:049_062 @atom:*_b049*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:049_082 @atom:*_b049*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:049_083 @atom:*_b049*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:049_084 @atom:*_b049*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:049_085 @atom:*_b049*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:049_087 @atom:*_b049*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:049_088 @atom:*_b049*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:050_050 @atom:*_b050*_a*_d*_i* @atom:*_b050*_a*_d*_i* + @bond:050_056 @atom:*_b050*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:050_084 @atom:*_b050*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:050_109 @atom:*_b050*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:051_105 @atom:*_b051*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:052_064 @atom:*_b052*_a*_d*_i* @atom:*_b064*_a*_d*_i* + @bond:053_054 @atom:*_b053*_a*_d*_i* @atom:*_b054*_a*_d*_i* + @bond:054_055 @atom:*_b054*_a*_d*_i* @atom:*_b055*_a*_d*_i* + @bond:055_059 @atom:*_b055*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:055_082 @atom:*_b055*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:056_056 @atom:*_b056*_a*_d*_i* @atom:*_b056*_a*_d*_i* + @bond:056_059 @atom:*_b056*_a*_d*_i* @atom:*_b059*_a*_d*_i* + @bond:056_060 @atom:*_b056*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:056_082 @atom:*_b056*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:056_086 @atom:*_b056*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:056_103 @atom:*_b056*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:056_109 @atom:*_b056*_a*_d*_i* @atom:*_b109*_a*_d*_i* + @bond:057_060 @atom:*_b057*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:057_061 @atom:*_b057*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:057_062 @atom:*_b057*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:057_081 @atom:*_b057*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:057_082 @atom:*_b057*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:057_084 @atom:*_b057*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:057_085 @atom:*_b057*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:057_086 @atom:*_b057*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:058_083 @atom:*_b058*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:058_084 @atom:*_b058*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:059_063 @atom:*_b059*_a*_d*_i* @atom:*_b063*_a*_d*_i* + @bond:060_060 @atom:*_b060*_a*_d*_i* @atom:*_b060*_a*_d*_i* + @bond:060_061 @atom:*_b060*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:060_080 @atom:*_b060*_a*_d*_i* @atom:*_b080*_a*_d*_i* + @bond:060_081 @atom:*_b060*_a*_d*_i* @atom:*_b081*_a*_d*_i* + @bond:060_087 @atom:*_b060*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:060_105 @atom:*_b060*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:061_061 @atom:*_b061*_a*_d*_i* @atom:*_b061*_a*_d*_i* + @bond:061_062 @atom:*_b061*_a*_d*_i* @atom:*_b062*_a*_d*_i* + @bond:061_082 @atom:*_b061*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:061_083 @atom:*_b061*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:061_084 @atom:*_b061*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:061_088 @atom:*_b061*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:062_063 @atom:*_b062*_a*_d*_i* @atom:*_b063*_a*_d*_i* + @bond:062_105 @atom:*_b062*_a*_d*_i* @atom:*_b105*_a*_d*_i* + @bond:063_082 @atom:*_b063*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:064_108 @atom:*_b064*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:065_082 @atom:*_b065*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:065_083 @atom:*_b065*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:065_084 @atom:*_b065*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:065_087 @atom:*_b065*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:065_088 @atom:*_b065*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:065_108 @atom:*_b065*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:066_082 @atom:*_b066*_a*_d*_i* @atom:*_b082*_a*_d*_i* + @bond:066_083 @atom:*_b066*_a*_d*_i* @atom:*_b083*_a*_d*_i* + @bond:066_084 @atom:*_b066*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:066_087 @atom:*_b066*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:066_088 @atom:*_b066*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:066_108 @atom:*_b066*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:077_078 @atom:*_b077*_a*_d*_i* @atom:*_b078*_a*_d*_i* + @bond:080_084 @atom:*_b080*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:082_086 @atom:*_b082*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:082_087 @atom:*_b082*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:083_084 @atom:*_b083*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:083_086 @atom:*_b083*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:084_084 @atom:*_b084*_a*_d*_i* @atom:*_b084*_a*_d*_i* + @bond:084_086 @atom:*_b084*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:084_087 @atom:*_b084*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:084_088 @atom:*_b084*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:085_085 @atom:*_b085*_a*_d*_i* @atom:*_b085*_a*_d*_i* + @bond:086_086 @atom:*_b086*_a*_d*_i* @atom:*_b086*_a*_d*_i* + @bond:086_087 @atom:*_b086*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:086_088 @atom:*_b086*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:087_087 @atom:*_b087*_a*_d*_i* @atom:*_b087*_a*_d*_i* + @bond:087_088 @atom:*_b087*_a*_d*_i* @atom:*_b088*_a*_d*_i* + @bond:089_090 @atom:*_b089*_a*_d*_i* @atom:*_b090*_a*_d*_i* + @bond:089_091 @atom:*_b089*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:090_091 @atom:*_b090*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:091_091 @atom:*_b091*_a*_d*_i* @atom:*_b091*_a*_d*_i* + @bond:102_103 @atom:*_b102*_a*_d*_i* @atom:*_b103*_a*_d*_i* + @bond:108_108 @atom:*_b108*_a*_d*_i* @atom:*_b108*_a*_d*_i* + @bond:109_109 @atom:*_b109*_a*_d*_i* @atom:*_b109*_a*_d*_i* } #(end of bonds by type) @@ -4465,1026 +4478,1026 @@ OPLSAA { # ------- Angle Interactions: ------- # http://lammps.sandia.gov/doc/angle_harmonic.html # Syntax: - # angle_coeff AngleTypeName AngleStyle parameters... + # angle_coeff AngleTypeName parameters... write_once("In Settings") { - angle_coeff @angle:25-1-25 harmonic 33.0 109.47 - angle_coeff @angle:1-2-2 harmonic 50.0 109.5 - angle_coeff @angle:2-2-2 harmonic 63.0 112.4 - angle_coeff @angle:2-2-3 harmonic 63.0 112.4 - angle_coeff @angle:2-2-5 harmonic 80.0 109.5 - angle_coeff @angle:2-2-6 harmonic 63.0 112.4 - angle_coeff @angle:6-2-6 harmonic 63.0 112.4 - angle_coeff @angle:5-2-6 harmonic 80.0 109.5 - angle_coeff @angle:2-2-10 harmonic 63.0 112.4 - angle_coeff @angle:3-2-10 harmonic 63.0 112.4 - angle_coeff @angle:6-2-10 harmonic 63.0 112.4 - angle_coeff @angle:10-2-10 harmonic 63.0 112.4 - angle_coeff @angle:5-2-10 harmonic 80.0 109.5 - angle_coeff @angle:10-2-12 harmonic 63.0 114.0 - angle_coeff @angle:6-2-13 harmonic 63.0 112.4 - angle_coeff @angle:10-2-15 harmonic 50.0 108.6 - angle_coeff @angle:2-2-16 harmonic 50.0 114.7 - angle_coeff @angle:10-2-16 harmonic 50.0 114.7 - angle_coeff @angle:2-2-20 harmonic 80.0 109.5 - angle_coeff @angle:6-2-20 harmonic 80.0 109.5 - angle_coeff @angle:10-2-20 harmonic 80.0 109.5 - angle_coeff @angle:3-2-24 harmonic 80.0 110.3 - angle_coeff @angle:2-2-24 harmonic 80.0 111.2 - angle_coeff @angle:2-2-44 harmonic 56.2 109.47 - angle_coeff @angle:6-2-44 harmonic 56.2 109.47 - angle_coeff @angle:10-2-44 harmonic 56.2 109.47 - angle_coeff @angle:13-2-44 harmonic 56.2 109.47 - angle_coeff @angle:3-2-44 harmonic 80.0 111.2 - angle_coeff @angle:2-2-48 harmonic 63.0 112.4 - angle_coeff @angle:10-2-48 harmonic 63.0 114.0 - angle_coeff @angle:2-2-51 harmonic 63.0 112.4 - angle_coeff @angle:6-2-51 harmonic 63.0 112.4 - angle_coeff @angle:2-2-53 harmonic 80.0 111.2 - angle_coeff @angle:2-2-55 harmonic 80.0 111.2 - angle_coeff @angle:10-2-80 harmonic 63.0 115.6 - angle_coeff @angle:2-3-4 harmonic 80.0 120.4 - angle_coeff @angle:1-3-4 harmonic 80.0 121.0 - angle_coeff @angle:3-3-4 harmonic 80.0 121.4 - angle_coeff @angle:4-3-4 harmonic 80.0 126.0 - angle_coeff @angle:4-3-5 harmonic 80.0 121.0 - angle_coeff @angle:4-3-6 harmonic 80.0 120.4 - angle_coeff @angle:5-3-10 harmonic 70.0 115.0 - angle_coeff @angle:4-3-10 harmonic 80.0 120.4 - angle_coeff @angle:5-3-12 harmonic 70.0 120.0 - angle_coeff @angle:12-3-12 harmonic 85.0 120.0 - angle_coeff @angle:5-3-13 harmonic 70.0 108.0 - angle_coeff @angle:13-3-13 harmonic 70.0 116.0 - angle_coeff @angle:1-3-13 harmonic 80.0 111.0 - angle_coeff @angle:3-3-13 harmonic 80.0 117.2 - angle_coeff @angle:4-3-13 harmonic 80.0 120.4 - angle_coeff @angle:10-3-20 harmonic 81.0 111.4 - angle_coeff @angle:13-3-20 harmonic 81.0 111.4 - angle_coeff @angle:4-3-20 harmonic 83.0 123.4 - angle_coeff @angle:13-3-21 harmonic 75.0 109.0 - angle_coeff @angle:4-3-21 harmonic 75.0 119.0 - angle_coeff @angle:24-3-24 harmonic 70.0 114.2 - angle_coeff @angle:2-3-24 harmonic 70.0 116.6 - angle_coeff @angle:3-3-24 harmonic 70.0 116.6 - angle_coeff @angle:6-3-24 harmonic 70.0 116.6 - angle_coeff @angle:10-3-24 harmonic 70.0 116.6 - angle_coeff @angle:13-3-24 harmonic 70.0 116.6 - angle_coeff @angle:4-3-24 harmonic 80.0 122.9 - angle_coeff @angle:20-3-24 harmonic 81.0 111.4 - angle_coeff @angle:13-3-44 harmonic 70.0 116.0 - angle_coeff @angle:4-3-44 harmonic 80.0 120.4 - angle_coeff @angle:13-3-46 harmonic 35.0 115.0 - angle_coeff @angle:46-3-46 harmonic 35.0 115.0 - angle_coeff @angle:4-3-46 harmonic 35.0 123.0 - angle_coeff @angle:24-3-46 harmonic 40.0 114.0 - angle_coeff @angle:5-3-46 harmonic 40.0 115.0 - angle_coeff @angle:20-3-46 harmonic 40.0 115.0 - angle_coeff @angle:24-3-47 harmonic 70.0 115.5 - angle_coeff @angle:4-3-47 harmonic 80.0 125.3 - angle_coeff @angle:46-3-48 harmonic 35.0 115.0 - angle_coeff @angle:24-3-48 harmonic 70.0 115.5 - angle_coeff @angle:13-3-48 harmonic 70.0 116.0 - angle_coeff @angle:5-3-48 harmonic 70.0 120.0 - angle_coeff @angle:4-3-48 harmonic 80.0 120.4 - angle_coeff @angle:20-3-48 harmonic 81.0 111.4 - angle_coeff @angle:48-3-48 harmonic 85.0 120.0 - angle_coeff @angle:13-3-50 harmonic 70.0 116.0 - angle_coeff @angle:46-3-50 harmonic 80.0 116.0 - angle_coeff @angle:4-3-50 harmonic 80.0 124.0 - angle_coeff @angle:10-3-52 harmonic 65.0 117.0 - angle_coeff @angle:2-3-52 harmonic 70.0 117.0 - angle_coeff @angle:6-3-52 harmonic 70.0 117.0 - angle_coeff @angle:13-3-52 harmonic 70.0 117.0 - angle_coeff @angle:48-3-52 harmonic 70.0 117.0 - angle_coeff @angle:4-3-52 harmonic 80.0 126.0 - angle_coeff @angle:52-3-52 harmonic 80.0 126.0 - angle_coeff @angle:46-3-56 harmonic 35.0 122.0 - angle_coeff @angle:4-3-56 harmonic 80.0 122.5 - angle_coeff @angle:47-3-57 harmonic 70.0 114.1 - angle_coeff @angle:56-3-57 harmonic 70.0 118.6 - angle_coeff @angle:57-3-57 harmonic 70.0 118.6 - angle_coeff @angle:4-3-57 harmonic 80.0 120.6 - angle_coeff @angle:24-3-60 harmonic 70.0 111.3 - angle_coeff @angle:57-3-60 harmonic 70.0 111.3 - angle_coeff @angle:4-3-60 harmonic 80.0 128.8 - angle_coeff @angle:13-3-65 harmonic 75.0 109.0 - angle_coeff @angle:4-3-65 harmonic 75.0 119.0 - angle_coeff @angle:44-3-84 harmonic 70.0 116.0 - angle_coeff @angle:4-3-84 harmonic 80.0 120.4 - angle_coeff @angle:4-3-87 harmonic 80.0 128.2 - angle_coeff @angle:57-3-105 harmonic 70.0 115.4 - angle_coeff @angle:56-3-105 harmonic 70.0 118.6 - angle_coeff @angle:4-3-105 harmonic 80.0 120.9 - angle_coeff @angle:13-3-107 harmonic 70.0 116.6 - angle_coeff @angle:4-3-107 harmonic 80.0 122.9 - angle_coeff @angle:25-4-25 harmonic 10.0 117.0 - angle_coeff @angle:3-4-25 harmonic 35.0 113.0 - angle_coeff @angle:3-5-7 harmonic 35.0 113.0 - angle_coeff @angle:2-5-7 harmonic 55.0 108.5 - angle_coeff @angle:6-5-7 harmonic 55.0 108.5 - angle_coeff @angle:7-5-10 harmonic 55.0 108.5 - angle_coeff @angle:7-5-13 harmonic 55.0 108.5 - angle_coeff @angle:7-5-24 harmonic 49.0 105.4 - angle_coeff @angle:25-5-25 harmonic 5.0 109.47 - angle_coeff @angle:7-5-25 harmonic 10.0 109.47 - angle_coeff @angle:13-5-25 harmonic 10.0 109.47 - angle_coeff @angle:7-5-47 harmonic 35.0 109.0 - angle_coeff @angle:25-5-48 harmonic 10.0 109.47 - angle_coeff @angle:7-5-48 harmonic 35.0 113.0 - angle_coeff @angle:7-5-51 harmonic 55.0 108.5 - angle_coeff @angle:7-5-64 harmonic 55.0 108.5 - angle_coeff @angle:13-5-64 harmonic 100.0 120.5 - angle_coeff @angle:7-5-79 harmonic 74.0 110.0 - angle_coeff @angle:7-5-106 harmonic 100.0 126.0 - angle_coeff @angle:5-7-25 harmonic 10.0 109.47 - angle_coeff @angle:25-7-25 harmonic 33.0 109.47 - angle_coeff @angle:2-10-2 harmonic 63.0 112.4 - angle_coeff @angle:2-10-3 harmonic 63.0 111.1 - angle_coeff @angle:2-10-5 harmonic 80.0 109.5 - angle_coeff @angle:3-10-6 harmonic 63.0 111.1 - angle_coeff @angle:6-10-6 harmonic 63.0 111.5 - angle_coeff @angle:2-10-6 harmonic 63.0 112.4 - angle_coeff @angle:5-10-6 harmonic 80.0 109.5 - angle_coeff @angle:3-10-10 harmonic 63.0 111.1 - angle_coeff @angle:2-10-10 harmonic 63.0 111.5 - angle_coeff @angle:6-10-10 harmonic 63.0 111.5 - angle_coeff @angle:10-10-10 harmonic 63.0 111.5 - angle_coeff @angle:5-10-10 harmonic 80.0 109.5 - angle_coeff @angle:2-10-20 harmonic 80.0 109.5 - angle_coeff @angle:6-10-20 harmonic 80.0 109.5 - angle_coeff @angle:10-10-20 harmonic 80.0 109.5 - angle_coeff @angle:3-10-24 harmonic 63.0 110.1 - angle_coeff @angle:6-10-24 harmonic 80.0 109.5 - angle_coeff @angle:2-10-24 harmonic 80.0 109.7 - angle_coeff @angle:10-10-24 harmonic 80.0 109.7 - angle_coeff @angle:2-10-44 harmonic 56.2 109.47 - angle_coeff @angle:6-10-44 harmonic 56.2 109.47 - angle_coeff @angle:10-10-44 harmonic 56.2 109.47 - angle_coeff @angle:13-10-44 harmonic 56.2 109.47 - angle_coeff @angle:3-10-44 harmonic 80.0 109.7 - angle_coeff @angle:2-10-48 harmonic 63.0 112.4 - angle_coeff @angle:20-10-48 harmonic 80.0 109.5 - angle_coeff @angle:2-10-105 harmonic 80.0 109.5 - angle_coeff @angle:10-10-105 harmonic 80.0 109.5 - angle_coeff @angle:20-10-105 harmonic 80.0 109.5 - angle_coeff @angle:2-11-2 harmonic 70.0 124.0 - angle_coeff @angle:2-11-6 harmonic 70.0 124.0 - angle_coeff @angle:6-11-6 harmonic 70.0 124.0 - angle_coeff @angle:2-11-9 harmonic 70.0 118.0 - angle_coeff @angle:6-11-9 harmonic 70.0 118.0 - angle_coeff @angle:9-11-10 harmonic 70.0 118.0 - angle_coeff @angle:2-11-10 harmonic 70.0 124.0 - angle_coeff @angle:6-11-10 harmonic 70.0 124.0 - angle_coeff @angle:10-11-10 harmonic 70.0 124.0 - angle_coeff @angle:2-11-11 harmonic 70.0 118.0 - angle_coeff @angle:6-11-11 harmonic 70.0 118.0 - angle_coeff @angle:9-11-11 harmonic 70.0 118.0 - angle_coeff @angle:10-11-11 harmonic 70.0 118.0 - angle_coeff @angle:11-11-11 harmonic 70.0 118.0 - angle_coeff @angle:9-11-13 harmonic 70.0 118.0 - angle_coeff @angle:11-11-13 harmonic 70.0 118.0 - angle_coeff @angle:2-11-13 harmonic 70.0 124.0 - angle_coeff @angle:6-11-13 harmonic 70.0 124.0 - angle_coeff @angle:10-11-13 harmonic 70.0 124.0 - angle_coeff @angle:13-11-13 harmonic 70.0 124.0 - angle_coeff @angle:9-11-14 harmonic 70.0 118.0 - angle_coeff @angle:11-11-14 harmonic 70.0 118.0 - angle_coeff @angle:9-11-79 harmonic 70.0 118.0 - angle_coeff @angle:2-12-12 harmonic 70.0 120.0 - angle_coeff @angle:3-12-12 harmonic 85.0 120.0 - angle_coeff @angle:12-12-12 harmonic 85.0 120.0 - angle_coeff @angle:12-12-48 harmonic 85.0 120.0 - angle_coeff @angle:12-12-60 harmonic 85.0 120.0 - angle_coeff @angle:12-12-81 harmonic 85.0 120.0 - angle_coeff @angle:1-13-1 harmonic 77.0 109.1 - angle_coeff @angle:2-13-2 harmonic 40.0 109.5 - angle_coeff @angle:1-13-3 harmonic 50.0 109.5 - angle_coeff @angle:2-13-3 harmonic 63.0 111.1 - angle_coeff @angle:3-13-3 harmonic 63.0 111.1 - angle_coeff @angle:2-13-6 harmonic 40.0 109.5 - angle_coeff @angle:6-13-6 harmonic 40.0 109.5 - angle_coeff @angle:3-13-6 harmonic 63.0 109.5 - angle_coeff @angle:1-13-13 harmonic 50.0 109.5 - angle_coeff @angle:5-13-13 harmonic 50.0 109.5 - angle_coeff @angle:13-13-13 harmonic 58.35 112.7 - angle_coeff @angle:3-13-13 harmonic 63.0 111.1 - angle_coeff @angle:13-13-15 harmonic 50.0 108.6 - angle_coeff @angle:13-13-16 harmonic 50.0 114.7 - angle_coeff @angle:13-13-19 harmonic 58.35 112.7 - angle_coeff @angle:3-13-20 harmonic 50.0 109.5 - angle_coeff @angle:13-13-20 harmonic 50.0 109.5 - angle_coeff @angle:3-13-21 harmonic 69.0 109.8 - angle_coeff @angle:13-13-21 harmonic 69.0 109.8 - angle_coeff @angle:21-13-21 harmonic 78.0 111.7 - angle_coeff @angle:13-13-22 harmonic 50.0 108.6 - angle_coeff @angle:20-13-24 harmonic 50.0 109.5 - angle_coeff @angle:3-13-24 harmonic 63.0 110.1 - angle_coeff @angle:2-13-24 harmonic 80.0 109.7 - angle_coeff @angle:13-13-24 harmonic 80.0 109.7 - angle_coeff @angle:16-13-44 harmonic 50.0 114.7 - angle_coeff @angle:2-13-44 harmonic 56.2 109.47 - angle_coeff @angle:6-13-44 harmonic 56.2 109.47 - angle_coeff @angle:10-13-44 harmonic 56.2 109.47 - angle_coeff @angle:13-13-44 harmonic 56.2 109.47 - angle_coeff @angle:3-13-44 harmonic 80.0 111.2 - angle_coeff @angle:46-13-46 harmonic 33.0 107.8 - angle_coeff @angle:18-13-46 harmonic 35.0 108.5 - angle_coeff @angle:19-13-46 harmonic 35.0 108.5 - angle_coeff @angle:2-13-46 harmonic 35.0 109.5 - angle_coeff @angle:3-13-46 harmonic 35.0 109.5 - angle_coeff @angle:5-13-46 harmonic 35.0 109.5 - angle_coeff @angle:15-13-46 harmonic 35.0 109.5 - angle_coeff @angle:16-13-46 harmonic 35.0 109.5 - angle_coeff @angle:20-13-46 harmonic 35.0 109.5 - angle_coeff @angle:22-13-46 harmonic 35.0 109.5 - angle_coeff @angle:24-13-46 harmonic 35.0 109.5 - angle_coeff @angle:44-13-46 harmonic 35.0 109.5 - angle_coeff @angle:13-13-46 harmonic 37.5 110.7 - angle_coeff @angle:1-13-46 harmonic 40.0 107.0 - angle_coeff @angle:21-13-46 harmonic 51.0 107.6 - angle_coeff @angle:46-13-47 harmonic 35.0 109.5 - angle_coeff @angle:1-13-47 harmonic 50.0 109.5 - angle_coeff @angle:13-13-47 harmonic 63.0 111.1 - angle_coeff @angle:47-13-47 harmonic 63.0 112.4 - angle_coeff @angle:46-13-48 harmonic 35.0 109.5 - angle_coeff @angle:47-13-48 harmonic 40.0 109.5 - angle_coeff @angle:48-13-48 harmonic 40.0 109.5 - angle_coeff @angle:1-13-48 harmonic 50.0 109.5 - angle_coeff @angle:5-13-48 harmonic 50.0 109.5 - angle_coeff @angle:20-13-48 harmonic 50.0 109.5 - angle_coeff @angle:16-13-48 harmonic 50.0 114.7 - angle_coeff @angle:3-13-48 harmonic 63.0 112.0 - angle_coeff @angle:2-13-48 harmonic 63.0 114.0 - angle_coeff @angle:13-13-48 harmonic 63.0 114.0 - angle_coeff @angle:44-13-48 harmonic 80.0 111.2 - angle_coeff @angle:46-13-50 harmonic 35.0 109.5 - angle_coeff @angle:46-13-51 harmonic 37.5 110.7 - angle_coeff @angle:5-13-51 harmonic 50.0 109.5 - angle_coeff @angle:13-13-51 harmonic 58.35 112.7 - angle_coeff @angle:46-13-53 harmonic 35.0 109.5 - angle_coeff @angle:3-13-53 harmonic 80.0 111.2 - angle_coeff @angle:13-13-53 harmonic 80.0 111.2 - angle_coeff @angle:46-13-55 harmonic 35.0 109.5 - angle_coeff @angle:13-13-55 harmonic 80.0 111.2 - angle_coeff @angle:46-13-56 harmonic 35.0 109.5 - angle_coeff @angle:3-13-56 harmonic 63.0 110.1 - angle_coeff @angle:13-13-56 harmonic 65.0 109.0 - angle_coeff @angle:46-13-57 harmonic 35.0 109.5 - angle_coeff @angle:48-13-57 harmonic 80.0 111.2 - angle_coeff @angle:46-13-60 harmonic 35.0 109.5 - angle_coeff @angle:13-13-60 harmonic 63.0 114.0 - angle_coeff @angle:46-13-64 harmonic 41.0 109.5 - angle_coeff @angle:13-13-64 harmonic 43.0 109.5 - angle_coeff @angle:48-13-64 harmonic 43.0 109.5 - angle_coeff @angle:46-13-65 harmonic 51.0 107.6 - angle_coeff @angle:3-13-65 harmonic 69.0 109.8 - angle_coeff @angle:13-13-65 harmonic 69.0 110.0 - angle_coeff @angle:48-13-65 harmonic 69.0 110.0 - angle_coeff @angle:65-13-65 harmonic 78.0 111.7 - angle_coeff @angle:46-13-66 harmonic 75.0 111.0 - angle_coeff @angle:13-13-66 harmonic 75.0 112.0 - angle_coeff @angle:46-13-79 harmonic 35.0 109.5 - angle_coeff @angle:13-13-79 harmonic 50.0 108.6 - angle_coeff @angle:1-13-79 harmonic 50.0 109.5 - angle_coeff @angle:46-13-80 harmonic 35.0 109.5 - angle_coeff @angle:13-13-80 harmonic 63.0 115.6 - angle_coeff @angle:46-13-83 harmonic 35.0 109.5 - angle_coeff @angle:13-13-83 harmonic 63.0 114.0 - angle_coeff @angle:46-13-84 harmonic 35.0 109.5 - angle_coeff @angle:16-13-84 harmonic 50.0 114.7 - angle_coeff @angle:13-13-84 harmonic 63.0 114.0 - angle_coeff @angle:46-13-85 harmonic 35.0 109.5 - angle_coeff @angle:13-13-85 harmonic 63.0 114.0 - angle_coeff @angle:46-13-87 harmonic 35.0 109.5 - angle_coeff @angle:13-13-87 harmonic 63.0 115.6 - angle_coeff @angle:46-13-90 harmonic 35.0 109.5 - angle_coeff @angle:13-13-90 harmonic 80.0 110.0 - angle_coeff @angle:3-13-90 harmonic 80.0 113.0 - angle_coeff @angle:46-13-91 harmonic 37.5 110.7 - angle_coeff @angle:46-13-95 harmonic 35.0 105.0 - angle_coeff @angle:13-13-95 harmonic 63.0 105.0 - angle_coeff @angle:46-13-101 harmonic 35.0 109.5 - angle_coeff @angle:13-13-101 harmonic 80.0 111.2 - angle_coeff @angle:46-13-102 harmonic 35.0 105.0 - angle_coeff @angle:13-13-102 harmonic 63.0 111.1 - angle_coeff @angle:46-13-104 harmonic 41.0 109.5 - angle_coeff @angle:13-13-104 harmonic 43.0 109.5 - angle_coeff @angle:46-13-105 harmonic 35.0 109.5 - angle_coeff @angle:13-13-105 harmonic 50.0 109.5 - angle_coeff @angle:20-13-105 harmonic 50.0 109.5 - angle_coeff @angle:46-13-107 harmonic 35.0 109.5 - angle_coeff @angle:13-13-107 harmonic 80.0 109.7 - angle_coeff @angle:46-13-108 harmonic 35.0 109.5 - angle_coeff @angle:13-13-108 harmonic 60.0 112.0 - angle_coeff @angle:2-14-2 harmonic 70.0 124.0 - angle_coeff @angle:2-14-6 harmonic 70.0 124.0 - angle_coeff @angle:6-14-6 harmonic 70.0 124.0 - angle_coeff @angle:2-14-9 harmonic 70.0 118.0 - angle_coeff @angle:6-14-9 harmonic 70.0 118.0 - angle_coeff @angle:9-14-10 harmonic 70.0 118.0 - angle_coeff @angle:2-14-10 harmonic 70.0 124.0 - angle_coeff @angle:6-14-10 harmonic 70.0 124.0 - angle_coeff @angle:10-14-10 harmonic 70.0 124.0 - angle_coeff @angle:2-14-11 harmonic 70.0 118.0 - angle_coeff @angle:6-14-11 harmonic 70.0 118.0 - angle_coeff @angle:9-14-11 harmonic 70.0 118.0 - angle_coeff @angle:10-14-11 harmonic 70.0 118.0 - angle_coeff @angle:11-14-11 harmonic 70.0 118.0 - angle_coeff @angle:9-14-13 harmonic 70.0 118.0 - angle_coeff @angle:11-14-13 harmonic 70.0 118.0 - angle_coeff @angle:2-14-13 harmonic 70.0 124.0 - angle_coeff @angle:6-14-13 harmonic 70.0 124.0 - angle_coeff @angle:10-14-13 harmonic 70.0 124.0 - angle_coeff @angle:13-14-13 harmonic 70.0 124.0 - angle_coeff @angle:2-14-14 harmonic 70.0 118.0 - angle_coeff @angle:6-14-14 harmonic 70.0 118.0 - angle_coeff @angle:9-14-14 harmonic 70.0 118.0 - angle_coeff @angle:10-14-14 harmonic 70.0 118.0 - angle_coeff @angle:11-14-14 harmonic 70.0 118.0 - angle_coeff @angle:13-14-14 harmonic 70.0 118.0 - angle_coeff @angle:14-14-14 harmonic 70.0 118.0 - angle_coeff @angle:17-15-17 harmonic 35.0 92.07 - angle_coeff @angle:2-15-17 harmonic 44.0 96.0 - angle_coeff @angle:6-15-17 harmonic 44.0 96.0 - angle_coeff @angle:13-15-17 harmonic 44.0 96.0 - angle_coeff @angle:25-15-25 harmonic 5.0 109.47 - angle_coeff @angle:13-15-25 harmonic 10.0 109.47 - angle_coeff @angle:33-15-33 harmonic 10.0 160.0 - angle_coeff @angle:2-15-33 harmonic 150.0 96.7 - angle_coeff @angle:6-15-33 harmonic 150.0 96.7 - angle_coeff @angle:13-15-33 harmonic 150.0 96.7 - angle_coeff @angle:17-15-33 harmonic 150.0 96.7 - angle_coeff @angle:17-15-48 harmonic 50.0 96.0 - angle_coeff @angle:2-16-6 harmonic 62.0 98.9 - angle_coeff @angle:13-16-13 harmonic 62.0 98.9 - angle_coeff @angle:2-16-16 harmonic 68.0 103.7 - angle_coeff @angle:6-16-16 harmonic 68.0 103.7 - angle_coeff @angle:13-16-16 harmonic 68.0 103.7 - angle_coeff @angle:13-16-19 harmonic 65.0 100.0 - angle_coeff @angle:25-16-25 harmonic 5.0 109.47 - angle_coeff @angle:13-16-25 harmonic 10.0 109.47 - angle_coeff @angle:33-16-33 harmonic 10.0 160.0 - angle_coeff @angle:2-16-33 harmonic 150.0 96.7 - angle_coeff @angle:6-16-33 harmonic 150.0 96.7 - angle_coeff @angle:13-16-33 harmonic 150.0 96.7 - angle_coeff @angle:16-16-33 harmonic 150.0 96.7 - angle_coeff @angle:13-16-48 harmonic 62.0 104.2 - angle_coeff @angle:47-16-48 harmonic 62.0 104.2 - angle_coeff @angle:24-16-60 harmonic 74.0 92.4 - angle_coeff @angle:25-16-61 harmonic 10.0 130.0 - angle_coeff @angle:25-16-82 harmonic 10.0 130.0 - angle_coeff @angle:60-16-82 harmonic 74.0 97.0 - angle_coeff @angle:25-16-84 harmonic 10.0 130.0 - angle_coeff @angle:82-16-84 harmonic 74.0 90.0 - angle_coeff @angle:60-16-84 harmonic 74.0 97.0 - angle_coeff @angle:84-16-84 harmonic 74.0 97.0 - angle_coeff @angle:13-16-91 harmonic 62.0 94.0 - angle_coeff @angle:15-17-25 harmonic 10.0 109.47 - angle_coeff @angle:25-17-25 harmonic 33.0 109.47 - angle_coeff @angle:13-18-19 harmonic 150.0 180.0 - angle_coeff @angle:19-18-48 harmonic 170.0 180.0 - angle_coeff @angle:18-18-56 harmonic 100.0 180.0 - angle_coeff @angle:13-19-18 harmonic 150.0 180.0 - angle_coeff @angle:16-19-19 harmonic 140.0 180.0 - angle_coeff @angle:13-19-19 harmonic 150.0 180.0 - angle_coeff @angle:18-19-25 harmonic 10.0 90.0 - angle_coeff @angle:19-19-46 harmonic 112.0 180.0 - angle_coeff @angle:18-19-47 harmonic 150.0 180.0 - angle_coeff @angle:19-19-47 harmonic 160.0 180.0 - angle_coeff @angle:18-19-48 harmonic 150.0 180.0 - angle_coeff @angle:19-19-48 harmonic 160.0 180.0 - angle_coeff @angle:19-19-50 harmonic 160.0 180.0 - angle_coeff @angle:18-19-55 harmonic 150.0 180.0 - angle_coeff @angle:18-19-88 harmonic 150.0 180.0 - angle_coeff @angle:2-20-2 harmonic 100.0 111.8 - angle_coeff @angle:2-20-3 harmonic 83.0 116.9 - angle_coeff @angle:3-20-6 harmonic 83.0 116.9 - angle_coeff @angle:2-20-6 harmonic 100.0 111.8 - angle_coeff @angle:2-20-7 harmonic 55.0 108.5 - angle_coeff @angle:7-20-10 harmonic 55.0 108.5 - angle_coeff @angle:3-20-10 harmonic 83.0 116.9 - angle_coeff @angle:10-20-10 harmonic 100.0 111.8 - angle_coeff @angle:13-20-13 harmonic 60.0 109.5 - angle_coeff @angle:3-20-13 harmonic 83.0 116.9 - angle_coeff @angle:25-20-25 harmonic 5.0 109.47 - angle_coeff @angle:13-20-25 harmonic 10.0 109.47 - angle_coeff @angle:13-20-47 harmonic 75.0 111.0 - angle_coeff @angle:25-20-48 harmonic 10.0 109.47 - angle_coeff @angle:13-20-48 harmonic 75.0 111.0 - angle_coeff @angle:47-20-48 harmonic 75.0 111.0 - angle_coeff @angle:48-20-48 harmonic 75.0 111.0 - angle_coeff @angle:3-20-48 harmonic 83.0 116.9 - angle_coeff @angle:2-20-48 harmonic 100.0 111.8 - angle_coeff @angle:13-20-51 harmonic 60.0 109.5 - angle_coeff @angle:2-20-51 harmonic 100.0 113.0 - angle_coeff @angle:6-20-51 harmonic 100.0 113.0 - angle_coeff @angle:10-20-51 harmonic 100.0 113.0 - angle_coeff @angle:24-20-60 harmonic 70.0 104.5 - angle_coeff @angle:25-20-61 harmonic 10.0 125.0 - angle_coeff @angle:2-20-64 harmonic 100.0 120.5 - angle_coeff @angle:6-20-64 harmonic 100.0 120.5 - angle_coeff @angle:10-20-64 harmonic 100.0 120.5 - angle_coeff @angle:13-20-64 harmonic 100.0 120.5 - angle_coeff @angle:48-20-64 harmonic 100.0 120.5 - angle_coeff @angle:64-20-64 harmonic 100.0 120.5 - angle_coeff @angle:25-20-82 harmonic 10.0 125.0 - angle_coeff @angle:60-20-82 harmonic 70.0 106.5 - angle_coeff @angle:82-20-82 harmonic 70.0 107.0 - angle_coeff @angle:25-20-84 harmonic 10.0 125.0 - angle_coeff @angle:82-20-84 harmonic 70.0 104.0 - angle_coeff @angle:60-20-84 harmonic 70.0 106.5 - angle_coeff @angle:84-20-84 harmonic 70.0 106.5 - angle_coeff @angle:61-20-84 harmonic 70.0 108.9 - angle_coeff @angle:108-20-108 harmonic 20.0 145.0 - angle_coeff @angle:13-20-108 harmonic 40.0 130.0 - angle_coeff @angle:25-21-25 harmonic 33.0 109.47 - angle_coeff @angle:13-22-13 harmonic 62.0 96.0 - angle_coeff @angle:13-22-23 harmonic 74.0 107.0 - angle_coeff @angle:23-22-25 harmonic 10.0 90.0 - angle_coeff @angle:2-24-3 harmonic 50.0 121.9 - angle_coeff @angle:3-24-3 harmonic 70.0 126.4 - angle_coeff @angle:3-24-5 harmonic 46.0 115.7 - angle_coeff @angle:2-24-6 harmonic 50.0 121.9 - angle_coeff @angle:3-24-6 harmonic 50.0 121.9 - angle_coeff @angle:2-24-10 harmonic 50.0 118.0 - angle_coeff @angle:3-24-10 harmonic 50.0 121.9 - angle_coeff @angle:13-24-13 harmonic 50.0 118.0 - angle_coeff @angle:3-24-13 harmonic 50.0 121.9 - angle_coeff @angle:3-24-16 harmonic 70.0 112.0 - angle_coeff @angle:3-24-20 harmonic 70.0 108.6 - angle_coeff @angle:3-24-25 harmonic 10.0 109.5 - angle_coeff @angle:25-24-45 harmonic 10.0 100.0 - angle_coeff @angle:5-24-45 harmonic 35.0 110.2 - angle_coeff @angle:3-24-45 harmonic 35.0 119.8 - angle_coeff @angle:45-24-45 harmonic 35.0 120.0 - angle_coeff @angle:2-24-45 harmonic 38.0 118.4 - angle_coeff @angle:6-24-45 harmonic 38.0 118.4 - angle_coeff @angle:10-24-45 harmonic 38.0 118.4 - angle_coeff @angle:13-24-45 harmonic 38.0 118.4 - angle_coeff @angle:45-24-48 harmonic 35.0 119.8 - angle_coeff @angle:13-24-48 harmonic 50.0 118.0 - angle_coeff @angle:3-24-48 harmonic 50.0 121.9 - angle_coeff @angle:48-24-48 harmonic 70.0 118.0 - angle_coeff @angle:54-24-54 harmonic 35.0 120.0 - angle_coeff @angle:45-24-59 harmonic 35.0 118.0 - angle_coeff @angle:3-24-59 harmonic 70.0 125.2 - angle_coeff @angle:13-24-79 harmonic 50.0 120.0 - angle_coeff @angle:45-24-79 harmonic 100.0 111.0 - angle_coeff @angle:45-24-84 harmonic 35.0 119.8 - angle_coeff @angle:48-24-84 harmonic 70.0 118.0 - angle_coeff @angle:16-24-86 harmonic 70.0 117.0 - angle_coeff @angle:45-24-87 harmonic 35.0 119.8 - angle_coeff @angle:48-24-87 harmonic 70.0 118.0 - angle_coeff @angle:45-24-88 harmonic 35.0 119.8 - angle_coeff @angle:48-24-88 harmonic 70.0 118.0 - angle_coeff @angle:45-24-91 harmonic 40.0 113.0 - angle_coeff @angle:3-24-91 harmonic 55.0 128.0 - angle_coeff @angle:48-24-103 harmonic 70.0 121.0 - angle_coeff @angle:3-24-106 harmonic 20.0 126.0 - angle_coeff @angle:25-25-25 harmonic 33.0 109.47 - angle_coeff @angle:32-31-32 harmonic 75.0 104.52 - angle_coeff @angle:32-31-33 harmonic 50.0 52.26 - angle_coeff @angle:35-34-35 harmonic 34.05 104.52 - angle_coeff @angle:37-36-37 harmonic 75.0 109.5 - angle_coeff @angle:37-36-38 harmonic 50.0 54.75 - angle_coeff @angle:40-39-40 harmonic 75.0 104.52 - angle_coeff @angle:41-39-41 harmonic 50.0 109.47 - angle_coeff @angle:40-39-41 harmonic 50.0 110.6948 - angle_coeff @angle:43-42-43 harmonic 75.0 109.47 - angle_coeff @angle:2-44-2 harmonic 51.8 107.2 - angle_coeff @angle:2-44-6 harmonic 51.8 107.2 - angle_coeff @angle:6-44-6 harmonic 51.8 107.2 - angle_coeff @angle:2-44-10 harmonic 51.8 107.2 - angle_coeff @angle:6-44-10 harmonic 51.8 107.2 - angle_coeff @angle:10-44-10 harmonic 51.8 107.2 - angle_coeff @angle:2-44-13 harmonic 51.8 107.2 - angle_coeff @angle:6-44-13 harmonic 51.8 107.2 - angle_coeff @angle:10-44-13 harmonic 51.8 107.2 - angle_coeff @angle:13-44-13 harmonic 51.8 107.2 - angle_coeff @angle:3-44-13 harmonic 63.0 111.1 - angle_coeff @angle:25-44-45 harmonic 10.0 100.0 - angle_coeff @angle:13-44-45 harmonic 35.0 109.5 - angle_coeff @angle:2-44-45 harmonic 43.2 108.1 - angle_coeff @angle:6-44-45 harmonic 43.2 108.1 - angle_coeff @angle:10-44-45 harmonic 43.2 108.1 - angle_coeff @angle:45-44-45 harmonic 43.6 106.4 - angle_coeff @angle:25-44-48 harmonic 10.0 109.5 - angle_coeff @angle:45-44-48 harmonic 35.0 116.0 - angle_coeff @angle:13-44-48 harmonic 50.0 116.0 - angle_coeff @angle:48-44-48 harmonic 50.0 116.0 - angle_coeff @angle:3-44-48 harmonic 63.0 112.0 - angle_coeff @angle:45-44-79 harmonic 35.0 115.0 - angle_coeff @angle:13-44-79 harmonic 50.0 108.6 - angle_coeff @angle:48-44-79 harmonic 50.0 108.6 - angle_coeff @angle:48-44-91 harmonic 50.0 109.5 - angle_coeff @angle:25-45-25 harmonic 33.0 109.47 - angle_coeff @angle:25-45-44 harmonic 10.0 109.5 - angle_coeff @angle:25-46-25 harmonic 33.0 109.47 - angle_coeff @angle:13-46-25 harmonic 37.5 109.47 - angle_coeff @angle:1-47-1 harmonic 80.0 108.0 - angle_coeff @angle:1-47-3 harmonic 80.0 121.5 - angle_coeff @angle:3-47-6 harmonic 85.0 119.7 - angle_coeff @angle:3-47-13 harmonic 70.0 119.7 - angle_coeff @angle:13-47-13 harmonic 70.0 130.0 - angle_coeff @angle:25-47-46 harmonic 10.0 90.0 - angle_coeff @angle:20-47-46 harmonic 35.0 114.5 - angle_coeff @angle:13-47-46 harmonic 35.0 117.0 - angle_coeff @angle:46-47-46 harmonic 35.0 117.0 - angle_coeff @angle:3-47-46 harmonic 35.0 119.7 - angle_coeff @angle:19-47-46 harmonic 35.0 120.0 - angle_coeff @angle:1-47-46 harmonic 50.0 112.0 - angle_coeff @angle:21-47-46 harmonic 60.0 114.0 - angle_coeff @angle:25-47-47 harmonic 2.0 90.0 - angle_coeff @angle:46-47-47 harmonic 35.0 120.0 - angle_coeff @angle:5-47-47 harmonic 70.0 123.0 - angle_coeff @angle:20-47-47 harmonic 70.0 123.0 - angle_coeff @angle:13-47-47 harmonic 70.0 124.0 - angle_coeff @angle:19-47-47 harmonic 70.0 124.0 - angle_coeff @angle:21-47-47 harmonic 75.0 121.5 - angle_coeff @angle:1-47-47 harmonic 80.0 121.5 - angle_coeff @angle:16-47-47 harmonic 85.0 119.4 - angle_coeff @angle:3-47-47 harmonic 85.0 120.7 - angle_coeff @angle:46-47-48 harmonic 35.0 123.3 - angle_coeff @angle:47-47-48 harmonic 85.0 117.0 - angle_coeff @angle:13-47-48 harmonic 85.0 119.7 - angle_coeff @angle:25-47-50 harmonic 2.0 90.0 - angle_coeff @angle:46-47-50 harmonic 35.0 120.0 - angle_coeff @angle:5-47-50 harmonic 70.0 123.0 - angle_coeff @angle:20-47-50 harmonic 70.0 123.0 - angle_coeff @angle:13-47-50 harmonic 70.0 124.0 - angle_coeff @angle:46-47-57 harmonic 35.0 119.1 - angle_coeff @angle:13-47-57 harmonic 70.0 120.0 - angle_coeff @angle:20-47-57 harmonic 70.0 120.0 - angle_coeff @angle:47-47-57 harmonic 70.0 121.2 - angle_coeff @angle:16-47-57 harmonic 85.0 119.4 - angle_coeff @angle:57-47-58 harmonic 35.0 119.1 - angle_coeff @angle:47-47-58 harmonic 35.0 119.7 - angle_coeff @angle:46-47-65 harmonic 60.0 114.0 - angle_coeff @angle:47-47-65 harmonic 75.0 120.0 - angle_coeff @angle:46-47-91 harmonic 35.0 135.0 - angle_coeff @angle:3-47-91 harmonic 70.0 119.7 - angle_coeff @angle:47-47-91 harmonic 70.0 124.0 - angle_coeff @angle:46-47-105 harmonic 35.0 119.1 - angle_coeff @angle:58-47-105 harmonic 35.0 119.1 - angle_coeff @angle:13-47-105 harmonic 70.0 120.0 - angle_coeff @angle:20-47-105 harmonic 70.0 120.0 - angle_coeff @angle:47-47-105 harmonic 70.0 121.2 - angle_coeff @angle:16-47-105 harmonic 85.0 119.4 - angle_coeff @angle:46-47-110 harmonic 40.0 121.0 - angle_coeff @angle:13-47-110 harmonic 80.0 122.0 - angle_coeff @angle:48-47-110 harmonic 80.0 122.0 - angle_coeff @angle:1-47-110 harmonic 80.0 125.0 - angle_coeff @angle:2-48-12 harmonic 70.0 120.0 - angle_coeff @angle:12-48-12 harmonic 85.0 120.0 - angle_coeff @angle:3-48-13 harmonic 70.0 119.7 - angle_coeff @angle:25-48-48 harmonic 10.0 90.0 - angle_coeff @angle:48-48-48 harmonic 63.0 120.0 - angle_coeff @angle:2-48-48 harmonic 70.0 120.0 - angle_coeff @angle:5-48-48 harmonic 70.0 120.0 - angle_coeff @angle:10-48-48 harmonic 70.0 120.0 - angle_coeff @angle:13-48-48 harmonic 70.0 120.0 - angle_coeff @angle:15-48-48 harmonic 70.0 120.0 - angle_coeff @angle:19-48-48 harmonic 70.0 120.0 - angle_coeff @angle:20-48-48 harmonic 70.0 120.0 - angle_coeff @angle:24-48-48 harmonic 70.0 120.0 - angle_coeff @angle:44-48-48 harmonic 70.0 120.0 - angle_coeff @angle:47-48-48 harmonic 70.0 124.0 - angle_coeff @angle:21-48-48 harmonic 75.0 120.0 - angle_coeff @angle:1-48-48 harmonic 80.0 120.0 - angle_coeff @angle:18-48-48 harmonic 80.0 120.0 - angle_coeff @angle:16-48-48 harmonic 85.0 119.4 - angle_coeff @angle:3-48-48 harmonic 85.0 120.0 - angle_coeff @angle:25-48-49 harmonic 2.0 90.0 - angle_coeff @angle:24-48-49 harmonic 35.0 119.1 - angle_coeff @angle:3-48-49 harmonic 35.0 120.0 - angle_coeff @angle:48-48-49 harmonic 35.0 120.0 - angle_coeff @angle:48-48-50 harmonic 70.0 124.0 - angle_coeff @angle:48-48-53 harmonic 70.0 120.0 - angle_coeff @angle:55-48-55 harmonic 70.0 120.0 - angle_coeff @angle:47-48-55 harmonic 70.0 120.1 - angle_coeff @angle:48-48-55 harmonic 70.0 120.1 - angle_coeff @angle:49-48-56 harmonic 35.0 116.0 - angle_coeff @angle:13-48-56 harmonic 70.0 116.0 - angle_coeff @angle:44-48-56 harmonic 70.0 116.0 - angle_coeff @angle:55-48-56 harmonic 70.0 119.3 - angle_coeff @angle:5-48-56 harmonic 70.0 120.0 - angle_coeff @angle:47-48-56 harmonic 70.0 121.5 - angle_coeff @angle:50-48-56 harmonic 70.0 121.5 - angle_coeff @angle:48-48-56 harmonic 70.0 124.0 - angle_coeff @angle:21-48-56 harmonic 75.0 120.0 - angle_coeff @angle:49-48-57 harmonic 35.0 120.0 - angle_coeff @angle:48-48-57 harmonic 70.0 108.7 - angle_coeff @angle:55-48-57 harmonic 70.0 116.0 - angle_coeff @angle:13-48-57 harmonic 70.0 120.0 - angle_coeff @angle:47-48-57 harmonic 70.0 121.5 - angle_coeff @angle:56-48-57 harmonic 70.0 123.3 - angle_coeff @angle:49-48-60 harmonic 35.0 120.0 - angle_coeff @angle:48-48-60 harmonic 63.0 120.0 - angle_coeff @angle:57-48-60 harmonic 70.0 108.7 - angle_coeff @angle:56-48-60 harmonic 70.0 117.3 - angle_coeff @angle:55-48-60 harmonic 70.0 123.5 - angle_coeff @angle:2-48-60 harmonic 70.0 128.6 - angle_coeff @angle:13-48-60 harmonic 70.0 128.6 - angle_coeff @angle:49-48-61 harmonic 35.0 119.1 - angle_coeff @angle:48-48-61 harmonic 70.0 108.7 - angle_coeff @angle:57-48-61 harmonic 70.0 123.3 - angle_coeff @angle:48-48-64 harmonic 85.0 119.4 - angle_coeff @angle:48-48-65 harmonic 75.0 120.0 - angle_coeff @angle:48-48-66 harmonic 75.0 120.0 - angle_coeff @angle:48-48-79 harmonic 85.0 119.4 - angle_coeff @angle:49-48-81 harmonic 35.0 120.0 - angle_coeff @angle:48-48-81 harmonic 85.0 120.0 - angle_coeff @angle:49-48-84 harmonic 35.0 126.9 - angle_coeff @angle:60-48-84 harmonic 63.0 106.4 - angle_coeff @angle:48-48-84 harmonic 70.0 107.4 - angle_coeff @angle:49-48-86 harmonic 35.0 120.0 - 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angle_coeff @angle:45-53-45 harmonic 43.6 109.5 - angle_coeff @angle:25-53-48 harmonic 10.0 100.0 - angle_coeff @angle:13-53-48 harmonic 55.0 114.0 - angle_coeff @angle:2-53-54 harmonic 35.0 109.5 - angle_coeff @angle:6-53-54 harmonic 35.0 109.5 - angle_coeff @angle:13-53-54 harmonic 35.0 109.5 - angle_coeff @angle:48-53-54 harmonic 35.0 109.5 - angle_coeff @angle:54-53-54 harmonic 35.0 109.5 - angle_coeff @angle:25-53-82 harmonic 10.0 100.0 - angle_coeff @angle:13-55-13 harmonic 50.0 118.0 - angle_coeff @angle:45-55-45 harmonic 35.0 113.0 - angle_coeff @angle:13-55-45 harmonic 35.0 118.4 - angle_coeff @angle:45-55-48 harmonic 35.0 120.0 - angle_coeff @angle:2-55-48 harmonic 50.0 123.2 - angle_coeff @angle:6-55-48 harmonic 50.0 123.2 - angle_coeff @angle:13-55-48 harmonic 50.0 123.2 - angle_coeff @angle:2-55-54 harmonic 35.0 118.4 - angle_coeff @angle:13-55-54 harmonic 35.0 118.4 - angle_coeff @angle:48-55-54 harmonic 35.0 120.0 - angle_coeff @angle:54-55-54 harmonic 35.0 120.0 - angle_coeff @angle:45-55-59 harmonic 35.0 120.0 - angle_coeff @angle:3-56-13 harmonic 70.0 120.5 - angle_coeff @angle:13-56-18 harmonic 70.0 120.0 - angle_coeff @angle:25-56-48 harmonic 5.0 120.0 - angle_coeff @angle:45-56-48 harmonic 35.0 113.0 - angle_coeff @angle:13-56-48 harmonic 50.0 118.0 - angle_coeff @angle:48-56-48 harmonic 70.0 117.0 - angle_coeff @angle:3-56-48 harmonic 70.0 120.5 - angle_coeff @angle:13-56-56 harmonic 70.0 117.0 - angle_coeff @angle:48-56-56 harmonic 70.0 117.0 - angle_coeff @angle:25-56-59 harmonic 5.0 119.8 - angle_coeff @angle:48-56-59 harmonic 70.0 118.6 - angle_coeff @angle:59-56-59 harmonic 70.0 118.6 - angle_coeff @angle:59-56-60 harmonic 70.0 111.0 - angle_coeff @angle:48-56-60 harmonic 70.0 112.2 - angle_coeff @angle:59-56-82 harmonic 70.0 111.0 - angle_coeff @angle:48-56-86 harmonic 70.0 117.0 - angle_coeff @angle:13-56-103 harmonic 70.0 114.0 - angle_coeff @angle:3-57-3 harmonic 70.0 126.4 - angle_coeff @angle:3-57-45 harmonic 35.0 116.8 - angle_coeff @angle:45-57-47 harmonic 35.0 119.2 - angle_coeff @angle:3-57-47 harmonic 70.0 121.6 - angle_coeff @angle:45-57-48 harmonic 35.0 118.0 - angle_coeff @angle:3-57-48 harmonic 70.0 125.2 - angle_coeff @angle:48-57-48 harmonic 70.0 125.2 - angle_coeff @angle:45-57-60 harmonic 30.0 125.8 - angle_coeff @angle:13-57-60 harmonic 70.0 125.8 - angle_coeff @angle:60-57-61 harmonic 56.0 113.1 - angle_coeff @angle:45-57-61 harmonic 56.0 118.4 - angle_coeff @angle:13-57-61 harmonic 70.0 118.4 - angle_coeff @angle:48-57-61 harmonic 70.0 118.4 - angle_coeff @angle:45-57-62 harmonic 30.0 128.8 - angle_coeff @angle:60-57-62 harmonic 70.0 105.4 - angle_coeff @angle:48-57-62 harmonic 70.0 109.8 - angle_coeff @angle:13-57-62 harmonic 70.0 128.8 - angle_coeff @angle:45-57-81 harmonic 35.0 123.1 - angle_coeff @angle:45-57-82 harmonic 35.0 120.0 - angle_coeff @angle:61-57-82 harmonic 56.0 113.1 - angle_coeff @angle:60-57-82 harmonic 70.0 109.8 - angle_coeff @angle:45-57-84 harmonic 35.0 120.0 - angle_coeff @angle:61-57-84 harmonic 56.0 113.1 - angle_coeff @angle:60-57-84 harmonic 70.0 109.8 - angle_coeff @angle:82-57-84 harmonic 70.0 109.8 - angle_coeff @angle:84-57-84 harmonic 70.0 109.8 - angle_coeff @angle:81-57-84 harmonic 70.0 111.6 - angle_coeff @angle:45-57-85 harmonic 35.0 120.0 - angle_coeff @angle:82-57-85 harmonic 70.0 109.8 - angle_coeff @angle:24-59-55 harmonic 70.0 116.0 - angle_coeff @angle:49-59-56 harmonic 35.0 115.45 - angle_coeff @angle:13-59-56 harmonic 70.0 115.5 - angle_coeff @angle:55-59-56 harmonic 70.0 119.3 - angle_coeff @angle:24-59-56 harmonic 70.0 123.3 - angle_coeff @angle:56-59-56 harmonic 70.0 129.1 - angle_coeff @angle:56-59-63 harmonic 35.0 115.45 - angle_coeff @angle:13-60-48 harmonic 70.0 120.0 - angle_coeff @angle:48-60-48 harmonic 85.0 134.9 - angle_coeff @angle:56-60-57 harmonic 70.0 126.2 - angle_coeff @angle:57-60-60 harmonic 70.0 106.2 - angle_coeff @angle:20-60-60 harmonic 70.0 110.6 - angle_coeff @angle:16-60-60 harmonic 70.0 111.0 - angle_coeff @angle:13-60-60 harmonic 70.0 120.0 - angle_coeff @angle:24-60-60 harmonic 70.0 127.7 - angle_coeff @angle:56-60-60 harmonic 70.0 127.7 - angle_coeff @angle:48-60-60 harmonic 85.0 117.3 - angle_coeff @angle:3-60-60 harmonic 85.0 119.2 - angle_coeff @angle:60-60-61 harmonic 70.0 111.0 - angle_coeff @angle:24-60-61 harmonic 70.0 126.2 - angle_coeff @angle:3-60-61 harmonic 70.0 130.0 - angle_coeff @angle:48-60-61 harmonic 70.0 132.4 - angle_coeff @angle:12-60-80 harmonic 85.0 134.9 - angle_coeff @angle:48-60-80 harmonic 85.0 134.9 - angle_coeff @angle:80-60-81 harmonic 85.0 108.8 - angle_coeff @angle:12-60-81 harmonic 85.0 116.2 - angle_coeff @angle:48-60-81 harmonic 85.0 116.2 - angle_coeff @angle:3-60-84 harmonic 70.0 130.0 - angle_coeff @angle:60-60-87 harmonic 70.0 107.3 - angle_coeff @angle:57-60-87 harmonic 70.0 107.7 - angle_coeff @angle:81-60-87 harmonic 85.0 108.8 - angle_coeff @angle:12-60-87 harmonic 85.0 134.9 - angle_coeff @angle:48-60-87 harmonic 85.0 134.9 - angle_coeff @angle:60-60-105 harmonic 70.0 106.2 - angle_coeff @angle:56-60-105 harmonic 70.0 126.2 - angle_coeff @angle:48-61-48 harmonic 70.0 125.2 - angle_coeff @angle:25-61-57 harmonic 10.0 125.0 - angle_coeff @angle:25-61-61 harmonic 10.0 125.0 - angle_coeff @angle:60-61-62 harmonic 70.0 103.8 - angle_coeff @angle:25-61-82 harmonic 10.0 125.0 - angle_coeff @angle:61-61-82 harmonic 70.0 109.0 - angle_coeff @angle:60-61-82 harmonic 70.0 110.0 - angle_coeff @angle:82-61-83 harmonic 70.0 110.0 - angle_coeff @angle:57-61-84 harmonic 70.0 104.1 - angle_coeff @angle:82-61-84 harmonic 70.0 110.0 - angle_coeff @angle:57-61-88 harmonic 70.0 104.1 - angle_coeff @angle:20-61-88 harmonic 70.0 105.3 - angle_coeff @angle:49-62-57 harmonic 35.0 120.0 - angle_coeff @angle:49-62-61 harmonic 35.0 120.0 - angle_coeff @angle:57-62-61 harmonic 70.0 113.9 - angle_coeff @angle:57-62-63 harmonic 35.0 123.05 - angle_coeff @angle:61-62-63 harmonic 35.0 123.05 - angle_coeff @angle:49-62-105 harmonic 35.0 120.0 - angle_coeff @angle:63-62-105 harmonic 35.0 123.05 - angle_coeff @angle:61-62-105 harmonic 70.0 113.9 - angle_coeff @angle:5-64-5 harmonic 45.0 102.6 - angle_coeff @angle:4-64-5 harmonic 100.0 108.23 - angle_coeff @angle:4-64-13 harmonic 45.0 109.5 - angle_coeff @angle:5-64-20 harmonic 45.0 102.6 - angle_coeff @angle:20-64-20 harmonic 45.0 102.6 - angle_coeff @angle:13-64-20 harmonic 45.0 109.5 - angle_coeff @angle:4-64-20 harmonic 100.0 108.23 - angle_coeff @angle:4-64-48 harmonic 45.0 109.5 - angle_coeff @angle:5-64-48 harmonic 45.0 109.5 - angle_coeff @angle:20-64-48 harmonic 45.0 109.5 - angle_coeff @angle:5-64-52 harmonic 45.0 108.23 - angle_coeff @angle:13-64-52 harmonic 45.0 109.5 - angle_coeff @angle:20-64-52 harmonic 100.0 108.23 - angle_coeff @angle:52-64-52 harmonic 140.0 119.9 - angle_coeff @angle:25-65-25 harmonic 33.0 109.47 - angle_coeff @angle:25-66-25 harmonic 33.0 109.47 - angle_coeff @angle:78-77-78 harmonic 150.0 180.0 - angle_coeff @angle:6-79-11 harmonic 62.0 98.9 - angle_coeff @angle:13-79-13 harmonic 62.0 102.0 - angle_coeff @angle:5-79-13 harmonic 75.0 96.4 - angle_coeff @angle:5-79-23 harmonic 74.0 108.7 - angle_coeff @angle:13-79-23 harmonic 74.0 108.9 - angle_coeff @angle:23-79-23 harmonic 104.0 119.0 - angle_coeff @angle:13-79-24 harmonic 100.0 103.0 - angle_coeff @angle:23-79-24 harmonic 120.0 107.0 - angle_coeff @angle:13-79-44 harmonic 62.0 102.0 - angle_coeff @angle:23-79-44 harmonic 74.0 108.9 - angle_coeff @angle:13-79-48 harmonic 62.0 102.0 - angle_coeff @angle:23-79-48 harmonic 74.0 107.2 - angle_coeff @angle:5-79-48 harmonic 75.0 96.4 - angle_coeff @angle:24-79-48 harmonic 100.0 103.0 - angle_coeff @angle:13-79-82 harmonic 62.0 102.0 - angle_coeff @angle:46-80-60 harmonic 35.0 126.8 - angle_coeff @angle:2-80-60 harmonic 70.0 128.6 - angle_coeff @angle:13-80-60 harmonic 70.0 128.6 - angle_coeff @angle:46-80-84 harmonic 35.0 126.8 - angle_coeff @angle:2-80-84 harmonic 70.0 125.0 - angle_coeff @angle:13-80-84 harmonic 70.0 125.0 - angle_coeff @angle:60-80-84 harmonic 85.0 106.4 - angle_coeff @angle:12-81-57 harmonic 70.0 132.8 - angle_coeff @angle:48-81-57 harmonic 70.0 132.8 - angle_coeff @angle:57-81-60 harmonic 70.0 104.4 - angle_coeff @angle:12-81-60 harmonic 85.0 122.7 - angle_coeff @angle:48-81-60 harmonic 85.0 122.7 - angle_coeff @angle:13-82-16 harmonic 70.0 125.0 - angle_coeff @angle:16-82-24 harmonic 70.0 125.0 - angle_coeff @angle:16-82-44 harmonic 70.0 120.2 - angle_coeff @angle:20-82-49 harmonic 35.0 117.0 - angle_coeff @angle:16-82-49 harmonic 35.0 125.0 - angle_coeff @angle:49-82-57 harmonic 35.0 120.0 - angle_coeff @angle:57-82-57 harmonic 70.0 120.0 - angle_coeff @angle:13-82-57 harmonic 70.0 125.0 - angle_coeff @angle:48-82-57 harmonic 70.0 125.0 - angle_coeff @angle:56-82-57 harmonic 70.0 126.2 - angle_coeff @angle:49-82-61 harmonic 35.0 120.0 - angle_coeff @angle:16-82-61 harmonic 70.0 115.0 - angle_coeff @angle:20-82-61 harmonic 70.0 115.0 - angle_coeff @angle:57-82-61 harmonic 70.0 120.0 - angle_coeff @angle:13-82-61 harmonic 70.0 125.0 - angle_coeff @angle:44-82-61 harmonic 70.0 126.1 - angle_coeff @angle:24-82-61 harmonic 70.0 126.2 - angle_coeff @angle:57-82-79 harmonic 70.0 120.0 - angle_coeff @angle:61-82-79 harmonic 70.0 120.0 - angle_coeff @angle:20-82-86 harmonic 70.0 122.0 - angle_coeff @angle:61-82-86 harmonic 70.0 130.0 - angle_coeff @angle:57-82-87 harmonic 70.0 106.2 - angle_coeff @angle:56-82-87 harmonic 70.0 127.7 - angle_coeff @angle:49-83-61 harmonic 35.0 120.0 - angle_coeff @angle:48-83-61 harmonic 70.0 111.0 - angle_coeff @angle:13-83-61 harmonic 70.0 124.5 - angle_coeff @angle:49-83-84 harmonic 35.0 128.2 - angle_coeff @angle:61-83-84 harmonic 70.0 111.0 - angle_coeff @angle:13-83-84 harmonic 70.0 130.7 - angle_coeff @angle:13-84-16 harmonic 70.0 125.0 - angle_coeff @angle:13-84-20 harmonic 70.0 121.6 - angle_coeff @angle:16-84-24 harmonic 70.0 125.0 - angle_coeff @angle:20-84-49 harmonic 35.0 113.4 - angle_coeff @angle:16-84-49 harmonic 35.0 125.0 - angle_coeff @angle:48-84-49 harmonic 35.0 130.7 - angle_coeff @angle:49-84-50 harmonic 35.0 130.7 - angle_coeff @angle:20-84-50 harmonic 70.0 110.0 - angle_coeff @angle:49-84-57 harmonic 35.0 121.6 - angle_coeff @angle:13-84-57 harmonic 70.0 121.6 - angle_coeff @angle:48-84-57 harmonic 70.0 121.6 - angle_coeff @angle:3-84-57 harmonic 85.0 120.0 - angle_coeff @angle:57-84-58 harmonic 35.0 120.0 - angle_coeff @angle:13-84-61 harmonic 70.0 118.9 - angle_coeff @angle:49-84-80 harmonic 35.0 120.0 - angle_coeff @angle:57-84-80 harmonic 70.0 108.7 - angle_coeff @angle:49-84-83 harmonic 35.0 130.7 - angle_coeff @angle:57-84-83 harmonic 70.0 106.3 - angle_coeff @angle:20-84-83 harmonic 70.0 108.0 - angle_coeff @angle:16-84-83 harmonic 70.0 111.0 - angle_coeff @angle:13-84-83 harmonic 70.0 130.7 - angle_coeff @angle:13-84-84 harmonic 70.0 120.0 - angle_coeff @angle:57-84-84 harmonic 70.0 120.0 - angle_coeff @angle:61-84-84 harmonic 70.0 120.0 - angle_coeff @angle:20-84-86 harmonic 70.0 121.6 - angle_coeff @angle:57-84-86 harmonic 70.0 121.6 - angle_coeff @angle:49-84-87 harmonic 35.0 132.1 - angle_coeff @angle:57-84-87 harmonic 70.0 107.7 - angle_coeff @angle:20-84-87 harmonic 70.0 110.6 - angle_coeff @angle:16-84-87 harmonic 70.0 111.0 - angle_coeff @angle:61-84-87 harmonic 70.0 111.9 - angle_coeff @angle:13-84-87 harmonic 70.0 132.1 - angle_coeff @angle:48-84-87 harmonic 70.0 132.1 - angle_coeff @angle:86-84-87 harmonic 70.0 132.1 - angle_coeff @angle:3-84-87 harmonic 85.0 120.0 - angle_coeff @angle:49-85-57 harmonic 35.0 120.0 - angle_coeff @angle:13-85-57 harmonic 70.0 121.6 - angle_coeff @angle:49-85-85 harmonic 35.0 130.7 - angle_coeff @angle:57-85-85 harmonic 70.0 106.3 - angle_coeff @angle:13-85-85 harmonic 70.0 130.7 - angle_coeff @angle:48-86-48 harmonic 63.0 120.0 - angle_coeff @angle:48-86-56 harmonic 70.0 124.0 - angle_coeff @angle:48-86-82 harmonic 63.0 120.0 - angle_coeff @angle:48-86-83 harmonic 63.0 120.0 - angle_coeff @angle:48-86-84 harmonic 63.0 120.0 - angle_coeff @angle:48-86-86 harmonic 63.0 120.0 - angle_coeff @angle:56-86-86 harmonic 70.0 124.0 - angle_coeff @angle:48-86-87 harmonic 63.0 120.0 - angle_coeff @angle:48-86-88 harmonic 63.0 120.0 - angle_coeff @angle:49-87-60 harmonic 35.0 120.0 - angle_coeff @angle:46-87-60 harmonic 35.0 126.8 - angle_coeff @angle:13-87-60 harmonic 70.0 128.6 - angle_coeff @angle:49-87-84 harmonic 35.0 125.7 - angle_coeff @angle:46-87-84 harmonic 35.0 126.8 - angle_coeff @angle:84-87-84 harmonic 70.0 103.8 - angle_coeff @angle:82-87-84 harmonic 70.0 110.4 - angle_coeff @angle:2-87-84 harmonic 70.0 125.0 - angle_coeff @angle:13-87-84 harmonic 70.0 125.0 - angle_coeff @angle:3-87-84 harmonic 70.0 130.0 - angle_coeff @angle:60-87-84 harmonic 85.0 106.4 - angle_coeff @angle:84-87-86 harmonic 70.0 125.7 - angle_coeff @angle:49-87-87 harmonic 35.0 127.5 - angle_coeff @angle:60-87-87 harmonic 70.0 107.3 - angle_coeff @angle:84-87-87 harmonic 70.0 107.3 - angle_coeff @angle:86-87-87 harmonic 70.0 127.5 - angle_coeff @angle:84-87-88 harmonic 70.0 103.8 - angle_coeff @angle:48-88-49 harmonic 35.0 128.6 - angle_coeff @angle:49-88-61 harmonic 35.0 118.9 - angle_coeff @angle:13-88-61 harmonic 70.0 118.9 - angle_coeff @angle:19-88-61 harmonic 70.0 118.9 - angle_coeff @angle:61-88-87 harmonic 70.0 111.9 - angle_coeff @angle:4-89-90 harmonic 80.0 134.0 - angle_coeff @angle:90-89-91 harmonic 70.0 91.0 - angle_coeff @angle:4-89-91 harmonic 80.0 134.0 - angle_coeff @angle:13-90-89 harmonic 55.0 127.0 - angle_coeff @angle:89-90-91 harmonic 50.0 94.0 - angle_coeff @angle:13-90-91 harmonic 50.0 126.0 - angle_coeff @angle:24-91-46 harmonic 35.0 108.0 - angle_coeff @angle:13-91-46 harmonic 35.0 114.3 - angle_coeff @angle:44-91-46 harmonic 35.0 114.3 - angle_coeff @angle:46-91-46 harmonic 35.0 114.3 - angle_coeff @angle:16-91-46 harmonic 37.5 108.0 - angle_coeff @angle:46-91-47 harmonic 35.0 109.5 - angle_coeff @angle:46-91-89 harmonic 37.5 110.0 - angle_coeff @angle:24-91-89 harmonic 70.0 117.0 - angle_coeff @angle:46-91-90 harmonic 35.0 111.0 - angle_coeff @angle:16-91-90 harmonic 55.0 109.0 - angle_coeff @angle:91-91-91 harmonic 30.0 79.2 - angle_coeff @angle:13-91-91 harmonic 37.5 117.2 - angle_coeff @angle:44-91-91 harmonic 37.5 117.2 - angle_coeff @angle:46-91-91 harmonic 37.5 117.2 - angle_coeff @angle:24-91-91 harmonic 37.5 126.0 - angle_coeff @angle:16-91-91 harmonic 55.0 128.0 - angle_coeff @angle:89-91-91 harmonic 63.0 85.0 - angle_coeff @angle:47-91-91 harmonic 63.0 114.0 - angle_coeff @angle:90-91-91 harmonic 80.0 89.0 - angle_coeff @angle:13-95-13 harmonic 172.8 120.0 - angle_coeff @angle:13-95-46 harmonic 144.0 120.0 - angle_coeff @angle:13-101-45 harmonic 35.0 109.5 - angle_coeff @angle:45-101-45 harmonic 43.6 106.4 - angle_coeff @angle:45-101-48 harmonic 50.0 112.5 - angle_coeff @angle:13-101-48 harmonic 50.0 120.5 - angle_coeff @angle:13-102-103 harmonic 80.0 117.5 - angle_coeff @angle:48-102-103 harmonic 80.0 117.5 - angle_coeff @angle:103-102-103 harmonic 80.0 125.0 - angle_coeff @angle:25-103-25 harmonic 10.0 109.5 - angle_coeff @angle:25-103-102 harmonic 10.0 109.5 - angle_coeff @angle:13-104-13 harmonic 45.0 109.5 - angle_coeff @angle:3-105-10 harmonic 70.0 117.6 - angle_coeff @angle:3-105-13 harmonic 70.0 117.6 - angle_coeff @angle:3-105-45 harmonic 35.0 119.2 - angle_coeff @angle:45-105-47 harmonic 35.0 119.2 - angle_coeff @angle:13-105-47 harmonic 70.0 121.2 - angle_coeff @angle:3-105-47 harmonic 70.0 121.6 - angle_coeff @angle:3-105-51 harmonic 70.0 117.6 - angle_coeff @angle:47-105-51 harmonic 70.0 121.2 - angle_coeff @angle:45-105-60 harmonic 30.0 125.8 - angle_coeff @angle:6-105-60 harmonic 70.0 125.8 - angle_coeff @angle:10-105-60 harmonic 70.0 125.8 - angle_coeff @angle:13-105-60 harmonic 70.0 125.8 - angle_coeff @angle:51-105-60 harmonic 70.0 125.8 - angle_coeff @angle:45-105-62 harmonic 30.0 128.8 - angle_coeff @angle:60-105-62 harmonic 70.0 105.4 - angle_coeff @angle:6-105-62 harmonic 70.0 128.8 - angle_coeff @angle:10-105-62 harmonic 70.0 128.8 - angle_coeff @angle:13-105-62 harmonic 70.0 128.8 - angle_coeff @angle:51-105-62 harmonic 70.0 128.8 - angle_coeff @angle:4-106-24 harmonic 20.0 109.5 - angle_coeff @angle:24-106-24 harmonic 20.0 109.5 - angle_coeff @angle:13-107-13 harmonic 50.0 118.0 - angle_coeff @angle:3-107-13 harmonic 50.0 121.9 - angle_coeff @angle:1-108-13 harmonic 35.0 110.5 - angle_coeff @angle:13-108-13 harmonic 60.0 110.0 - angle_coeff @angle:13-108-20 harmonic 60.0 100.0 - angle_coeff @angle:20-108-20 harmonic 60.0 110.0 - angle_coeff @angle:13-108-21 harmonic 35.0 110.5 - angle_coeff @angle:45-108-45 harmonic 35.0 109.5 - angle_coeff @angle:13-108-45 harmonic 35.0 110.5 - angle_coeff @angle:46-108-46 harmonic 35.0 109.5 - angle_coeff @angle:13-108-46 harmonic 35.0 110.5 - angle_coeff @angle:13-108-65 harmonic 35.0 110.5 - angle_coeff @angle:13-108-66 harmonic 35.0 110.5 - angle_coeff @angle:13-108-108 harmonic 50.0 112.0 - angle_coeff @angle:46-109-48 harmonic 35.0 123.3 - angle_coeff @angle:46-109-50 harmonic 35.0 120.0 - angle_coeff @angle:13-109-50 harmonic 70.0 124.0 - angle_coeff @angle:46-109-109 harmonic 35.0 120.0 - angle_coeff @angle:13-109-109 harmonic 70.0 124.0 - angle_coeff @angle:50-109-109 harmonic 70.0 124.0 - angle_coeff @angle:48-109-109 harmonic 85.0 117.0 - angle_coeff @angle:4-110-47 harmonic 160.0 180.0 - angle_coeff @angle:47-110-47 harmonic 160.0 180.0 + angle_coeff @angle:025_001_025 33.0 109.47 + angle_coeff @angle:001_002_002 50.0 109.5 + angle_coeff @angle:002_002_002 63.0 112.4 + angle_coeff @angle:002_002_003 63.0 112.4 + angle_coeff @angle:002_002_005 80.0 109.5 + angle_coeff @angle:002_002_006 63.0 112.4 + angle_coeff @angle:006_002_006 63.0 112.4 + angle_coeff @angle:005_002_006 80.0 109.5 + angle_coeff @angle:002_002_010 63.0 112.4 + angle_coeff @angle:003_002_010 63.0 112.4 + angle_coeff @angle:006_002_010 63.0 112.4 + angle_coeff @angle:010_002_010 63.0 112.4 + angle_coeff @angle:005_002_010 80.0 109.5 + 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@angle:013_064_052 45.0 109.5 + angle_coeff @angle:020_064_052 100.0 108.23 + angle_coeff @angle:052_064_052 140.0 119.9 + angle_coeff @angle:025_065_025 33.0 109.47 + angle_coeff @angle:025_066_025 33.0 109.47 + angle_coeff @angle:078_077_078 150.0 180.0 + angle_coeff @angle:006_079_011 62.0 98.9 + angle_coeff @angle:013_079_013 62.0 102.0 + angle_coeff @angle:005_079_013 75.0 96.4 + angle_coeff @angle:005_079_023 74.0 108.7 + angle_coeff @angle:013_079_023 74.0 108.9 + angle_coeff @angle:023_079_023 104.0 119.0 + angle_coeff @angle:013_079_024 100.0 103.0 + angle_coeff @angle:023_079_024 120.0 107.0 + angle_coeff @angle:013_079_044 62.0 102.0 + angle_coeff @angle:023_079_044 74.0 108.9 + angle_coeff @angle:013_079_048 62.0 102.0 + angle_coeff @angle:023_079_048 74.0 107.2 + angle_coeff @angle:005_079_048 75.0 96.4 + angle_coeff @angle:024_079_048 100.0 103.0 + angle_coeff @angle:013_079_082 62.0 102.0 + angle_coeff @angle:046_080_060 35.0 126.8 + angle_coeff @angle:002_080_060 70.0 128.6 + angle_coeff @angle:013_080_060 70.0 128.6 + angle_coeff @angle:046_080_084 35.0 126.8 + angle_coeff @angle:002_080_084 70.0 125.0 + angle_coeff @angle:013_080_084 70.0 125.0 + angle_coeff @angle:060_080_084 85.0 106.4 + angle_coeff @angle:012_081_057 70.0 132.8 + angle_coeff @angle:048_081_057 70.0 132.8 + angle_coeff @angle:057_081_060 70.0 104.4 + angle_coeff @angle:012_081_060 85.0 122.7 + angle_coeff @angle:048_081_060 85.0 122.7 + angle_coeff @angle:013_082_016 70.0 125.0 + angle_coeff @angle:016_082_024 70.0 125.0 + angle_coeff @angle:016_082_044 70.0 120.2 + angle_coeff @angle:020_082_049 35.0 117.0 + angle_coeff @angle:016_082_049 35.0 125.0 + angle_coeff @angle:049_082_057 35.0 120.0 + angle_coeff @angle:057_082_057 70.0 120.0 + angle_coeff @angle:013_082_057 70.0 125.0 + angle_coeff @angle:048_082_057 70.0 125.0 + angle_coeff @angle:056_082_057 70.0 126.2 + angle_coeff @angle:049_082_061 35.0 120.0 + angle_coeff @angle:016_082_061 70.0 115.0 + angle_coeff @angle:020_082_061 70.0 115.0 + angle_coeff @angle:057_082_061 70.0 120.0 + angle_coeff @angle:013_082_061 70.0 125.0 + angle_coeff @angle:044_082_061 70.0 126.1 + angle_coeff @angle:024_082_061 70.0 126.2 + angle_coeff @angle:057_082_079 70.0 120.0 + angle_coeff @angle:061_082_079 70.0 120.0 + angle_coeff @angle:020_082_086 70.0 122.0 + angle_coeff @angle:061_082_086 70.0 130.0 + angle_coeff @angle:057_082_087 70.0 106.2 + angle_coeff @angle:056_082_087 70.0 127.7 + angle_coeff @angle:049_083_061 35.0 120.0 + angle_coeff @angle:048_083_061 70.0 111.0 + angle_coeff @angle:013_083_061 70.0 124.5 + angle_coeff @angle:049_083_084 35.0 128.2 + angle_coeff @angle:061_083_084 70.0 111.0 + angle_coeff @angle:013_083_084 70.0 130.7 + angle_coeff @angle:013_084_016 70.0 125.0 + angle_coeff @angle:013_084_020 70.0 121.6 + angle_coeff @angle:016_084_024 70.0 125.0 + angle_coeff @angle:020_084_049 35.0 113.4 + angle_coeff @angle:016_084_049 35.0 125.0 + angle_coeff @angle:048_084_049 35.0 130.7 + angle_coeff @angle:049_084_050 35.0 130.7 + angle_coeff @angle:020_084_050 70.0 110.0 + angle_coeff @angle:049_084_057 35.0 121.6 + angle_coeff @angle:013_084_057 70.0 121.6 + angle_coeff @angle:048_084_057 70.0 121.6 + angle_coeff @angle:003_084_057 85.0 120.0 + angle_coeff @angle:057_084_058 35.0 120.0 + angle_coeff @angle:013_084_061 70.0 118.9 + angle_coeff @angle:049_084_080 35.0 120.0 + angle_coeff @angle:057_084_080 70.0 108.7 + angle_coeff @angle:049_084_083 35.0 130.7 + angle_coeff @angle:057_084_083 70.0 106.3 + angle_coeff @angle:020_084_083 70.0 108.0 + angle_coeff @angle:016_084_083 70.0 111.0 + angle_coeff @angle:013_084_083 70.0 130.7 + angle_coeff @angle:013_084_084 70.0 120.0 + angle_coeff @angle:057_084_084 70.0 120.0 + angle_coeff @angle:061_084_084 70.0 120.0 + angle_coeff @angle:020_084_086 70.0 121.6 + angle_coeff @angle:057_084_086 70.0 121.6 + angle_coeff @angle:049_084_087 35.0 132.1 + angle_coeff @angle:057_084_087 70.0 107.7 + angle_coeff @angle:020_084_087 70.0 110.6 + angle_coeff @angle:016_084_087 70.0 111.0 + angle_coeff @angle:061_084_087 70.0 111.9 + angle_coeff @angle:013_084_087 70.0 132.1 + angle_coeff @angle:048_084_087 70.0 132.1 + angle_coeff @angle:086_084_087 70.0 132.1 + angle_coeff @angle:003_084_087 85.0 120.0 + angle_coeff @angle:049_085_057 35.0 120.0 + angle_coeff @angle:013_085_057 70.0 121.6 + angle_coeff @angle:049_085_085 35.0 130.7 + angle_coeff @angle:057_085_085 70.0 106.3 + angle_coeff @angle:013_085_085 70.0 130.7 + angle_coeff @angle:048_086_048 63.0 120.0 + angle_coeff @angle:048_086_056 70.0 124.0 + angle_coeff @angle:048_086_082 63.0 120.0 + angle_coeff @angle:048_086_083 63.0 120.0 + angle_coeff @angle:048_086_084 63.0 120.0 + angle_coeff @angle:048_086_086 63.0 120.0 + angle_coeff @angle:056_086_086 70.0 124.0 + angle_coeff @angle:048_086_087 63.0 120.0 + angle_coeff @angle:048_086_088 63.0 120.0 + angle_coeff @angle:049_087_060 35.0 120.0 + angle_coeff @angle:046_087_060 35.0 126.8 + angle_coeff @angle:013_087_060 70.0 128.6 + angle_coeff @angle:049_087_084 35.0 125.7 + angle_coeff @angle:046_087_084 35.0 126.8 + angle_coeff @angle:084_087_084 70.0 103.8 + angle_coeff @angle:082_087_084 70.0 110.4 + angle_coeff @angle:002_087_084 70.0 125.0 + angle_coeff @angle:013_087_084 70.0 125.0 + angle_coeff @angle:003_087_084 70.0 130.0 + angle_coeff @angle:060_087_084 85.0 106.4 + angle_coeff @angle:084_087_086 70.0 125.7 + angle_coeff @angle:049_087_087 35.0 127.5 + angle_coeff @angle:060_087_087 70.0 107.3 + angle_coeff @angle:084_087_087 70.0 107.3 + angle_coeff @angle:086_087_087 70.0 127.5 + angle_coeff @angle:084_087_088 70.0 103.8 + angle_coeff @angle:048_088_049 35.0 128.6 + angle_coeff @angle:049_088_061 35.0 118.9 + angle_coeff @angle:013_088_061 70.0 118.9 + angle_coeff @angle:019_088_061 70.0 118.9 + angle_coeff @angle:061_088_087 70.0 111.9 + angle_coeff @angle:004_089_090 80.0 134.0 + angle_coeff @angle:090_089_091 70.0 91.0 + angle_coeff @angle:004_089_091 80.0 134.0 + angle_coeff @angle:013_090_089 55.0 127.0 + angle_coeff @angle:089_090_091 50.0 94.0 + angle_coeff @angle:013_090_091 50.0 126.0 + angle_coeff @angle:024_091_046 35.0 108.0 + angle_coeff @angle:013_091_046 35.0 114.3 + angle_coeff @angle:044_091_046 35.0 114.3 + angle_coeff @angle:046_091_046 35.0 114.3 + angle_coeff @angle:016_091_046 37.5 108.0 + angle_coeff @angle:046_091_047 35.0 109.5 + angle_coeff @angle:046_091_089 37.5 110.0 + angle_coeff @angle:024_091_089 70.0 117.0 + angle_coeff @angle:046_091_090 35.0 111.0 + angle_coeff @angle:016_091_090 55.0 109.0 + angle_coeff @angle:091_091_091 30.0 79.2 + angle_coeff @angle:013_091_091 37.5 117.2 + angle_coeff @angle:044_091_091 37.5 117.2 + angle_coeff @angle:046_091_091 37.5 117.2 + angle_coeff @angle:024_091_091 37.5 126.0 + angle_coeff @angle:016_091_091 55.0 128.0 + angle_coeff @angle:089_091_091 63.0 85.0 + angle_coeff @angle:047_091_091 63.0 114.0 + angle_coeff @angle:090_091_091 80.0 89.0 + angle_coeff @angle:013_095_013 172.8 120.0 + angle_coeff @angle:013_095_046 144.0 120.0 + angle_coeff @angle:013_101_045 35.0 109.5 + angle_coeff @angle:045_101_045 43.6 106.4 + angle_coeff @angle:045_101_048 50.0 112.5 + angle_coeff @angle:013_101_048 50.0 120.5 + angle_coeff @angle:013_102_103 80.0 117.5 + angle_coeff @angle:048_102_103 80.0 117.5 + angle_coeff @angle:103_102_103 80.0 125.0 + angle_coeff @angle:025_103_025 10.0 109.5 + angle_coeff @angle:025_103_102 10.0 109.5 + angle_coeff @angle:013_104_013 45.0 109.5 + angle_coeff @angle:003_105_010 70.0 117.6 + angle_coeff @angle:003_105_013 70.0 117.6 + angle_coeff @angle:003_105_045 35.0 119.2 + angle_coeff @angle:045_105_047 35.0 119.2 + angle_coeff @angle:013_105_047 70.0 121.2 + angle_coeff @angle:003_105_047 70.0 121.6 + angle_coeff @angle:003_105_051 70.0 117.6 + angle_coeff @angle:047_105_051 70.0 121.2 + angle_coeff @angle:045_105_060 30.0 125.8 + angle_coeff @angle:006_105_060 70.0 125.8 + angle_coeff @angle:010_105_060 70.0 125.8 + angle_coeff @angle:013_105_060 70.0 125.8 + angle_coeff @angle:051_105_060 70.0 125.8 + angle_coeff @angle:045_105_062 30.0 128.8 + angle_coeff @angle:060_105_062 70.0 105.4 + angle_coeff @angle:006_105_062 70.0 128.8 + angle_coeff @angle:010_105_062 70.0 128.8 + angle_coeff @angle:013_105_062 70.0 128.8 + angle_coeff @angle:051_105_062 70.0 128.8 + angle_coeff @angle:004_106_024 20.0 109.5 + angle_coeff @angle:024_106_024 20.0 109.5 + angle_coeff @angle:013_107_013 50.0 118.0 + angle_coeff @angle:003_107_013 50.0 121.9 + angle_coeff @angle:001_108_013 35.0 110.5 + angle_coeff @angle:013_108_013 60.0 110.0 + angle_coeff @angle:013_108_020 60.0 100.0 + angle_coeff @angle:020_108_020 60.0 110.0 + angle_coeff @angle:013_108_021 35.0 110.5 + angle_coeff @angle:045_108_045 35.0 109.5 + angle_coeff @angle:013_108_045 35.0 110.5 + angle_coeff @angle:046_108_046 35.0 109.5 + angle_coeff @angle:013_108_046 35.0 110.5 + angle_coeff @angle:013_108_065 35.0 110.5 + angle_coeff @angle:013_108_066 35.0 110.5 + angle_coeff @angle:013_108_108 50.0 112.0 + angle_coeff @angle:046_109_048 35.0 123.3 + angle_coeff @angle:046_109_050 35.0 120.0 + angle_coeff @angle:013_109_050 70.0 124.0 + angle_coeff @angle:046_109_109 35.0 120.0 + angle_coeff @angle:013_109_109 70.0 124.0 + angle_coeff @angle:050_109_109 70.0 124.0 + angle_coeff @angle:048_109_109 85.0 117.0 + angle_coeff @angle:004_110_047 160.0 180.0 + angle_coeff @angle:047_110_047 160.0 180.0 } #(end of angle_coeffs) # Rules for creating angle interactions according to atom type: @@ -5492,1023 +5505,1023 @@ OPLSAA { # (* = wildcard) write_once("Data Angles By Type") { - @angle:25-1-25 @atom:*_b*_a25_d*_i* @atom:*_b*_a1_d*_i* @atom:*_b*_a25_d*_i* - @angle:1-2-2 @atom:*_b*_a1_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* - @angle:2-2-2 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* - @angle:2-2-3 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* - @angle:2-2-5 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a5_d*_i* - @angle:2-2-6 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:6-2-6 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:5-2-6 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a6_d*_i* - @angle:2-2-10 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:3-2-10 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:6-2-10 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:10-2-10 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:5-2-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a10_d*_i* - @angle:10-2-12 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a12_d*_i* - @angle:6-2-13 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a13_d*_i* - @angle:10-2-15 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a15_d*_i* - @angle:2-2-16 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i* - @angle:10-2-16 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a16_d*_i* - @angle:2-2-20 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:6-2-20 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:10-2-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a20_d*_i* - @angle:3-2-24 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-2-24 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-2-44 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:6-2-44 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:10-2-44 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:13-2-44 @atom:*_b*_a13_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:3-2-44 @atom:*_b*_a3_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a44_d*_i* - @angle:2-2-48 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i* - @angle:10-2-48 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a48_d*_i* - @angle:2-2-51 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i* - @angle:6-2-51 @atom:*_b*_a6_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a51_d*_i* - @angle:2-2-53 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a53_d*_i* - @angle:2-2-55 @atom:*_b*_a2_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a55_d*_i* - @angle:10-2-80 @atom:*_b*_a10_d*_i* @atom:*_b*_a2_d*_i* @atom:*_b*_a80_d*_i* - @angle:2-3-4 @atom:*_b*_a2_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:1-3-4 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:3-3-4 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:4-3-4 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a4_d*_i* - @angle:4-3-5 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a5_d*_i* - @angle:4-3-6 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a6_d*_i* - @angle:5-3-10 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i* - @angle:4-3-10 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a10_d*_i* - @angle:5-3-12 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i* - @angle:12-3-12 @atom:*_b*_a12_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a12_d*_i* - @angle:5-3-13 @atom:*_b*_a5_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:13-3-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:1-3-13 @atom:*_b*_a1_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:3-3-13 @atom:*_b*_a3_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:4-3-13 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a13_d*_i* - @angle:10-3-20 @atom:*_b*_a10_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:13-3-20 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:4-3-20 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a20_d*_i* - @angle:13-3-21 @atom:*_b*_a13_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i* - @angle:4-3-21 @atom:*_b*_a4_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a21_d*_i* - @angle:24-3-24 @atom:*_b*_a24_d*_i* @atom:*_b*_a3_d*_i* @atom:*_b*_a24_d*_i* - @angle:2-3-24 @atom:*_b*_a2_d*_i* 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@angle:002_011_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_011_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_011_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_011_011 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:006_011_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_011_011 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:010_011_011 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:011_011_011 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_011_013 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:011_011_013 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:002_011_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:006_011_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:010_011_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_011_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:009_011_014 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:011_011_014 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:009_011_079 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:002_012_012 @atom:*_b*_a002*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:003_012_012 @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:012_012_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:012_012_048 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:012_012_060 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:012_012_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:001_013_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a001*_d*_i* + @angle:002_013_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:001_013_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:002_013_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_013_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:002_013_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_013_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_013_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:001_013_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_013_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_013_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_013_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_013_015 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* + @angle:013_013_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:013_013_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:003_013_020 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_013_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:003_013_021 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:013_013_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:021_013_021 @atom:*_b*_a021*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:013_013_022 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* + @angle:020_013_024 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:003_013_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:002_013_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:013_013_024 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:016_013_044 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:002_013_044 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:006_013_044 @atom:*_b*_a006*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:010_013_044 @atom:*_b*_a010*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:013_013_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:003_013_044 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:046_013_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:018_013_046 @atom:*_b*_a018*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:019_013_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:002_013_046 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:003_013_046 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:005_013_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:015_013_046 @atom:*_b*_a015*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:016_013_046 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:020_013_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:022_013_046 @atom:*_b*_a022*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:024_013_046 @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:044_013_046 @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* + 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@angle:046_013_102 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:013_013_102 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:046_013_104 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* + @angle:013_013_104 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* + @angle:046_013_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_013_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_013_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:046_013_107 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* + @angle:013_013_107 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* + @angle:046_013_108 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:013_013_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:002_014_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_014_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_014_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_014_009 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a009*_d*_i* + @angle:006_014_009 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a009*_d*_i* + @angle:009_014_010 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_014_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_014_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_014_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_014_011 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:006_014_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_014_011 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:010_014_011 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:011_014_011 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:009_014_013 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:011_014_013 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:002_014_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:006_014_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:010_014_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_014_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:002_014_014 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:006_014_014 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:009_014_014 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:010_014_014 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:011_014_014 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:013_014_014 @atom:*_b*_a013*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:014_014_014 @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* + @angle:017_015_017 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* + @angle:002_015_017 @atom:*_b*_a002*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* + @angle:006_015_017 @atom:*_b*_a006*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* + @angle:013_015_017 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* + @angle:025_015_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_015_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:033_015_033 @atom:*_b*_a033*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:002_015_033 @atom:*_b*_a002*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:006_015_033 @atom:*_b*_a006*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:013_015_033 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:017_015_033 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:017_015_048 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_016_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:013_016_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:002_016_016 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:006_016_016 @atom:*_b*_a006*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:013_016_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:013_016_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:025_016_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_016_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:033_016_033 @atom:*_b*_a033*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:002_016_033 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:006_016_033 @atom:*_b*_a006*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:013_016_033 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:016_016_033 @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:013_016_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_016_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:024_016_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:025_016_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:025_016_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_016_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:025_016_084 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_016_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_016_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_016_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_016_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:015_017_025 @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_017_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_018_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:019_018_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:018_018_056 @atom:*_b*_a018*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_019_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* + @angle:016_019_019 @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:013_019_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* + @angle:018_019_025 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:019_019_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:018_019_047 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:019_019_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:018_019_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_019_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_019_050 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:018_019_055 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:018_019_088 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:002_020_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_020_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_020_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_020_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_020_007 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a007*_d*_i* + @angle:007_020_010 @atom:*_b*_a007*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:003_020_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_020_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:013_020_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_020_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_020_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_020_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_020_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:025_020_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_020_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_020_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_020_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_020_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_020_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_020_051 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:002_020_051 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:006_020_051 @atom:*_b*_a006*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:010_020_051 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:024_020_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:025_020_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:002_020_064 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:006_020_064 @atom:*_b*_a006*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:010_020_064 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:013_020_064 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:048_020_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:064_020_064 @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:025_020_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_020_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:082_020_082 @atom:*_b*_a082*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:025_020_084 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_020_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_020_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_020_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:061_020_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:108_020_108 @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:013_020_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:025_021_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a021*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_022_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_022_023 @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a023*_d*_i* + @angle:023_022_025 @atom:*_b*_a023*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:002_024_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_024_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_024_005 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:002_024_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_024_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_024_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:003_024_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:013_024_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_024_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_024_016 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* + @angle:003_024_020 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:003_024_025 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_024_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:005_024_045 @atom:*_b*_a005*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:003_024_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_024_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:002_024_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:006_024_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:010_024_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_024_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_024_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_024_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_024_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_024_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:054_024_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:045_024_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:003_024_059 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:013_024_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:045_024_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:045_024_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:048_024_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:016_024_086 @atom:*_b*_a016*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:045_024_087 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:048_024_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:045_024_088 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:048_024_088 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:045_024_091 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:003_024_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:048_024_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:003_024_106 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* + @angle:025_025_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:032_031_032 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a032*_d*_i* + @angle:032_031_033 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a033*_d*_i* + @angle:035_034_035 @atom:*_b*_a035*_d*_i* @atom:*_b*_a034*_d*_i* @atom:*_b*_a035*_d*_i* + @angle:037_036_037 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a037*_d*_i* + @angle:037_036_038 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a038*_d*_i* + @angle:040_039_040 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a040*_d*_i* + @angle:041_039_041 @atom:*_b*_a041*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* + @angle:040_039_041 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* + @angle:043_042_043 @atom:*_b*_a043*_d*_i* @atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i* + @angle:002_044_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a002*_d*_i* + @angle:002_044_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:006_044_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:002_044_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:006_044_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:010_044_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:002_044_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:006_044_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:010_044_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_044_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_044_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_044_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_044_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:002_044_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:006_044_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:010_044_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_044_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:025_044_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_044_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_044_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_044_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_044_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_044_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:013_044_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:048_044_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:048_044_091 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:025_045_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_045_044 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:025_046_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:013_046_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:001_047_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a001*_d*_i* + @angle:001_047_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_047_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:003_047_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_047_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_047_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:020_047_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_047_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_047_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:003_047_046 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:019_047_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:001_047_046 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:021_047_046 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:025_047_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_047_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:005_047_047 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:020_047_047 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_047_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:019_047_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:021_047_047 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:001_047_047 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:016_047_047 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_047_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_047_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_047_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_047_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_047_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_047_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:005_047_050 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:020_047_050 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_047_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_047_057 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_047_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:020_047_057 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:047_047_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:016_047_057 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_047_058 @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* + @angle:047_047_058 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* + @angle:046_047_065 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:047_047_065 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:046_047_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:003_047_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:047_047_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:046_047_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:058_047_105 @atom:*_b*_a058*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_047_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_047_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:047_047_105 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:016_047_105 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:046_047_110 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:013_047_110 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:048_047_110 @atom:*_b*_a048*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:001_047_110 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* + @angle:002_048_012 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:012_048_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* + @angle:003_048_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:025_048_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_048_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_048_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_048_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:010_048_048 @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_048_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:015_048_048 @atom:*_b*_a015*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:019_048_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_048_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:024_048_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:044_048_048 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_048_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:021_048_048 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:001_048_048 @atom:*_b*_a001*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:018_048_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:016_048_048 @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_048_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_048_049 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:024_048_049 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:003_048_049 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:048_048_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* + @angle:048_048_050 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:048_048_053 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* + @angle:055_048_055 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:047_048_055 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:048_048_055 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:049_048_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_048_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:044_048_056 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:055_048_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:005_048_056 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:047_048_056 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:050_048_056 @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:048_048_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:021_048_056 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:049_048_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_048_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:055_048_057 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:013_048_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:047_048_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:056_048_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:049_048_060 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_048_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:057_048_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:056_048_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:055_048_060 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:002_048_060 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_048_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:049_048_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_048_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_048_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_048_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a064*_d*_i* + @angle:048_048_065 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:048_048_066 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a066*_d*_i* + @angle:048_048_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a079*_d*_i* + @angle:049_048_081 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:048_048_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:049_048_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_048_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:048_048_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:049_048_086 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:048_048_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:056_048_086 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:049_048_088 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:101_048_101 @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* + @angle:056_048_101 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* + @angle:048_048_102 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:048_048_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:025_050_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:019_050_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:025_050_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_050_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_050_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_050_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:046_050_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:047_050_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_050_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_050_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_050_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:047_050_050 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:050_050_084 @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_050_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:046_050_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:013_050_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:047_050_109 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:006_051_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a006*_d*_i* + @angle:005_051_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_051_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:002_051_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:006_051_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:005_051_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_051_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:046_051_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:005_051_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:020_051_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_051_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:046_051_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_051_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:020_051_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:013_053_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_053_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:045_053_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:025_053_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_053_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_053_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:006_053_054 @atom:*_b*_a006*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:013_053_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:048_053_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:054_053_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:025_053_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:013_055_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:045_055_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_055_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_055_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_055_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:006_055_048 @atom:*_b*_a006*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_055_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:002_055_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:013_055_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:048_055_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:054_055_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* + @angle:045_055_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:003_056_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_056_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a018*_d*_i* + @angle:025_056_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_056_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_056_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_056_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_056_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_056_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:048_056_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:025_056_059 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:048_056_059 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:059_056_059 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* + @angle:059_056_060 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_056_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:059_056_082 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:048_056_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a086*_d*_i* + @angle:013_056_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:003_057_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* + @angle:003_057_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_057_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_057_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:045_057_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:003_057_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_057_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:045_057_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_057_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:060_057_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:045_057_061 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:013_057_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_057_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:045_057_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:060_057_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:048_057_062 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:013_057_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:045_057_081 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:045_057_082 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:061_057_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_057_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:045_057_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:061_057_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_057_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_057_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:084_057_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:081_057_084 @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:045_057_085 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:082_057_085 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* + @angle:024_059_055 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a055*_d*_i* + @angle:049_059_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:013_059_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:055_059_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:024_059_056 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:056_059_056 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* + @angle:056_059_063 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a063*_d*_i* + @angle:013_060_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:048_060_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:056_060_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_060_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:020_060_060 @atom:*_b*_a020*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:016_060_060 @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_060_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:024_060_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:056_060_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_060_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:003_060_060 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:060_060_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:024_060_061 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:003_060_061 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:048_060_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:012_060_080 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:048_060_080 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* + @angle:080_060_081 @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:012_060_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:048_060_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* + @angle:003_060_084 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_060_087 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:057_060_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:081_060_087 @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:012_060_087 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:048_060_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* + @angle:060_060_105 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:056_060_105 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:048_061_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:025_061_057 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:025_061_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:060_061_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:025_061_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:061_061_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:060_061_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:082_061_083 @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a083*_d*_i* + @angle:057_061_084 @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:082_061_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:057_061_088 @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:020_061_088 @atom:*_b*_a020*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* + @angle:049_062_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:049_062_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_062_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a061*_d*_i* + @angle:057_062_063 @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a063*_d*_i* + @angle:061_062_063 @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a063*_d*_i* + @angle:049_062_105 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:063_062_105 @atom:*_b*_a063*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:061_062_105 @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* + @angle:005_064_005 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:004_064_005 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* + @angle:004_064_013 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_064_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_064_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_064_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:004_064_020 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:004_064_048 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_064_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:020_064_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_064_052 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:013_064_052 @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:020_064_052 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:052_064_052 @atom:*_b*_a052*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* + @angle:025_065_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a065*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_066_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a066*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:078_077_078 @atom:*_b*_a078*_d*_i* @atom:*_b*_a077*_d*_i* @atom:*_b*_a078*_d*_i* + @angle:006_079_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a011*_d*_i* + @angle:013_079_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_079_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:005_079_023 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* + @angle:013_079_023 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* + @angle:023_079_023 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* + @angle:013_079_024 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:023_079_024 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:013_079_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:023_079_044 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a044*_d*_i* + @angle:013_079_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:023_079_048 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:005_079_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:024_079_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_079_082 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a082*_d*_i* + @angle:046_080_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:002_080_060 @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_080_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:046_080_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:002_080_084 @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:013_080_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:060_080_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* + @angle:012_081_057 @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:048_081_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* + @angle:057_081_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:012_081_060 @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:048_081_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* + 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@angle:016_091_091 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:089_091_091 @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:047_091_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:090_091_091 @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* + @angle:013_095_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_095_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_101_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_101_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_101_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_101_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:013_102_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:048_102_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:103_102_103 @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* + @angle:025_103_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a025*_d*_i* + @angle:025_103_102 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* + @angle:013_104_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_105_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a010*_d*_i* + @angle:003_105_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_105_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:045_105_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:013_105_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_105_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:003_105_051 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:047_105_051 @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* + @angle:045_105_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:006_105_060 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:010_105_060 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:013_105_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:051_105_060 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* + @angle:045_105_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:060_105_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:006_105_062 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:010_105_062 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:013_105_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:051_105_062 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* + @angle:004_106_024 @atom:*_b*_a004*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:024_106_024 @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* + @angle:013_107_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:003_107_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:001_108_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_108_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* + @angle:013_108_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:020_108_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* + @angle:013_108_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a021*_d*_i* + @angle:045_108_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:013_108_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* + @angle:046_108_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_108_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* + @angle:013_108_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a065*_d*_i* + @angle:013_108_066 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a066*_d*_i* + @angle:013_108_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a108*_d*_i* + @angle:046_109_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a048*_d*_i* + @angle:046_109_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:013_109_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* + @angle:046_109_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:013_109_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:050_109_109 @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:048_109_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* + @angle:004_110_047 @atom:*_b*_a004*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* + @angle:047_110_047 @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* } #(end of angles by type) @@ -6517,809 +6530,809 @@ OPLSAA { # ----------- Dihedral Interactions: ------------ # http://lammps.sandia.gov/doc/dihedral_opls.html # Syntax: - # dihedral_coeff DihedralTypeName DihedralStyle parameters... + # dihedral_coeff DihedralTypeName parameters... write_once("In Settings") { - dihedral_coeff @dihedral:X-2-2-2 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:X-2-2-6 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:1-2-2-2 opls -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:1-2-2-6 opls -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:2-2-2-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-6 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-10 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-13 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-2-65 opls -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:6-2-2-6 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:6-2-2-65 opls -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:10-2-2-10 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:6-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:10-2-5-7 opls 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:X-2-10-2 opls -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-10-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:2-2-13-2 opls -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:6-2-20-2 opls -7.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:6-2-20-6 opls -8.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:4-3-3-4 opls 1.6 3.2 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-13 opls 0.0 0.5 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-24 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-3-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-13 opls 0.7 -1.5 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-24 opls -0.5 0.2 0.0 0.0 - dihedral_coeff @dihedral:13-3-3-46 opls 0.8 -0.76 0.0 0.0 - dihedral_coeff @dihedral:24-3-3-46 opls -0.9 0.3 0.0 0.0 - dihedral_coeff @dihedral:46-3-3-46 opls 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:3-3-5-7 opls 3.0 5.5 0.0 0.0 - dihedral_coeff @dihedral:4-3-5-7 opls 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-5-7 opls 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:24-3-5-7 opls -2.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-5-7 opls 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:48-3-5-7 opls 4.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:1-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:1-3-13-46 opls 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:3-3-13-46 opls 0.0 0.0 0.085 0.0 - dihedral_coeff @dihedral:4-3-13-X opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-21 opls -0.65 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-44 opls 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-24 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-13-48 opls 0.0 0.546 0.0 0.0 - dihedral_coeff @dihedral:5-3-13-13 opls 0.0 1.412 0.0 0.0 - dihedral_coeff @dihedral:5-3-13-44 opls 5.26 0.82 0.0 0.0 - dihedral_coeff @dihedral:5-3-13-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-13-13 opls 1.454 -0.144 -0.775 0.0 - dihedral_coeff @dihedral:13-3-13-46 opls 0.0 0.0 0.275 0.0 - dihedral_coeff @dihedral:20-3-13-13 opls 0.0 0.0 -0.553 0.0 - dihedral_coeff @dihedral:20-3-13-46 opls 0.0 0.0 0.132 0.0 - dihedral_coeff @dihedral:21-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:21-3-13-46 opls 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:24-3-13-13 opls 1.173 0.189 -1.2 0.0 - dihedral_coeff @dihedral:24-3-13-21 opls 0.65 0.0 0.0 0.0 - dihedral_coeff @dihedral:24-3-13-24 opls 1.816 1.222 1.581 0.0 - dihedral_coeff @dihedral:24-3-13-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-13-46 opls 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:48-3-13-46 opls 0.0 0.0 0.275 0.0 - dihedral_coeff @dihedral:52-3-13-13 opls 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:52-3-13-44 opls 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:52-3-13-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:65-3-13-13 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:65-3-13-46 opls 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:107-3-13-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-20-13 opls 0.0 5.124 0.0 0.0 - dihedral_coeff @dihedral:4-3-20-48 opls 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-20-13 opls 4.669 5.124 0.0 0.0 - dihedral_coeff @dihedral:13-3-20-48 opls 1.5 5.0 0.0 0.0 - dihedral_coeff @dihedral:24-3-20-13 opls -2.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-20-13 opls 4.669 5.124 0.0 0.0 - dihedral_coeff @dihedral:48-3-20-13 opls 4.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:3-3-24-13 opls 0.4 4.9 0.0 0.0 - dihedral_coeff @dihedral:3-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-5 opls 0.0 6.603 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-13 opls 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-47 opls 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-48 opls 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:4-3-24-91 opls 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:5-3-24-13 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:5-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:13-3-24-5 opls 4.542 6.603 1.045 0.0 - dihedral_coeff @dihedral:13-3-24-13 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:13-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:13-3-24-48 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:20-3-24-13 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:20-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:24-3-24-3 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:24-3-24-13 opls 4.6 0.0 0.0 0.0 - dihedral_coeff @dihedral:24-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:46-3-24-13 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:46-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:47-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:48-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:48-3-24-48 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:48-3-24-84 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:48-3-24-87 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:84-3-24-48 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:84-3-24-84 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:84-3-24-87 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:87-3-24-45 opls 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:87-3-24-48 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:87-3-24-84 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:87-3-24-87 opls 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:X-3-47-13 opls 0.9 0.23 -0.505 0.0 - dihedral_coeff @dihedral:4-3-47-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-47-47 opls 2.5 6.0 0.0 0.0 - dihedral_coeff @dihedral:5-3-47-47 opls 3.2 -3.0 0.0 0.0 - dihedral_coeff @dihedral:24-3-47-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:24-3-47-47 opls 2.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:107-3-47-46 opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:107-3-47-47 opls 2.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-48-48 opls 0.0 2.1 0.0 0.0 - dihedral_coeff @dihedral:5-3-48-48 opls 0.0 2.1 0.0 0.0 - dihedral_coeff @dihedral:13-3-48-48 opls 0.0 0.2 0.0 0.0 - dihedral_coeff @dihedral:20-3-48-48 opls 0.0 2.1 0.0 0.0 - dihedral_coeff @dihedral:24-3-48-48 opls 0.0 1.1 0.0 0.0 - dihedral_coeff @dihedral:46-3-48-48 opls 0.0 0.2 0.0 0.0 - dihedral_coeff @dihedral:X-3-50-13 opls 0.9 0.23 -0.505 0.0 - dihedral_coeff @dihedral:4-3-50-47 opls 2.5 6.0 0.0 0.0 - dihedral_coeff @dihedral:5-3-50-47 opls 3.2 -3.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-50-47 opls 0.8 -3.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-56-X opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:13-3-56-13 opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-56-X opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:46-3-56-45 opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:X-3-60-X opls 0.0 7.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-60-X opls 0.0 7.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-82-X opls 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-82-57 opls 2.0 1.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-82-61 opls 0.0 1.0 0.0 0.0 - dihedral_coeff @dihedral:82-3-82-57 opls -2.0 1.0 0.0 0.0 - dihedral_coeff @dihedral:82-3-82-61 opls 0.0 1.0 0.0 0.0 - dihedral_coeff @dihedral:4-3-84-20 opls -0.75 1.5 0.0 0.0 - dihedral_coeff @dihedral:4-3-84-87 opls 0.75 1.5 0.0 0.0 - 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@dihedral:002_002_002_002 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_002_006 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_002_010 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_002_013 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_002_065 -2.0 0.5 3.25 0.0 + dihedral_coeff @dihedral:006_002_002_006 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:006_002_002_065 -2.0 0.5 3.25 0.0 + dihedral_coeff @dihedral:010_002_002_010 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_005_007 0.3 0.0 1.3 0.0 + dihedral_coeff @dihedral:006_002_005_007 0.3 0.0 1.3 0.0 + dihedral_coeff @dihedral:010_002_005_007 0.3 0.0 1.3 0.0 + dihedral_coeff @dihedral:X_002_010_002 -2.5 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_010_002 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:002_002_013_002 -3.4 1.25 3.1 0.0 + dihedral_coeff @dihedral:006_002_020_002 -7.4 3.0 1.8 0.0 + dihedral_coeff @dihedral:006_002_020_006 -8.4 3.0 1.8 0.0 + dihedral_coeff @dihedral:004_003_003_004 1.6 3.2 0.0 0.0 + dihedral_coeff @dihedral:004_003_003_013 0.0 0.5 0.0 0.0 + dihedral_coeff @dihedral:004_003_003_024 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_003_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_003_013 0.7 -1.5 0.0 0.0 + dihedral_coeff @dihedral:013_003_003_024 -0.5 0.2 0.0 0.0 + dihedral_coeff @dihedral:013_003_003_046 0.8 -0.76 0.0 0.0 + dihedral_coeff @dihedral:024_003_003_046 -0.9 0.3 0.0 0.0 + dihedral_coeff @dihedral:046_003_003_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:003_003_005_007 3.0 5.5 0.0 0.0 + dihedral_coeff @dihedral:004_003_005_007 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_005_007 1.5 5.5 0.0 0.0 + dihedral_coeff @dihedral:024_003_005_007 -2.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_005_007 1.5 5.5 0.0 0.0 + dihedral_coeff @dihedral:048_003_005_007 4.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:001_003_013_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:001_003_013_046 0.0 0.0 0.36 0.0 + dihedral_coeff @dihedral:003_003_013_046 0.0 0.0 0.085 0.0 + dihedral_coeff @dihedral:004_003_013_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_021 -0.65 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_044 0.0 0.82 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_024 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_013_048 0.0 0.546 0.0 0.0 + dihedral_coeff @dihedral:005_003_013_013 0.0 1.412 0.0 0.0 + dihedral_coeff @dihedral:005_003_013_044 5.26 0.82 0.0 0.0 + dihedral_coeff @dihedral:005_003_013_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_013_013 1.454 -0.144 -0.775 0.0 + dihedral_coeff @dihedral:013_003_013_046 0.0 0.0 0.275 0.0 + dihedral_coeff @dihedral:020_003_013_013 0.0 0.0 -0.553 0.0 + dihedral_coeff @dihedral:020_003_013_046 0.0 0.0 0.132 0.0 + dihedral_coeff @dihedral:021_003_013_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:021_003_013_046 0.0 0.0 0.36 0.0 + dihedral_coeff @dihedral:024_003_013_013 1.173 0.189 -1.2 0.0 + dihedral_coeff @dihedral:024_003_013_021 0.65 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_003_013_024 1.816 1.222 1.581 0.0 + dihedral_coeff @dihedral:024_003_013_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_013_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_013_046 0.0 0.0 0.36 0.0 + dihedral_coeff @dihedral:048_003_013_046 0.0 0.0 0.275 0.0 + dihedral_coeff @dihedral:052_003_013_013 0.0 0.82 0.0 0.0 + dihedral_coeff @dihedral:052_003_013_044 0.0 0.82 0.0 0.0 + dihedral_coeff @dihedral:052_003_013_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:065_003_013_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:065_003_013_046 0.0 0.0 0.36 0.0 + dihedral_coeff @dihedral:107_003_013_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_003_020_013 0.0 5.124 0.0 0.0 + dihedral_coeff @dihedral:004_003_020_048 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:013_003_020_013 4.669 5.124 0.0 0.0 + dihedral_coeff @dihedral:013_003_020_048 1.5 5.0 0.0 0.0 + dihedral_coeff @dihedral:024_003_020_013 -2.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:046_003_020_013 4.669 5.124 0.0 0.0 + dihedral_coeff @dihedral:048_003_020_013 4.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:003_003_024_013 0.4 4.9 0.0 0.0 + dihedral_coeff @dihedral:003_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_005 0.0 6.603 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_013 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_047 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_048 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_003_024_091 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:005_003_024_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:005_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:013_003_024_005 4.542 6.603 1.045 0.0 + dihedral_coeff @dihedral:013_003_024_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:013_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:013_003_024_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:020_003_024_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:020_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:024_003_024_003 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:024_003_024_013 4.6 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:046_003_024_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:046_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:047_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:048_003_024_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:048_003_024_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:048_003_024_084 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:048_003_024_087 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:084_003_024_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:084_003_024_084 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:084_003_024_087 2.3 6.089 0.0 0.0 + dihedral_coeff 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@dihedral:003_013_013_046 0.0 0.0 -0.1 0.0 + dihedral_coeff @dihedral:003_013_013_048 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_080 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:005_013_013_005 9.508 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_013 -1.552 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_020 4.319 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_044 8.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:005_013_013_024 6.28 -1.467 2.03 0.0 + dihedral_coeff @dihedral:005_013_013_046 0.0 0.0 0.468 0.0 + dihedral_coeff @dihedral:013_013_013_013 1.3 -0.05 0.2 0.0 + dihedral_coeff @dihedral:013_013_013_015 1.262 -0.198 0.465 0.0 + dihedral_coeff @dihedral:013_013_013_016 2.619 -0.62 0.258 0.0 + dihedral_coeff @dihedral:013_013_013_019 0.0 -0.65 0.0 0.0 + dihedral_coeff @dihedral:013_013_013_021 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:013_013_013_044 2.392 -0.674 0.55 0.0 + dihedral_coeff @dihedral:013_013_013_024 0.845 -0.962 0.713 0.0 + 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@dihedral:044_013_013_044 11.035 -0.968 0.27 0.0 + dihedral_coeff @dihedral:044_013_013_046 -1.013 -0.709 0.473 0.0 + dihedral_coeff @dihedral:044_013_013_048 -0.8 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_046 0.0 0.0 0.464 0.0 + dihedral_coeff @dihedral:024_013_013_048 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:024_013_013_080 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:046_013_013_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_013_047 0.0 0.0 0.366 0.0 + dihedral_coeff @dihedral:046_013_013_048 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_051 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_013_013_053 0.0 0.0 0.384 0.0 + dihedral_coeff @dihedral:046_013_013_055 0.0 0.0 -0.582 0.0 + dihedral_coeff @dihedral:046_013_013_059 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_062 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:046_013_013_065 0.0 0.0 0.4 0.0 + dihedral_coeff @dihedral:046_013_013_066 0.0 0.0 0.4 0.0 + dihedral_coeff 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0.925 -0.576 0.677 0.0 + dihedral_coeff @dihedral:013_013_016_016 1.941 -0.836 0.935 0.0 + dihedral_coeff @dihedral:046_013_016_013 0.0 0.0 0.647 0.0 + dihedral_coeff @dihedral:046_013_016_016 0.0 0.0 0.558 0.0 + dihedral_coeff @dihedral:046_013_016_048 0.0 0.0 0.647 0.0 + dihedral_coeff @dihedral:X_013_018_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_018_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_019_018 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_013_019_019 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_013_020_013 -0.521 -2.018 1.996 0.0 + dihedral_coeff @dihedral:056_013_020_013 -0.5 -1.5 1.0 0.0 + dihedral_coeff @dihedral:057_013_020_013 -0.5 -1.5 1.0 0.0 + dihedral_coeff @dihedral:013_013_020_003 -1.22 -0.126 0.422 0.0 + dihedral_coeff @dihedral:013_013_020_013 0.65 -0.25 0.67 0.0 + dihedral_coeff @dihedral:013_013_020_064 -1.42 -0.62 0.1 0.0 + 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dihedral_coeff @dihedral:013_016_016_013 0.0 -7.414 1.705 0.0 + dihedral_coeff @dihedral:013_016_048_048 0.0 0.6 0.0 0.0 + dihedral_coeff @dihedral:013_016_048_056 1.6 5.1 0.0 0.0 + dihedral_coeff @dihedral:013_016_059_056 0.0 4.8 0.0 0.0 + dihedral_coeff @dihedral:084_016_082_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:084_016_082_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_016_084_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_016_084_083 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_016_084_088 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_016_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:019_018_048_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:019_018_048_048 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:018_018_056_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:018_018_056_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_019_019_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_019_019_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_019_019_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_019_019_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_019_019_109 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_019_019_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_019_019_109 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:019_019_047_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:019_019_047_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:019_019_047_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_020_044_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_020_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_020_047_013 0.65 -0.25 0.67 0.0 + dihedral_coeff @dihedral:013_020_047_046 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:013_020_047_047 -3.5 3.0 0.0 0.0 + dihedral_coeff @dihedral:013_020_047_050 -3.5 3.0 0.0 0.0 + dihedral_coeff @dihedral:003_020_048_048 0.0 2.5 0.0 0.0 + dihedral_coeff @dihedral:013_020_048_048 0.0 3.0 0.0 0.0 + dihedral_coeff @dihedral:013_020_048_056 0.4 5.5 0.0 0.0 + dihedral_coeff @dihedral:064_020_048_048 0.0 2.99 0.0 0.0 + dihedral_coeff @dihedral:013_020_051_005 -0.375 -1.358 0.004 0.0 + dihedral_coeff @dihedral:013_020_051_013 0.65 -0.25 0.67 0.0 + dihedral_coeff @dihedral:013_020_051_020 -0.375 -1.358 0.004 0.0 + dihedral_coeff @dihedral:013_020_051_046 0.0 0.0 0.76 0.0 + dihedral_coeff @dihedral:013_020_056_003 3.0 3.0 0.0 0.0 + dihedral_coeff @dihedral:013_020_059_056 0.0 5.2 0.0 0.0 + dihedral_coeff @dihedral:X_020_064_052 0.0 0.0 0.562 0.0 + dihedral_coeff @dihedral:013_020_064_013 3.5 -3.3 1.5 0.0 + dihedral_coeff @dihedral:013_020_064_052 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_020_064_004 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:084_020_082_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_020_084_088 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:084_020_084_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:084_020_084_087 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:108_020_108_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:108_020_108_020 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:003_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:013_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:059_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:082_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:084_024_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:X_024_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_059_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:045_024_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_024_079_023 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_024_079_048 2.074 -2.966 2.473 0.0 + dihedral_coeff @dihedral:045_024_079_048 1.671 -4.901 0.669 0.0 + dihedral_coeff @dihedral:013_024_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_082_020 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_024_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_024_082_020 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_024_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:X_024_084_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_024_084_084 0.0 3.0 0.0 0.0 + dihedral_coeff @dihedral:045_024_084_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_024_084_020 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_024_084_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_024_084_020 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:003_024_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_024_086_056 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_024_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:047_024_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:047_024_086_056 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_024_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_024_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_024_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_024_091_089 -1.396 -0.427 0.0 0.0 + dihedral_coeff @dihedral:003_024_091_091 -1.396 -0.427 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_089 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:045_024_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_024_106_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_044_044_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_044_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:045_044_044_045 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_044_048_048 -7.582 3.431 3.198 0.0 + dihedral_coeff @dihedral:045_044_048_048 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:059_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:082_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:084_044_048_048 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_044_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_044_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_044_082_016 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_044_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:047_046_047_013 0.0 -8.0 0.0 0.0 + dihedral_coeff @dihedral:047_046_047_046 0.0 -8.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_047_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_047_019 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:003_047_047_024 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:003_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:005_047_047_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:005_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_019 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_020 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:019_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:020_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:021_047_047_021 -1.6 14.0 0.0 0.0 + dihedral_coeff @dihedral:021_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_047_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_047_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_048_048 0.205 -0.531 0.0 0.0 + dihedral_coeff @dihedral:046_047_048_048 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_047_048_056 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_047_048_048 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:013_047_050_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_047_050_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:024_047_050_003 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_050_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:X_047_084_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_047_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:003_047_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_047_086_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_047_086_024 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_047_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_047_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:013_047_110_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_047_110_047 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:001_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:001_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:021_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:021_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:044_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:047_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_055 0.0 1.62 0.0 -0.44 + dihedral_coeff @dihedral:048_048_048_060 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_065 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_066 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_048_109 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_050 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_060 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_065 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_066 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_048_109 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_048_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_050_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:048_048_050_047 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:056_048_050_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:056_048_050_047 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:048_048_053_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_048_053_054 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_055_045 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:048_048_055_045 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_013 0.0 7.936 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_045 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:060_048_055_045 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:X_048_056_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_048_060_X 0.0 7.0 0.0 0.0 + dihedral_coeff @dihedral:X_048_079_023 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:048_048_079_013 0.0 -0.9 0.0 0.0 + dihedral_coeff @dihedral:048_048_079_024 1.656 -0.768 -0.117 0.0 + dihedral_coeff @dihedral:048_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_086_056 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_056 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_048_088_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:056_048_101_013 0.0 3.651 0.0 0.0 + dihedral_coeff @dihedral:048_048_102_103 0.0 1.15 0.0 0.0 + dihedral_coeff @dihedral:048_048_109_013 0.205 -0.531 0.0 0.0 + dihedral_coeff @dihedral:048_048_109_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:048_048_109_109 1.241 3.353 -0.286 0.0 + dihedral_coeff @dihedral:X_050_050_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:003_050_050_003 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_050_050_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_050_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_050_047 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_050_050_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_050_047 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_050_047 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:013_050_109_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:013_050_109_109 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:046_050_109_013 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_109_046 0.0 0.0 0.3 0.0 + dihedral_coeff @dihedral:046_050_109_109 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_013 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_046 0.0 0.0 -0.372 0.0 + dihedral_coeff @dihedral:047_050_109_109 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:013_053_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:048_053_082_061 0.0 2.1 0.0 0.0 + dihedral_coeff @dihedral:045_055_059_X 0.0 2.03 0.0 0.0 + dihedral_coeff @dihedral:013_056_056_013 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:013_056_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_056_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_059_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_059_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_056_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_056_082_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_086_048 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_056_086_086 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_057_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:045_057_060_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_061_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_081_X 0.0 3.05 0.0 0.0 + dihedral_coeff @dihedral:X_057_082_X 0.0 4.65 0.0 0.0 + dihedral_coeff @dihedral:X_057_082_049 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:045_057_082_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_057_084_X 0.0 2.8 0.0 0.0 + dihedral_coeff @dihedral:045_057_084_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:061_057_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:084_057_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_060_060_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_060_061_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_060_080_X 0.0 3.35 0.0 0.0 + dihedral_coeff @dihedral:X_060_081_X 0.0 6.0 0.0 0.0 + dihedral_coeff @dihedral:X_060_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_060_087_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:060_060_087_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_061_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_062_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_082_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_082_049 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:083_061_082_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:088_061_082_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:088_061_082_020 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_083_X 0.0 4.8 0.0 0.0 + dihedral_coeff @dihedral:082_061_083_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_061_083_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_061_084_X 0.0 10.0 0.0 0.0 + dihedral_coeff @dihedral:X_061_088_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:082_061_088_084 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_080_084_X 0.0 13.05 0.0 0.0 + dihedral_coeff @dihedral:X_082_084_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:016_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:020_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:057_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_082_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_082_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_083_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_083_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_016 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_083_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_016 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_020 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:061_083_084_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_083_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_083_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:061_083_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:084_083_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_084_084_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:016_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:049_084_084_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:X_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:016_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:020_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:057_084_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_084_087_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_084_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_084_088_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:016_084_088_049 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:016_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:020_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_088_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:049_084_088_061 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:048_086_086_048 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_086_056 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_087_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:048_086_088_061 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:056_086_088_X 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_020 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_057 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:X_087_087_087 0.0 2.17 0.0 0.0 + dihedral_coeff @dihedral:049_087_087_049 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_013 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_048 0.0 6.089 0.0 0.0 + dihedral_coeff @dihedral:004_089_090_091 0.0 20.0 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_013 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_045 0.0 4.9 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_048 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:091_089_090_091 2.3 6.089 0.0 0.0 + dihedral_coeff @dihedral:X_089_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_089_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:004_089_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:090_089_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:090_089_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_090_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_091_091_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_091_091_024 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_091_091_013 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_091_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_091_091_046 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:046_091_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:091_091_091_091 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:X_109_109_X 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_013 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:013_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_046 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:046_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_048 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:048_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:050_109_109_050 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:050_109_109_109 0.0 14.0 0.0 0.0 + dihedral_coeff @dihedral:109_109_109_109 1.423 4.055 0.858 0.0 + dihedral_coeff @dihedral:024_003_013_053 1.816 1.222 1.581 0.0 + dihedral_coeff @dihedral:052_003_013_024 0.0 0.82 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_053 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_013_083 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_084 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:003_013_013_085 -1.697 -0.456 0.585 0.0 + dihedral_coeff @dihedral:005_013_013_053 6.28 -1.467 2.03 0.0 + dihedral_coeff @dihedral:015_013_013_053 1.428 0.086 0.029 0.0 + dihedral_coeff @dihedral:016_013_013_053 1.428 0.086 0.029 0.0 + dihedral_coeff @dihedral:013_013_013_055 2.732 -0.229 0.485 0.0 + dihedral_coeff @dihedral:024_013_013_083 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:053_013_013_083 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_084 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:053_013_013_084 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:024_013_013_085 0.845 -0.962 0.713 0.0 + dihedral_coeff @dihedral:046_013_013_085 0.0 0.0 0.462 0.0 + dihedral_coeff @dihedral:053_013_013_085 1.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:003_013_053_013 1.438 -0.124 0.264 0.0 + dihedral_coeff @dihedral:003_013_053_054 0.0 0.0 0.347 0.0 + dihedral_coeff @dihedral:013_013_053_054 0.0 0.0 0.347 0.0 + dihedral_coeff @dihedral:046_013_055_054 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_085_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:013_013_085_057 1.7 -0.6 0.0 0.0 + dihedral_coeff @dihedral:046_013_085_X 0.0 0.0 0.0 0.0 + dihedral_coeff @dihedral:055_048_055_054 0.0 3.9 0.0 0.0 + dihedral_coeff @dihedral:X_048_081_X 0.0 7.25 0.0 0.0 + dihedral_coeff @dihedral:X_057_085_X 0.0 5.0 0.0 0.0 + dihedral_coeff @dihedral:X_085_085_X 0.0 10.75 0.0 0.0 + dihedral_coeff @dihedral:013_013_013_020 1.3 -0.05 0.2 0.0 + dihedral_coeff @dihedral:013_013_013_047 1.3 -0.05 0.2 0.0 } #(end of dihedral_coeffs) # Rules for creating dihedral interactions according to atom type: @@ -7327,806 +7340,806 @@ OPLSAA { # (* = wildcard) write_once("Data Dihedrals By Type") { - @dihedral:X-2-2-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:X-2-2-6 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:1-2-2-2 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:1-2-2-6 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:2-2-2-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-2-6 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:2-2-2-10 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* - @dihedral:2-2-2-13 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i* - @dihedral:2-2-2-65 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i* - @dihedral:6-2-2-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d6_i* - @dihedral:6-2-2-65 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d65_i* - @dihedral:10-2-2-10 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* - @dihedral:2-2-5-7 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:6-2-5-7 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:10-2-5-7 @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:X-2-10-2 @atom:* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-10-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:2-2-13-2 @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i* - @dihedral:6-2-20-2 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d2_i* - @dihedral:6-2-20-6 @atom:*_b*_a*_d6_i* @atom:*_b*_a*_d2_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d6_i* - @dihedral:4-3-3-4 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d4_i* - @dihedral:4-3-3-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-3-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-3-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-3-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-3-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* - @dihedral:13-3-3-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-3-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-3-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-5-7 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:4-3-5-7 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:13-3-5-7 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:24-3-5-7 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:46-3-5-7 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:48-3-5-7 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d7_i* - @dihedral:1-3-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:1-3-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-3-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:* - @dihedral:4-3-13-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-13-21 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:4-3-13-44 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:4-3-13-24 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:4-3-13-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-13-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:5-3-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:5-3-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-3-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:20-3-13-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:20-3-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:21-3-13-13 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:21-3-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-13-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:24-3-13-21 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:24-3-13-24 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:24-3-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:46-3-13-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:48-3-13-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:52-3-13-13 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:52-3-13-44 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:52-3-13-46 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:65-3-13-13 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:65-3-13-46 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-13-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-20-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-20-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:13-3-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-20-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-20-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-20-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:48-3-20-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:3-3-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:3-3-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:4-3-24-5 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:4-3-24-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-24-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:4-3-24-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i* - @dihedral:4-3-24-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:4-3-24-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:5-3-24-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:5-3-24-45 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d5_i* - @dihedral:13-3-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-3-24-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-24-13 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:20-3-24-45 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:24-3-24-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:24-3-24-13 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:24-3-24-45 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-3-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:47-3-24-45 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:48-3-24-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:48-3-24-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:48-3-24-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:48-3-24-87 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:84-3-24-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:84-3-24-84 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:84-3-24-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:87-3-24-45 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:87-3-24-48 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:87-3-24-84 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* - @dihedral:87-3-24-87 @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* - @dihedral:X-3-47-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-47-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:4-3-47-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:5-3-47-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:24-3-47-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:24-3-47-47 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:107-3-47-46 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:107-3-47-47 @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:4-3-48-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:5-3-48-48 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-3-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:20-3-48-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:24-3-48-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-3-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-50-13 @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-50-47 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:5-3-50-47 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-3-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-3-56-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:13-3-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:46-3-56-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:46-3-56-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d45_i* - @dihedral:X-3-60-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:4-3-60-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:4-3-82-X @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:4-3-82-57 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i* - @dihedral:4-3-82-61 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-3-82-57 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d57_i* - @dihedral:82-3-82-61 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:4-3-84-20 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:4-3-84-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:84-3-84-20 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:84-3-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:48-3-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-3-87-X @atom:* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:4-3-87-84 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:4-3-87-87 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:24-3-87-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:24-3-87-87 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:4-3-107-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:13-3-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:4-3-109-109 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:5-3-109-109 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:X-4-106-X @atom:* @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d106_i* @atom:* - @dihedral:7-5-10-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-10-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d10_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-2 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d2_i* - @dihedral:7-5-13-6 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d6_i* - @dihedral:7-5-13-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-13-46 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:7-5-13-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:7-5-13-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-13-50 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* - @dihedral:7-5-44-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-44-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:7-5-24-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:7-5-24-45 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:7-5-47-47 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:7-5-48-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:7-5-51-20 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:7-5-56-3 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:7-5-64-4 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i* - @dihedral:7-5-64-5 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d5_i* - @dihedral:7-5-79-13 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:7-5-79-23 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:7-5-79-48 @atom:*_b*_a*_d7_i* @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-13-3 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* - @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-13-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:1-13-13-1 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d1_i* - @dihedral:1-13-13-5 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:1-13-13-13 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:1-13-13-46 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-13-5 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:3-13-13-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-13-15 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* - @dihedral:3-13-13-16 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* - @dihedral:3-13-13-24 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:3-13-13-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:3-13-13-80 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:5-13-13-5 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d5_i* - @dihedral:5-13-13-13 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:5-13-13-20 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:5-13-13-44 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:5-13-13-24 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:5-13-13-46 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-13-15 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* - @dihedral:13-13-13-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* - @dihedral:13-13-13-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-13-21 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:13-13-13-44 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:13-13-13-24 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-13-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-13-51 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* - @dihedral:13-13-13-53 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-65 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i* - @dihedral:13-13-13-66 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i* - @dihedral:13-13-13-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-13-107 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* - @dihedral:13-13-13-108 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:15-13-13-46 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:16-13-13-46 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:19-13-13-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:20-13-13-20 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:20-13-13-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:21-13-13-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d21_i* - @dihedral:21-13-13-44 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:21-13-13-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-44 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* - @dihedral:44-13-13-46 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:44-13-13-48 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-46 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:24-13-13-48 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:24-13-13-80 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-13-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-13-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-13-53 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:46-13-13-55 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* - @dihedral:46-13-13-59 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* - @dihedral:46-13-13-62 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* - @dihedral:46-13-13-65 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d65_i* - @dihedral:46-13-13-66 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d66_i* - @dihedral:46-13-13-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* - @dihedral:46-13-13-80 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* - @dihedral:46-13-13-82 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* - @dihedral:46-13-13-83 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:46-13-13-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-13-87 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* - @dihedral:46-13-13-88 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* - @dihedral:46-13-13-102 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* - @dihedral:46-13-13-104 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* - @dihedral:46-13-13-107 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* - @dihedral:46-13-13-108 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:46-13-13-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* - @dihedral:48-13-13-53 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:108-13-13-108 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* - @dihedral:13-13-15-17 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:46-13-15-17 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d17_i* - @dihedral:13-13-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-16-16 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-16-16 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* - @dihedral:46-13-16-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-18-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-18-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-19-18 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-19-19 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:13-13-19-19 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:46-13-19-19 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* - @dihedral:X-13-20-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:56-13-20-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:57-13-20-13 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-20-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-20-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-20-64 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:46-13-20-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:* - @dihedral:46-13-20-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-20-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-20-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-20-51 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* - @dihedral:46-13-20-64 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* - @dihedral:X-13-24-45 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:3-13-24-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:3-13-24-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-24-45 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-24-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-24-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-24-59 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-24-79 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:13-13-24-91 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* - @dihedral:46-13-24-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-24-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-24-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-24-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-24-79 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* - @dihedral:48-13-24-59 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* - @dihedral:13-13-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-44-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-44-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:X-13-47-50 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:1-13-47-47 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-47-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-47-110 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* - @dihedral:47-13-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:47-13-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-48-48 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-13-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:21-13-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:64-13-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:65-13-48-48 @atom:*_b*_a*_d65_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-13-50-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-13-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:13-13-51-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:* - @dihedral:13-13-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-51-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-53-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-53-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-53-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-53-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d48_i* - @dihedral:46-13-53-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-55-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-55-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-55-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-55-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-55-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-56-18 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d18_i* - @dihedral:X-13-57-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:13-13-57-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-57-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-57-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:* - @dihedral:20-13-57-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-57-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* - @dihedral:13-13-59-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:46-13-59-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-13-62-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-62-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:46-13-64-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-64-52 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-13-64-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* - @dihedral:48-13-64-52 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:X-13-79-23 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:X-13-79-24 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:13-13-79-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-79-23 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-5 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d5_i* - @dihedral:46-13-79-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-79-23 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:46-13-79-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-80-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:13-13-80-60 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:13-13-80-84 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:46-13-80-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:46-13-80-60 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d60_i* - @dihedral:46-13-80-84 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* - @dihedral:13-13-82-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:46-13-82-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:13-13-83-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:46-13-83-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:1-13-84-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:13-13-84-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* - @dihedral:21-13-84-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:46-13-84-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:1-13-87-X @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-87-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:21-13-87-X @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:46-13-87-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:13-13-88-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:46-13-88-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-13-90-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-90-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d90_i* @atom:* - @dihedral:46-13-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:13-13-95-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-95-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d95_i* @atom:*_b*_a*_d46_i* - @dihedral:13-13-102-103 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:46-13-102-103 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:13-13-104-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-104-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d104_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-105-X @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:13-13-105-62 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:13-13-105-82 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:20-13-105-X @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:* - @dihedral:20-13-105-62 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d62_i* - @dihedral:20-13-105-82 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d105_i* @atom:*_b*_a*_d82_i* - @dihedral:3-13-107-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-107-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:13-13-107-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-107-3 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d3_i* - @dihedral:46-13-107-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-107-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d107_i* @atom:*_b*_a*_d48_i* - @dihedral:13-13-108-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-108-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:46-13-108-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-108-20 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:46-13-108-45 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d45_i* - @dihedral:13-13-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-13-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:17-15-48-X @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:17-15-48-48 @atom:*_b*_a*_d17_i* @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-16-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* - @dihedral:13-16-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-16-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:13-16-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:84-16-82-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:84-16-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-16-84-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:82-16-84-83 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i* - @dihedral:82-16-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* - @dihedral:X-16-91-X @atom:* @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:19-18-48-X @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:19-18-48-48 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:18-18-56-13 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:18-18-56-46 @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d18_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d46_i* - @dihedral:X-19-19-X @atom:* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:* - @dihedral:13-19-19-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d13_i* - @dihedral:13-19-19-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d46_i* - @dihedral:13-19-19-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* - @dihedral:13-19-19-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:46-19-19-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* - @dihedral:46-19-19-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d109_i* - @dihedral:19-19-47-13 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:19-19-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:19-19-47-47 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-20-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-20-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-20-47-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* - @dihedral:3-20-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-48-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:64-20-48-48 @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-20-51-5 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d5_i* - @dihedral:13-20-51-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-51-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d20_i* - @dihedral:13-20-51-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d51_i* @atom:*_b*_a*_d46_i* - @dihedral:13-20-56-3 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d3_i* - @dihedral:13-20-59-56 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d56_i* - @dihedral:X-20-64-52 @atom:* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:13-20-64-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d13_i* - @dihedral:13-20-64-52 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d52_i* - @dihedral:48-20-64-4 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d64_i* @atom:*_b*_a*_d4_i* - @dihedral:84-20-82-61 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:82-20-84-88 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* - @dihedral:84-20-84-49 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:84-20-84-87 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* - @dihedral:108-20-108-13 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d13_i* - @dihedral:108-20-108-20 @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d108_i* @atom:*_b*_a*_d20_i* - @dihedral:X-24-48-48 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:3-24-48-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-24-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:59-24-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:82-24-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:84-24-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-24-59-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-24-59-49 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i* - @dihedral:45-24-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-24-60-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-24-79-23 @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:13-24-79-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:45-24-79-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d48_i* - @dihedral:13-24-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:45-24-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:45-24-82-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:45-24-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-24-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:48-24-82-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:48-24-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:X-24-84-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:3-24-84-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* - @dihedral:45-24-84-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:45-24-84-20 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:48-24-84-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:48-24-84-20 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:3-24-86-48 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-24-86-56 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:3-24-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:47-24-86-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:47-24-86-56 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:X-24-87-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-24-88-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:3-24-91-46 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:3-24-91-89 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* - @dihedral:3-24-91-91 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:45-24-91-46 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:45-24-91-89 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* - @dihedral:45-24-91-91 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-24-106-X @atom:* @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d106_i* @atom:* - @dihedral:13-44-44-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d13_i* - @dihedral:13-44-44-45 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:45-44-44-45 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d45_i* - @dihedral:13-44-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-44-48-48 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:59-44-48-48 @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:82-44-48-48 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:84-44-48-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:45-44-82-16 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:45-44-82-61 @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-44-82-16 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:48-44-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:47-46-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - 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@atom:*_b*_a*_d47_i* @atom:*_b*_a*_d20_i* - @dihedral:13-47-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:19-47-47-46 @atom:*_b*_a*_d19_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:20-47-47-46 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:21-47-47-21 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d21_i* - @dihedral:21-47-47-46 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-47-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-48-56 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* - @dihedral:47-47-48-48 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:13-47-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-47-50-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:13-47-50-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:13-47-50-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:24-47-50-3 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:46-47-50-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:46-47-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-47-50-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d48_i* - @dihedral:46-47-50-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* - @dihedral:46-47-50-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* - @dihedral:X-47-84-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-47-86-48 @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:3-47-86-86 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-47-86-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:* - @dihedral:49-47-86-24 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d24_i* - @dihedral:X-47-87-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-47-88-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:13-47-110-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i* - @dihedral:46-47-110-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d110_i* @atom:*_b*_a*_d47_i* - @dihedral:X-48-48-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:* - @dihedral:X-48-48-13 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* - @dihedral:X-48-48-48 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:X-48-48-49 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:1-48-48-48 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:1-48-48-49 @atom:*_b*_a*_d1_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d13_i* - @dihedral:13-48-48-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:13-48-48-49 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:13-48-48-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:21-48-48-48 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:21-48-48-49 @atom:*_b*_a*_d21_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:44-48-48-49 @atom:*_b*_a*_d44_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:47-48-48-49 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-48-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* - @dihedral:48-48-48-49 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:48-48-48-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:48-48-48-55 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* - @dihedral:48-48-48-60 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* - @dihedral:48-48-48-65 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i* - @dihedral:48-48-48-66 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i* - @dihedral:48-48-48-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:48-48-48-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* - @dihedral:49-48-48-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d49_i* - @dihedral:49-48-48-50 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* - @dihedral:49-48-48-60 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* - @dihedral:49-48-48-65 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d65_i* - @dihedral:49-48-48-66 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d66_i* - @dihedral:49-48-48-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-48-109 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* - @dihedral:56-48-48-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* - @dihedral:48-48-50-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:48-48-50-47 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:56-48-50-46 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:56-48-50-47 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:48-48-53-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-53-54 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:X-48-55-45 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:48-48-55-45 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:55-48-55-13 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d13_i* - @dihedral:55-48-55-45 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:60-48-55-45 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d45_i* - @dihedral:X-48-56-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:* - @dihedral:48-48-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:49-48-56-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:X-48-60-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-48-79-23 @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d23_i* - @dihedral:48-48-79-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-79-24 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d79_i* @atom:*_b*_a*_d24_i* - @dihedral:48-48-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-48-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:48-48-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-86-48 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:49-48-86-56 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:49-48-86-86 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:56-48-86-48 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:56-48-86-86 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:49-48-88-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:56-48-101-13 @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d101_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-102-103 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d102_i* @atom:*_b*_a*_d103_i* - @dihedral:48-48-109-13 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:48-48-109-46 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:48-48-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:X-50-50-49 @atom:* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d49_i* - @dihedral:3-50-50-3 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d3_i* - @dihedral:13-50-50-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d13_i* - @dihedral:13-50-50-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:13-50-50-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:46-50-50-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d46_i* - @dihedral:46-50-50-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:47-50-50-47 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d47_i* - @dihedral:13-50-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:13-50-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-50-109-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:46-50-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-50-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:47-50-109-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:47-50-109-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:47-50-109-109 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:13-53-82-61 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:48-53-82-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* - @dihedral:45-55-59-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:13-56-56-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d13_i* - @dihedral:13-56-56-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:48-56-56-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d48_i* - @dihedral:X-56-59-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:* - @dihedral:X-56-59-49 @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d59_i* @atom:*_b*_a*_d49_i* - @dihedral:X-56-60-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-56-62-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-56-82-X @atom:* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:48-56-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-56-86-86 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* - @dihedral:X-57-60-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:45-57-60-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-57-61-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-57-62-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-57-81-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-57-82-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-57-82-49 @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i* - @dihedral:45-57-82-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-57-84-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:45-57-84-X @atom:*_b*_a*_d45_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:61-57-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:84-57-86-48 @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-60-60-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:* - @dihedral:X-60-61-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-60-80-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d80_i* @atom:* - @dihedral:X-60-81-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-60-87-X @atom:* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:48-60-87-84 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:60-60-87-84 @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d60_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d84_i* - @dihedral:X-61-61-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d61_i* @atom:* - @dihedral:X-61-62-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d62_i* @atom:* - @dihedral:X-61-82-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:* - @dihedral:X-61-82-49 @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d49_i* - @dihedral:83-61-82-16 @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:88-61-82-16 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d16_i* - @dihedral:88-61-82-20 @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d20_i* - @dihedral:X-61-83-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:* - @dihedral:82-61-83-49 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d49_i* - @dihedral:82-61-83-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* - @dihedral:X-61-84-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-61-88-X @atom:* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:82-61-88-84 @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d84_i* - @dihedral:X-80-84-X @atom:* @atom:*_b*_a*_d80_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-82-84-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:16-82-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:20-82-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:57-82-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-82-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-82-87-X @atom:* @atom:*_b*_a*_d82_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-83-84-X @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-83-84-49 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:49-83-84-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:49-83-84-16 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:49-83-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:61-83-84-16 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d16_i* - @dihedral:61-83-84-20 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d20_i* - @dihedral:61-83-84-49 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:X-83-86-48 @atom:* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-83-86-48 @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:61-83-87-X @atom:*_b*_a*_d61_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:84-83-87-X @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d83_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-84-84-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:* - @dihedral:X-84-84-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-84-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:49-84-84-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d49_i* - @dihedral:X-84-86-48 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:16-84-86-48 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:20-84-86-48 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:57-84-86-48 @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:X-84-87-X @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:X-84-87-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:49-84-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:X-84-88-49 @atom:* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-88-49 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d49_i* - @dihedral:16-84-88-61 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:20-84-88-61 @atom:*_b*_a*_d20_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:49-84-88-X @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:49-84-88-61 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d84_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:48-86-86-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d48_i* - @dihedral:48-86-86-56 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d56_i* - @dihedral:48-86-87-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d87_i* @atom:* - @dihedral:48-86-88-X @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:48-86-88-61 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:*_b*_a*_d61_i* - @dihedral:56-86-88-X @atom:*_b*_a*_d56_i* @atom:*_b*_a*_d86_i* @atom:*_b*_a*_d88_i* @atom:* - @dihedral:X-87-87-20 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d20_i* - @dihedral:X-87-87-57 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d57_i* - @dihedral:X-87-87-87 @atom:* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* - @dihedral:49-87-87-49 @atom:*_b*_a*_d49_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d87_i* @atom:*_b*_a*_d49_i* - @dihedral:4-89-90-13 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i* - @dihedral:4-89-90-45 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i* - @dihedral:4-89-90-48 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i* - @dihedral:4-89-90-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* - @dihedral:91-89-90-13 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d13_i* - @dihedral:91-89-90-45 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d45_i* - @dihedral:91-89-90-48 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d48_i* - @dihedral:91-89-90-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* - @dihedral:X-89-91-X @atom:* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:4-89-91-46 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:4-89-91-91 @atom:*_b*_a*_d4_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:90-89-91-46 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:90-89-91-91 @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d89_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-90-91-X @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:X-90-91-46 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:X-90-91-91 @atom:* @atom:*_b*_a*_d90_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-91-91-X @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:* - @dihedral:X-91-91-24 @atom:* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d24_i* - @dihedral:13-91-91-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d13_i* - @dihedral:13-91-91-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:46-91-91-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d46_i* - @dihedral:46-91-91-91 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:91-91-91-91 @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* @atom:*_b*_a*_d91_i* - @dihedral:X-109-109-X @atom:* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:* - @dihedral:13-109-109-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d13_i* - @dihedral:13-109-109-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:13-109-109-48 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:13-109-109-50 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:13-109-109-109 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:46-109-109-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d46_i* - @dihedral:46-109-109-48 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:46-109-109-50 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:46-109-109-109 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:48-109-109-48 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d48_i* - @dihedral:48-109-109-50 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:48-109-109-109 @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:50-109-109-50 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d50_i* - @dihedral:50-109-109-109 @atom:*_b*_a*_d50_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:109-109-109-109 @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* @atom:*_b*_a*_d109_i* - @dihedral:24-3-13-53 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:52-3-13-24 @atom:*_b*_a*_d52_i* @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d24_i* - @dihedral:3-13-13-53 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:3-13-13-83 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:3-13-13-84 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:3-13-13-85 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:5-13-13-53 @atom:*_b*_a*_d5_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:15-13-13-53 @atom:*_b*_a*_d15_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:16-13-13-53 @atom:*_b*_a*_d16_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* - @dihedral:13-13-13-55 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* - @dihedral:24-13-13-83 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:53-13-13-83 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d83_i* - @dihedral:24-13-13-84 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:53-13-13-84 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d84_i* - @dihedral:24-13-13-85 @atom:*_b*_a*_d24_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:46-13-13-85 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:53-13-13-85 @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* - @dihedral:3-13-53-13 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d13_i* - @dihedral:3-13-53-54 @atom:*_b*_a*_d3_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-53-54 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d53_i* @atom:*_b*_a*_d54_i* - @dihedral:46-13-55-54 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:13-13-85-X @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-85-57 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d57_i* - @dihedral:46-13-85-X @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:55-48-55-54 @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d55_i* @atom:*_b*_a*_d54_i* - @dihedral:X-48-81-X @atom:* @atom:*_b*_a*_d48_i* @atom:*_b*_a*_d81_i* @atom:* - @dihedral:X-57-85-X @atom:* @atom:*_b*_a*_d57_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:X-85-85-X @atom:* @atom:*_b*_a*_d85_i* @atom:*_b*_a*_d85_i* @atom:* - @dihedral:13-13-13-20 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d20_i* - @dihedral:13-13-13-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* + @dihedral:X_002_002_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:X_002_002_006 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:001_002_002_002 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:001_002_002_006 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:002_002_002_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_002_006 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:002_002_002_010 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* + @dihedral:002_002_002_013 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* + @dihedral:002_002_002_065 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* + @dihedral:006_002_002_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* + @dihedral:006_002_002_065 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* + @dihedral:010_002_002_010 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* + @dihedral:002_002_005_007 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:006_002_005_007 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:010_002_005_007 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:X_002_010_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_010_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:002_002_013_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* + @dihedral:006_002_020_002 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d002*_i* + @dihedral:006_002_020_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d006*_i* + @dihedral:004_003_003_004 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d004*_i* + @dihedral:004_003_003_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_003_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* + @dihedral:004_003_003_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_003_003_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_003_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_003_003_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_003_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_003_003_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_003_005_007 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:004_003_005_007 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:013_003_005_007 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:024_003_005_007 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:046_003_005_007 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:048_003_005_007 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* + @dihedral:001_003_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:001_003_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_003_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_013_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:* + @dihedral:004_003_013_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_013_021 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:004_003_013_044 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:004_003_013_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:004_003_013_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_013_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:005_003_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_003_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:005_003_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_003_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_003_013_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:020_003_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_003_013_013 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:021_003_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_013_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:024_003_013_021 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:024_003_013_024 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:024_003_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_003_013_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_003_013_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:052_003_013_013 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:052_003_013_044 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:052_003_013_046 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:065_003_013_013 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:065_003_013_046 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:107_003_013_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_020_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_020_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_003_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_020_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_003_020_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_020_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_003_020_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_003_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_003_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_003_024_005 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* + @dihedral:004_003_024_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_024_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_003_024_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* + @dihedral:004_003_024_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:004_003_024_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* + @dihedral:005_003_024_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_003_024_045 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_003_024_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* + @dihedral:013_003_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_003_024_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_003_024_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:020_003_024_045 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:024_003_024_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:024_003_024_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:024_003_024_045 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_003_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:047_003_024_045 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_003_024_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_003_024_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_003_024_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:048_003_024_087 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:084_003_024_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_003_024_084 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:084_003_024_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:087_003_024_045 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:087_003_024_048 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:087_003_024_084 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* + @dihedral:087_003_024_087 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* + @dihedral:X_003_047_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_047_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_003_047_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:005_003_047_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:024_003_047_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_003_047_047 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:107_003_047_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:107_003_047_047 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:004_003_048_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:005_003_048_048 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_003_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_003_048_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_003_048_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_003_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_003_050_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_050_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:005_003_050_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_003_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_003_056_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:013_003_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_003_056_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:046_003_056_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d045*_i* + @dihedral:X_003_060_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:004_003_060_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:004_003_082_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:004_003_082_057 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* + @dihedral:004_003_082_061 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_003_082_057 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* + @dihedral:082_003_082_061 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:004_003_084_020 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:004_003_084_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:084_003_084_020 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:084_003_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:048_003_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_003_087_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:004_003_087_084 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:004_003_087_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:024_003_087_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:024_003_087_087 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:004_003_107_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_003_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_003_109_109 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:005_003_109_109 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_004_106_X @atom:* @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d106*_i* @atom:* + @dihedral:007_005_010_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* + @dihedral:007_005_010_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d006*_i* + @dihedral:007_005_013_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* + @dihedral:007_005_013_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d006*_i* + @dihedral:007_005_013_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_013_046 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:007_005_013_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* + @dihedral:007_005_013_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:007_005_013_050 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* + @dihedral:007_005_044_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_044_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:007_005_024_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:007_005_024_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:007_005_047_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:007_005_048_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:007_005_051_020 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:007_005_056_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* + @dihedral:007_005_064_004 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* + @dihedral:007_005_064_005 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d005*_i* + @dihedral:007_005_079_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:007_005_079_023 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:007_005_079_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_013_003 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* + @dihedral:X_013_013_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_013_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:001_013_013_001 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d001*_i* + @dihedral:001_013_013_005 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:001_013_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:001_013_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_013_013_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* + @dihedral:003_013_013_005 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:003_013_013_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_013_015 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* + @dihedral:003_013_013_016 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* + @dihedral:003_013_013_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_013_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_013_013_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_013_013_080 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:005_013_013_005 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* + @dihedral:005_013_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_013_013_020 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:005_013_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:005_013_013_024 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:005_013_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_013_015 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* + @dihedral:013_013_013_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* + @dihedral:013_013_013_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_013_013_021 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:013_013_013_044 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:013_013_013_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_013_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_013_051 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* + @dihedral:013_013_013_053 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:013_013_013_065 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* + @dihedral:013_013_013_066 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* + @dihedral:013_013_013_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* + @dihedral:013_013_013_107 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* + @dihedral:013_013_013_108 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:015_013_013_046 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:016_013_013_046 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_013_013_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_013_013_020 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:020_013_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_013_013_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* + @dihedral:021_013_013_044 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:021_013_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:044_013_013_044 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* + @dihedral:044_013_013_046 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:044_013_013_048 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_013_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:024_013_013_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:024_013_013_080 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:046_013_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_013_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_013_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_013_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* + @dihedral:046_013_013_053 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:046_013_013_055 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* + @dihedral:046_013_013_059 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* + @dihedral:046_013_013_062 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* + @dihedral:046_013_013_065 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* + @dihedral:046_013_013_066 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* + @dihedral:046_013_013_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* + @dihedral:046_013_013_080 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* + @dihedral:046_013_013_082 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* + @dihedral:046_013_013_083 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:046_013_013_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:046_013_013_087 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* + @dihedral:046_013_013_088 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* + @dihedral:046_013_013_102 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* + @dihedral:046_013_013_104 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* + @dihedral:046_013_013_107 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* + @dihedral:046_013_013_108 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:046_013_013_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* + @dihedral:048_013_013_053 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:108_013_013_108 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* + @dihedral:013_013_015_017 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* + @dihedral:046_013_015_017 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* + @dihedral:013_013_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_016_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* + @dihedral:046_013_016_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_016_016 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* + @dihedral:046_013_016_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_018_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* + @dihedral:046_013_018_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* + @dihedral:X_013_019_018 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* + @dihedral:X_013_019_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_013_019_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:046_013_019_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* + @dihedral:X_013_020_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:056_013_020_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:057_013_020_013 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_020_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_020_064 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* + @dihedral:046_013_020_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:* + @dihedral:046_013_020_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_020_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_020_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_020_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* + @dihedral:046_013_020_064 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* + @dihedral:X_013_024_045 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:003_013_024_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:003_013_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_024_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_024_059 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* + @dihedral:013_013_024_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* + @dihedral:013_013_024_091 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* + @dihedral:046_013_024_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_024_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_024_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* + @dihedral:048_013_024_059 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* + @dihedral:013_013_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_044_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_044_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_044_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_047_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_047_046 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_013_047_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:X_013_047_050 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:001_013_047_047 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_047_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_047_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_047_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_047_110 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* + @dihedral:047_013_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_013_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_013_048_048 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:001_013_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:021_013_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:064_013_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:065_013_048_048 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_013_050_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_013_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_013_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_013_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:013_013_051_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:* + @dihedral:013_013_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_051_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_013_053_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_053_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_053_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_053_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_053_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_013_053_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_055_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_055_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_055_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:046_013_055_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_055_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_055_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_056_018 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d018*_i* + @dihedral:X_013_057_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:013_013_057_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:013_013_057_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* + @dihedral:013_013_057_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* + @dihedral:020_013_057_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* + @dihedral:020_013_057_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* + @dihedral:020_013_057_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* + @dihedral:013_013_059_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_013_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:046_013_059_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_013_062_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:046_013_062_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:046_013_064_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* + @dihedral:046_013_064_052 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:048_013_064_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_013_064_052 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:X_013_079_023 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:X_013_079_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_013_079_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_079_023 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:046_013_079_005 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d005*_i* + @dihedral:046_013_079_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_079_023 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:046_013_079_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_080_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:013_013_080_060 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* + @dihedral:013_013_080_084 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* + @dihedral:046_013_080_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:046_013_080_060 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* + @dihedral:046_013_080_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* + @dihedral:013_013_082_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:046_013_082_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:013_013_083_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:046_013_083_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:001_013_084_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:013_013_084_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:013_013_084_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* + @dihedral:021_013_084_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:046_013_084_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:001_013_087_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:013_013_087_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:021_013_087_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:046_013_087_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:013_013_088_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:046_013_088_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:X_013_090_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* + @dihedral:046_013_090_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* + @dihedral:046_013_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:013_013_095_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_095_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_013_102_103 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:046_013_102_103 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:013_013_104_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_104_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_013_105_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:013_013_105_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:013_013_105_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* + @dihedral:013_013_105_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* + @dihedral:020_013_105_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* + @dihedral:020_013_105_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* + @dihedral:020_013_105_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* + @dihedral:003_013_107_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_107_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_013_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_107_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_013_107_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_107_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_013_108_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_013_108_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* + @dihedral:046_013_108_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_108_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* + @dihedral:046_013_108_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_013_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_013_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_013_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_013_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:017_015_048_X @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:017_015_048_048 @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_016_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_016_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_016_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:013_016_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:084_016_082_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:084_016_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_016_084_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:082_016_084_083 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* + @dihedral:082_016_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* + @dihedral:X_016_091_X @atom:* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:019_018_048_X @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:019_018_048_048 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:018_018_056_013 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:018_018_056_046 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_019_019_X @atom:* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:* + @dihedral:013_019_019_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_019_019_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_019_019_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_019_019_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_019_019_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_019_019_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* + @dihedral:019_019_047_013 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:019_019_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_019_047_047 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_020_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_020_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_020_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_020_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* + @dihedral:003_020_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:064_020_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_020_051_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d005*_i* + @dihedral:013_020_051_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_051_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_020_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_020_056_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_020_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* + @dihedral:X_020_064_052 @atom:* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:013_020_064_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_020_064_052 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* + @dihedral:048_020_064_004 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* + @dihedral:084_020_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:082_020_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* + @dihedral:084_020_084_049 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:084_020_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* + @dihedral:108_020_108_013 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* + @dihedral:108_020_108_020 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_024_048_048 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_024_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_024_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_024_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:059_024_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:082_024_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_024_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_024_059_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_024_059_049 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* + @dihedral:045_024_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_024_060_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_024_079_023 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:013_024_079_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_024_079_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_024_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:045_024_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_024_082_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:045_024_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_024_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_024_082_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_024_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:X_024_084_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:003_024_084_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* + @dihedral:045_024_084_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_024_084_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:048_024_084_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_024_084_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:003_024_086_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_024_086_056 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:003_024_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:047_024_086_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:047_024_086_056 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:X_024_087_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_024_088_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:003_024_091_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:003_024_091_089 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* + @dihedral:003_024_091_091 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:045_024_091_046 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:045_024_091_089 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* + @dihedral:045_024_091_091 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_024_106_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d106*_i* @atom:* + @dihedral:013_044_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_044_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:045_044_044_045 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* + @dihedral:013_044_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_044_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:059_044_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:082_044_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_044_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:045_044_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:045_044_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_044_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:048_044_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:047_046_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_046_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_047_047_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:* + @dihedral:X_047_047_019 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* + @dihedral:003_047_047_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_047_047_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:005_047_047_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:005_047_047_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_047_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_047_047_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* + @dihedral:013_047_047_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_047_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:019_047_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:020_047_047_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:021_047_047_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d021*_i* + @dihedral:021_047_047_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_047_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_048_056 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* + @dihedral:047_047_048_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_047_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_047_050_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_047_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:013_047_050_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:024_047_050_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* + @dihedral:046_047_050_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_047_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_047_050_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_047_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_047_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_047_084_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_047_086_048 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:003_047_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_047_086_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:* + @dihedral:049_047_086_024 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d024*_i* + @dihedral:X_047_087_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_047_088_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:013_047_110_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_047_110_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* + @dihedral:X_048_048_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:* + @dihedral:X_048_048_013 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* + @dihedral:X_048_048_048 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_048_048_049 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:001_048_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:001_048_048_049 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:013_048_048_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_048_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_048_048_049 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:013_048_048_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:021_048_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:021_048_048_049 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:044_048_048_049 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:047_048_048_049 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:048_048_048_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_048_048_049 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:048_048_048_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:048_048_048_055 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* + @dihedral:048_048_048_060 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* + @dihedral:048_048_048_065 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* + @dihedral:048_048_048_066 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* + @dihedral:048_048_048_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:048_048_048_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* + @dihedral:049_048_048_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_048_048_050 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* + @dihedral:049_048_048_060 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* + @dihedral:049_048_048_065 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* + @dihedral:049_048_048_066 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* + @dihedral:049_048_048_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_048_109 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* + @dihedral:056_048_048_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* + @dihedral:048_048_050_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_048_050_047 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:056_048_050_046 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:056_048_050_047 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:048_048_053_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_053_054 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:X_048_055_045 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:048_048_055_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:055_048_055_013 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* + @dihedral:055_048_055_045 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:060_048_055_045 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* + @dihedral:X_048_056_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:* + @dihedral:048_048_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:049_048_056_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_048_060_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_048_079_023 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* + @dihedral:048_048_079_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_079_024 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* + @dihedral:048_048_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_048_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:048_048_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_086_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:049_048_086_056 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:049_048_086_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:056_048_086_048 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:056_048_086_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:049_048_088_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:056_048_101_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d101*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_102_103 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* + @dihedral:048_048_109_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:048_048_109_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:048_048_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:X_050_050_049 @atom:* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d049*_i* + @dihedral:003_050_050_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* + @dihedral:013_050_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_050_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_050_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:046_050_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_050_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:047_050_050_047 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* + @dihedral:013_050_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_050_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_050_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:046_050_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_050_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:047_050_109_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:047_050_109_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:047_050_109_109 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:013_053_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_053_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* + @dihedral:045_055_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:013_056_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_056_056_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_056_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_056_059_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:* + @dihedral:X_056_059_049 @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_056_060_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_056_062_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_056_082_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:048_056_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_056_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* + @dihedral:X_057_060_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:045_057_060_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_057_061_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_057_062_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_057_081_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_057_082_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_057_082_049 @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* + @dihedral:045_057_082_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_057_084_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:045_057_084_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:061_057_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:084_057_086_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_060_060_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:* + @dihedral:X_060_061_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_060_080_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d080*_i* @atom:* + @dihedral:X_060_081_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_060_087_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:048_060_087_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:060_060_087_084 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_061_061_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d061*_i* @atom:* + @dihedral:X_061_062_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d062*_i* @atom:* + @dihedral:X_061_082_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:* + @dihedral:X_061_082_049 @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* + @dihedral:083_061_082_016 @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:088_061_082_016 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* + @dihedral:088_061_082_020 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_061_083_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:* + @dihedral:082_061_083_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d049*_i* + @dihedral:082_061_083_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_061_084_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_061_088_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:082_061_088_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d084*_i* + @dihedral:X_080_084_X @atom:* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_082_084_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:016_082_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_082_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:057_082_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_082_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_082_087_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_083_084_X @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_083_084_049 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_083_084_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:049_083_084_016 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:049_083_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:061_083_084_016 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* + @dihedral:061_083_084_020 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* + @dihedral:061_083_084_049 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_083_086_048 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_083_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:061_083_087_X @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:084_083_087_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_084_084_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:* + @dihedral:X_084_084_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_084_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_084_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_084_086_048 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:016_084_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:020_084_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:057_084_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:X_084_087_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:X_084_087_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:049_084_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:X_084_088_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_088_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* + @dihedral:016_084_088_061 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:020_084_088_061 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:049_084_088_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:049_084_088_061 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:048_086_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_086_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* + @dihedral:048_086_087_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d087*_i* @atom:* + @dihedral:048_086_088_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:048_086_088_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* + @dihedral:056_086_088_X @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* + @dihedral:X_087_087_020 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d020*_i* + @dihedral:X_087_087_057 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d057*_i* + @dihedral:X_087_087_087 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* + @dihedral:049_087_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* + @dihedral:004_089_090_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* + @dihedral:004_089_090_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* + @dihedral:004_089_090_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* + @dihedral:004_089_090_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* + @dihedral:091_089_090_013 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* + @dihedral:091_089_090_045 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* + @dihedral:091_089_090_048 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* + @dihedral:091_089_090_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_089_091_X @atom:* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:004_089_091_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:004_089_091_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:090_089_091_046 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:090_089_091_091 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_090_091_X @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:X_090_091_046 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:X_090_091_091 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_091_091_X @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:* + @dihedral:X_091_091_024 @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d024*_i* + @dihedral:013_091_091_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_091_091_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_091_091_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_091_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:091_091_091_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* + @dihedral:X_109_109_X @atom:* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:* + @dihedral:013_109_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* + @dihedral:013_109_109_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:013_109_109_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:013_109_109_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:013_109_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:046_109_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* + @dihedral:046_109_109_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:046_109_109_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:046_109_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:048_109_109_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* + @dihedral:048_109_109_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:048_109_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:050_109_109_050 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* + @dihedral:050_109_109_109 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:109_109_109_109 @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* + @dihedral:024_003_013_053 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:052_003_013_024 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* + @dihedral:003_013_013_053 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:003_013_013_083 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:003_013_013_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:003_013_013_085 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:005_013_013_053 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:015_013_013_053 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:016_013_013_053 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* + @dihedral:013_013_013_055 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* + @dihedral:024_013_013_083 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:053_013_013_083 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* + @dihedral:024_013_013_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:053_013_013_084 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* + @dihedral:024_013_013_085 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:046_013_013_085 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:053_013_013_085 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* + @dihedral:003_013_053_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* + @dihedral:003_013_053_054 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_053_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* + @dihedral:046_013_055_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:013_013_085_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:013_013_085_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d057*_i* + @dihedral:046_013_085_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:055_048_055_054 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* + @dihedral:X_048_081_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d081*_i* @atom:* + @dihedral:X_057_085_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:X_085_085_X @atom:* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d085*_i* @atom:* + @dihedral:013_013_013_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* + @dihedral:013_013_013_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* } #(end of dihedrals by type) @@ -8135,25 +8148,61 @@ OPLSAA { # ---------- Improper Interactions: ---------- # http://lammps.sandia.gov/doc/improper_harmonic.html # Syntax: - # improper_coeff ImproperTypeName ImproperStyle parameters + # improper_coeff ImproperTypeName parameters write_once("In Settings") { - improper_coeff @improper:X-X-3-4 harmonic 10.5 180.0 - improper_coeff @improper:X-X-3-52 harmonic 10.5 180.0 - improper_coeff @improper:X-X-24-X harmonic 2.5 180.0 - improper_coeff @improper:X-X-47-X harmonic 15.0 180.0 - improper_coeff @improper:X-X-48-X harmonic 2.5 180.0 + # The following force field parameters were converted from + # the tinker parameter file (oplsaa.prm) and then edited by hand: + # Thanks to David Huang (adelaide.edu.au) for the corrections: + + improper_coeff @improper:X_X_003_004 10.5 180.0 # (moltemplate) + # <==> "imptors 0 0 3 4 21.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_003_052 10.5 180.0 # (moltemplate) + # <==> "imptors 0 0 3 52 21.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_024_X 1.0 180.0 # (moltemplate) + # <==> "imptors 0 0 24 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? + # <==> "define improper_Z_N_X_Y 180.0 4.18400 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_047_X 15.0 180.0 # (moltemplate) + # <==> "imptors 0 0 47 0 30.000 180.0 2" in oplsaa.prm (tinker) + # <==> "define improper_Z_CM_X_Y 180.0 62.76000 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:X_X_048_X 1.1 180.0 # (moltemplate) + # <==> "imptors 0 0 48 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? + # <==> "define improper_Z_CA_X_Y 180.0 4.60240 2" in oplsaa.ff (gromacs) + + improper_coeff @improper:055_055_X_055 10.5 180.0 + # <==> "define improper_N2_X_N2_N2 180.0 43.93200" in oplsaa.ff (gromacs) + # <==> no corresponding line found in oplsaa.prm (tinker) + + # --- As of 2017-9-13, I am unsure if I should add this rule: ---- + # The gromacs file for oplsaa include the following line: + # "define improper_X_NO_ON_NO 180.0 43.93200" in oplsaa.ff (gromacs) + # but there is no corresponding line found in oplsaa.prm (tinker) + # and there is no corresponding line from opls-a.prm (emc (BASF)) + # I'm not sure what the "NO" and "ON" correspond to. If I had to guess, + # the corresponding moltemplate line might be one of these two choices: + # improper_coeff @improper:X_103_102_102 10.5 180.0 ? + # improper_coeff @improper:X_102_103_103 10.5 180.0 ? + # but I'd prefer to leave this out. + } #(end of improper_coeffs) - # Rules for creating dihedral interactions according to atom type: + + # Rules for creating improper interactions according to atom type: # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4 # (* = wildcard) write_once("Data Impropers By Type (opls_imp.py)") { - @improper:X-X-3-4 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i4 - @improper:X-X-3-52 @atom:* @atom:* @atom:*_b*_a*_d*_i3 @atom:*_b*_a*_d*_i52 - @improper:X-X-24-X @atom:* @atom:* @atom:*_b*_a*_d*_i24 @atom:* - @improper:X-X-47-X @atom:* @atom:* @atom:*_b*_a*_d*_i47 @atom:* - @improper:X-X-48-X @atom:* @atom:* @atom:*_b*_a*_d*_i48 @atom:* + @improper:X_X_003_004 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i004* + @improper:X_X_003_052 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i052* + @improper:X_X_024_X @atom:* @atom:* @atom:*_b*_a*_d*_i024* @atom:* + @improper:X_X_047_X @atom:* @atom:* @atom:*_b*_a*_d*_i047* @atom:* + @improper:X_X_048_X @atom:* @atom:* @atom:*_b*_a*_d*_i048* @atom:* + @improper:055_055_X_055 @atom:*_b*_a*_d*_i55 @atom:*_b*_a*_d*_i55 @atom:* @atom:*_b*_a*_d*_i55 } #(end of impropers by type) @@ -8961,11 +9010,11 @@ OPLSAA { write_once("In Init") { units real atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style hybrid harmonic - pair_style hybrid lj/cut/coul/long 10.0 10.0 + bond_style harmonic + angle_style harmonic + dihedral_style opls + improper_style harmonic + pair_style lj/cut/coul/long 10.0 10.0 pair_modify mix geometric special_bonds lj/coul 0.0 0.0 0.5 kspace_style pppm 0.0001 @@ -8985,34 +9034,3 @@ OPLSAA { } # OPLSAA - - - - -############################### NOTES #################################### -# -# This file was generated (on 2017-7-18) using this script: -# -# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls -# -# The oplsaa.prm file was downloaded from the TINKER website -# https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# (You can build a smaller version of this file by editing the oplsaa.prm -# file and deleting the lines beginning with "atom" that you don't need, -# and subsequently running tinkerparm2lt.py on the new file. This can -# help reduce the number of atom types, which can help with visualization, -# and in some cases may also improve performance.) -# -# The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED: -# special_bonds lj/coul 0.0 0.0 0.5 -# (See http://lammps.sandia.gov/doc/special_bonds.html for details) -# -# WARNING: All Urey-Bradley interactions have been IGNORED including: -# ffid1 ffid2 ffid3 K r0 -# ureybrad 35 34 35 38.25 1.5537 -# -# WARNING: Many of these atoms are UNITED-ATOM (UA) atoms (#1-56). This means -# the hydrogen atoms have been absorbed into the heavy atoms, and the -# force-field modified accordingly. (Hopefully, moltemplate will -# complain if you attempt to bond these atoms to hydrogen atoms.) -########################################################################## diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt deleted file mode 100644 index a3e9f3ee787a06de02b12e953746910ca823865c..0000000000000000000000000000000000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa/AUTHOR.txt +++ /dev/null @@ -1,2 +0,0 @@ -OPLSAA force-field conversion tools provided by -Jason Lambert, Sebastian Echeverri, and Andrew Jewett diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt new file mode 100644 index 0000000000000000000000000000000000000000..5874b5926bc656bc91bde209af2ec130f8d7c9c6 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt @@ -0,0 +1,7 @@ + +OPLSAA force-field conversion tools provided by +Jason Lambert and Andrew Jewett. + +LOPLSAA force-field conversion provided by Sebastian Echeverri. + + diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..2412c4aa7dd0049c9347d0726d606bf64d996453 --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt @@ -0,0 +1,10 @@ +The "oplsaa.lt" file contains force field parameters which we found in the +"oplsaa.prm" file which is distributed with TINKER. +Jay Ponder, (the author of TINKER) preferred that we do not distribute +that file with moltemplate. However you can download that file here: + +https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm + +This directory does contain other files ("loplsaa.prm") containing additional +force field parameters that modify the original OPLSAA force field. + diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm similarity index 52% rename from tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm rename to tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm index ff0e3e445c4988e73a1cedefac0b50ac8a440899..bf89d9a3412364fdb73f4fd51858b8be7c93fc89 100644 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa/loplsaa_ext.prm +++ b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm @@ -1,19 +1,28 @@ - ########################################################################### - ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## - ## SOURCE: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 ## - ## CREDIT: Sebastian Echeverri (file format conversion) ## - ########################################################################### - ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ## - ########################################################################### + ############################################################################ + ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## + ## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 + ## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## + ## CREDIT: Sebastian Echeverri (file format conversion) ## + ############################################################################ + ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ## + ############################################################################ atom 80L 13L CT "Alkane CH3- (LOPLS CT_CH3)" 6 12.011 4 atom 81L 13L CT "Alkane -CH2- (LOPLS CT_CH2)" 6 12.011 4 +atom 81LL 13LL CT "Alkane -CH2- (LOPLS ALT)" 6 12.011 4 atom 85LCH3 46 HC "Alkane H-C CH3 (LOPLS HC_CH3)" 1 1.008 1 atom 85LCH2 46 HC "Alkane H-C CH2 (LOPLS HC_CH2)" 1 1.008 1 atom 87L 47L CM "Alkene RH-C= (LOPLS CM_CH)" 6 12.011 3 atom 89L 46 HC "Alkene H-C= (LOPLS HC_CH)" 1 1.008 1 atom 86L 47L CM "Alkene R2-C= (LOPLS)" 6 12.011 3 atom 88L 47L CM "Alkene H2-C= (LOPLS)" 6 12.011 3 +atom 96L 5L OH "Alcohol -OH (LOPLS)" 8 15.999 2 +atom 97L 7L HO "Alcohol -OH (LOPLS)" 1 1.008 1 +atom 111L 5L OH "Diol -OH (LOPLS)" 8 15.999 2 +atom 112L 7L HO "Diol -OH (LOPLS)" 1 1.008 1 +atom 113L 5L OH "Triol -OH (LOPLS)" 8 15.999 2 +atom 114L 7L HO "Triol -OH (LOPLS)" 1 1.008 1 +atom 118L 46L HC "Diol & Triol H-COH (LOPLS)" 1 1.008 1 atom 169L 47L CM "Chloroalkene Cl-CH= (LOPLS)" 6 12.011 3 atom 266L 47L CM "Uracil & Thymine C5 (LOPLS)" 6 12.011 3 atom 267L 47L CM "Uracil & Thymine C6 (LOPLS)" 6 12.011 3 @@ -23,21 +32,36 @@ atom 324L 47L CM "CytosineH+ C5 (LOPLS)" 6 12.011 3 atom 325L 47L CM "CytosineH+ C6 (LOPLS)" 6 12.011 3 atom 340L 47L CM "Trifluorothymine CF3- (LOPLS)" 6 12.011 4 atom 342L 47L CM "Chloroalkene Cl2-C= (LOPLS)" 6 12.011 3 +atom 406L 3L C_2 "Ester -COOR (LOPLS)" 6 12.011 3 +atom 407L 4L O_2 "Ester C=O (LOPLS)" 8 15.999 1 +atom 408L 20L OS "Ester CO-O-R (LOPLS)" 8 15.999 2 atom 458L 47L CM "Vinyl Ether =CH-OR (LOPLS)" 6 12.011 3 atom 459L 47L CM "Vinyl Ether =CR-OR (LOPLS)" 6 12.011 3 atom 649L 47L CM "Cl..CH3..Cl- Sn2 TS (LOPLS)" 6 12.011 5 +atom 718L 46L HC "Propylene Carbonate CH2 (LOPLS)" 1 1.008 1 +atom 718LL 46L HC "Propylene Carbonate CH2 (LOPLS ALT)" 1 1.008 1 atom 900L 47L CM "Allene/Ketene H2C=C=X (LOPLS)" 6 12.011 3 atom 901L 47L CM "Allene/Ketene HRC=C=X (LOPLS)" 6 12.011 3 atom 902L 47L CM "Allene/Ketene R2C=C=X (LOPLS)" 6 12.011 3 +###################### + vdw 80L 3.5000 0.0660 vdw 81L 3.5000 0.0660 +vdw 81LL 0.3500 0.0660 vdw 85LCH3 2.5000 0.0300 vdw 85LCH2 2.5000 0.026290630975 vdw 87L 3.5500 0.0760 vdw 89L 2.4200 0.0300 vdw 86L 3.5500 0.0760 vdw 88L 3.5500 0.0760 +vdw 96L 0.3120 0.1700 +vdw 97L 0.0000 0.0000 +vdw 111L 0.3070 0.1700 +vdw 112L 0.0000 0.0000 +vdw 113L 0.3070 0.1700 +vdw 114L 0.0000 0.0000 +vdw 118L 0.2500 0.0300 vdw 169L 3.5500 0.0760 vdw 266L 3.5000 0.0800 vdw 267L 3.5000 0.0800 @@ -47,13 +71,21 @@ vdw 324L 3.5000 0.0800 vdw 325L 3.5000 0.0800 vdw 340L 3.5000 0.0800 vdw 342L 3.5500 0.0760 +vdw 406L 0.31875 0.1050 +vdw 407L 0.3108 0.1680 +vdw 408L 0.2550 0.1700 vdw 458L 3.5500 0.0760 vdw 459L 3.5500 0.0760 vdw 649L 3.5500 0.0760 +vdw 718L 0.2420 0.1500 +vdw 718LL 0.2420 0.1500 vdw 900L 3.3000 0.0860 vdw 901L 3.3000 0.0860 vdw 902L 3.3000 0.0860 +###################### + + # New torsion angle parameters # Taken from table 2 of # Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 @@ -62,14 +94,42 @@ torsion 0 47L 47L 0 0.0 0 1 12.2502629063 180 2 0.0 torsion 47L 47L 13L 13L -0.8050121893 0 1 0.3218905354 180 2 -0.1032768881 0 3 0 180 4 # offset V0=-0.3574832696 torsion 13L 13L 13L 47L 0.4821902486 0 1 0.1343683078 180 2 0.1777461759 0 3 0 180 4 # offset V0=0.4405726577 +###################### +torsion 46L 13LL 5L 7L 0.00962596 0 1 -0.0145554 180 2 0.381091 0 3 0 180 4 # offset V0=0.00133126 +torsion 46L 13LL 13LL 5L 0.0143774 0 1 0.033021 180 2 0.26687 0 3 0 180 4 # offset V0=-0.0291993 +torsion 13LL 13LL 5L 7L -0.675785 0 1 -0.0160421 180 2 0.373199 0 3 0 180 4 # offset V0=-0.0225884 +torsion 13LL 13LL 13LL 5L 1.31261 0 1 -0.266307 180 2 0.637867 0 3 0 180 4 # offset V0=0.00224187 +torsion 5L 13LL 13LL 5L 2.69106 0 1 -0.849706 180 2 0.725731 0 3 0 180 4 # offset V0=-0.3326 +torsion 13LL 3L 20L 13LL 3.11923 0 1 5.73771 180 2 0.0 0 3 0 180 4 # offset V0=0.493475 +torsion 13LL 20L 3L 4L 0.0 0 1 5.73772 180 2 0.0 0 3 0 180 4 # offset V0=-0.28142 +torsion 46L 13LL 3L 20L -0.00742471 0 1 0.00217734 180 2 0.111803 0 3 0 180 4 # offset V0=-0.012512 +torsion 3L 20L 13LL 13LL -1.7354 0 1 -1.24844 180 2 0.623897 0 3 0 180 4 # offset V0=0.11706 +torsion 46L 13LL 13LL 20L 0.0113337 0 1 0.0236209 180 2 0.429747 0 3 0 180 4 # offset V0=-0.0255306 +torsion 13LL 13LL 3L 20L 0.884988 0 1 -0.626905 180 2 -0.493344 0 3 0 180 4 # offset V0=-0.0195172 +torsion 13LL 13LL 3L 4L -0.276019 0 1 1.23685 180 2 -0.670745 0 3 0 180 4 # offset V0=-0.0322467 +torsion 3L 13LL 13LL 46L -0.0021152 0 1 0.0173542 180 2 -0.295208 0 3 0 180 4 # offset V0=-0.0433963 +torsion 3L 13LL 13LL 13LL -2.30738 0 1 -0.627326 180 2 0.621951 0 3 0 180 4 # offset V0=0.0323566 +torsion 13LL 13LL 13LL 20L 2.25871 0 1 -1.02408 180 2 1.0071 0 3 0 180 4 # offset V0=0.0297084 +torsion 20L 13LL 13LL 20L 4.66787 0 1 -2.62698 180 2 1.3248 0 3 0 180 4 # offset V0=-1.48385 +torsion 5L 13LL 13LL 20L 5.03208 0 1 -2.37742 180 2 1.23809 0 3 0 180 4 # offset V0=0.223141 +###################### + charge 80L -0.222 #"Alkane CH3- (LOPLS)" "CT_CH3" 3.50 0.0660 charge 81L -0.148 #"Alkane -CH2- (LOPLS)" "CT_CH2" 3.50 0.0660 +charge 81LL 0.19 charge 85LCH3 0.074 #"Alkane H-C CH3 (LOPLS)" "HC_CH3" 2.50 0.0300 charge 85LCH2 0.074 #"Alkane H-C CH2 (LOPLS)" "HC_CH2" 2.50 0.0263 charge 87L -0.160 #"Alkene RH-C= (LOPLS)" "CM_CH" 3.55 0.0760 charge 89L 0.160 #"Alkene H-C= (LOPLS)" "HC_CH" 2.42 0.0300 charge 86L 0.0000 charge 88L -0.2300 +charge 96L -0.683 +charge 97L 0.418 +charge 111L -0.7 +charge 112L 0.435 +charge 113L -0.73 +charge 114L 0.465 +charge 118L 0.06 charge 169L 0.0050 charge 266L -0.0700 charge 267L 0.0800 @@ -79,9 +139,15 @@ charge 324L -0.0600 charge 325L 0.1000 charge 340L 0.1800 charge 342L 0.1200 +charge 406L 0.75 +charge 407L -0.55 +charge 408L -0.45 charge 458L -0.0300 charge 459L 0.0850 charge 649L -0.3440 +charge 718L 0.06 +charge 718LL 0.03 charge 900L -0.2500 charge 901L -0.1000 charge 902L 0.0500 + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt b/tools/moltemplate/moltemplate/force_fields/sdk.lt similarity index 98% rename from tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt rename to tools/moltemplate/moltemplate/force_fields/sdk.lt index f610085113381d4e5703f11fb3639e30f93b5a95..8207614282898596cf7be0cf0637c6b9824e00ff 100644 --- a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipid+chol.lt +++ b/tools/moltemplate/moltemplate/force_fields/sdk.lt @@ -1,11 +1,21 @@ # Autogenerated by EMC 2 LT tool v0.2 on 2017-06-29 # -# ./emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units +# cd sdk/ +# emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=sdk --units +# mv -f sdk.lt ../ +# +# This file contains force field parameters for lipids and cholesterol from: +# Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 +# MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 +# For details see the "README.txt" file (located in "force_fields/sdk/") # # Adapted from EMC by Pieter J. in 't Veld # Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 +# "emcprm2lt.py" was written by David Stelter. + SDK { + write_once("Data Masses") { @atom:CM 42.080400 # CM @atom:CMD2 26.037800 # CMD2 @@ -420,4 +430,6 @@ SDK { pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 special_bonds lj/coul 0.0 0.0 0.0 } # end init + } # SDK + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/README.txt b/tools/moltemplate/moltemplate/force_fields/sdk/README.txt deleted file mode 100644 index 6ca9e8f98ff3177c34239da0c92ae972d7c33942..0000000000000000000000000000000000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk/README.txt +++ /dev/null @@ -1,63 +0,0 @@ -README! - -v0.2 - -This is only part of the SDK force field and is to be used for lipids only. Only parameters from: - -Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 -http://dx.doi.org/10.1021/jp9107206 - -are used. - -NOTE: We extracted the parameters from that publication from the files -distributed with the "EMC" tool. If you use these files, please also cite: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358. - - -This works for any topology built using the following types: - -Name Structure Charge -NC -CH2CH2-N-(CH3)3 +1 -NH -CH2CH2-NH3 +1 -PH -PO4- -1 -PHE -PO4- (PE lipid) -1 -GL -CH2CH-CH2- -EST1 -CH2CO2- -EST2 -H2CO2- -CMD2 -HC=CH- (cis) -CM -CH2CH2CH2- -CT CH3CH2CH2- -CT2 CH3CH2- -W (H2O)3 - -This coarse-grainng allows for design of a wide variety of lipids. - -NEW! in v0.2: - SDK Cholesterol model has been added! Using parameters from: - -MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 -http://dx.doi.org/10.1063/1.4937153 - -are used. The following types are defined specifically for cholesterol: - -Name Structure Location -C2T -CH-(CH3)2 Tail -CM2 -CH2-CH2- Tail -CM2R -CH2-CH2- Ring A -CMDB -CH2-C=CH- Ring A/B -CMB -CH2-CH-CH- Ring B/C -CMR -CH-CH2-CH2- Ring B/C -CMR5 -CH2-CH2-CH- Ring D -CTB -CH2-CH-CH3- Tail -CTBA -C-CH3 Ring A/B -CTBB -C-CH3 Ring C/D -OAB -CH-OH Ring A - -See the provided reference for details on the CG cholesterol topology. -A 5-10 timestep is used when using cholesterol. - -Several limiations, due to missing parameters: --use of cholesterol with type "NH" is not possible. --use of cholesterol with type "PHE" is not possible. - ---- diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..eb2eed836df35e9a1ce729dbc14e83e2a474b0cd --- /dev/null +++ b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt @@ -0,0 +1,84 @@ +The files in this directory are used to create the "sdk.lt" file +(containing SDK force field parameters for moltemplate). +These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. + +Conversion from EMC (.PRM) format to moltemplate (.LT) format was +done using the "emcprm2lt.py" script written by David Stelter. +Here is an example how to use the emcprm2lt.py script: + +emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units + +This will generate a file named "sdk.lt" which (in this example) +only includes the force field parameters for lipids and cholestrol. +Later you can define new molecules in moltemplate using: + +import "sdk.lt" +NewMolecule inherits SDK { + write("Data Atoms") {...atom coordinates and types go here...} + write("Data Bond List") {...list of bonds goes here...} +} + +This is only part of the SDK force field and is to be used for lipids +and cholesterol only. Lipid parameters were taken from: + +Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 +http://dx.doi.org/10.1021/jp9107206 + +Cholesterol parameters were taken from: +MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 +http://dx.doi.org/10.1063/1.4937153 + +You can define lipids with any topology built using the following types: + +Name Structure Charge +NC -CH2CH2-N-(CH3)3 +1 +NH -CH2CH2-NH3 +1 +PH -PO4- -1 +PHE -PO4- (PE lipid) -1 +GL -CH2CH-CH2- +EST1 -CH2CO2- +EST2 -H2CO2- +CMD2 -HC=CH- (cis) +CM -CH2CH2CH2- +CT CH3CH2CH2- +CT2 CH3CH2- +W (H2O)3 + +This coarse-grainng allows for design of a wide variety of lipids. + +The following types are defined specifically for cholesterol: + +Name Structure Location +C2T -CH-(CH3)2 Tail +CM2 -CH2-CH2- Tail +CM2R -CH2-CH2- Ring A +CMDB -CH2-C=CH- Ring A/B +CMB -CH2-CH-CH- Ring B/C +CMR -CH-CH2-CH2- Ring B/C +CMR5 -CH2-CH2-CH- Ring D +CTB -CH2-CH-CH3- Tail +CTBA -C-CH3 Ring A/B +CTBB -C-CH3 Ring C/D +OAB -CH-OH Ring A + +See the provided reference for details on the CG cholesterol topology. +A 5.0-10.0 timestep is used when using cholesterol. + +Several limiations, due to missing parameters: +-use of cholesterol with type "NH" is not possible. +-use of cholesterol with type "PHE" is not possible. + +---- Credits: ---- + +emcprm2lt.py was written by David Stelter +EMC was written by Pieter J. in 't Veld +SDK was created by Shinoda, DeVane, Klein, J.Phys.Chem.B, Vol. 114, No. 20, 2010 + +---- additional citation request ---- + +Since we borrowed force field parameters from files distributed with EMC, +if you use files generated by "emcprm2lt.py", please also cite the EMC paper: +P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 + + + diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipidONLY.lt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/SDK_lipidONLY.lt rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/sdk_cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/sdk_cholesterol.prm rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm diff --git a/tools/moltemplate/moltemplate/force_fields/sdk/sdk_lipids.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm similarity index 100% rename from tools/moltemplate/moltemplate/force_fields/sdk/sdk_lipids.prm rename to tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm diff --git a/tools/moltemplate/moltemplate/genpoly_lt.py b/tools/moltemplate/moltemplate/genpoly_lt.py index 2c4014e5dbd851d08000de79323c06c81de17aa5..9d8ec846081eb21600ef2afea222314a21f7548a 100755 --- a/tools/moltemplate/moltemplate/genpoly_lt.py +++ b/tools/moltemplate/moltemplate/genpoly_lt.py @@ -256,7 +256,7 @@ class GPSettings(object): if i + 1 >= len(argv): raise InputError('Error: ' + argv[i] + ' flag should be followed ' + 'by 3 numbers separated by commas (no spaces)\n') - self.direction_orig = map(float, argv[i + 1].split(',')) + self.direction_orig = list(map(float, argv[i + 1].split(','))) del(argv[i:i + 2]) elif argv[i].lower() == '-circular': if i + 1 >= len(argv): @@ -294,7 +294,7 @@ class GPSettings(object): if i + 1 >= len(argv): raise InputError('Error: ' + argv[i] + ' flag should be followed ' + 'by 3 numbers separated by commas (no spaces)\n') - self.box_padding = map(float, argv[i + 1].split(',')) + self.box_padding = list(map(float, argv[i + 1].split(','))) if len(self.box_padding) == 1: self.box_padding = self.box_padding * 3 del(argv[i:i + 2]) @@ -340,7 +340,7 @@ class WrapPeriodic(object): @classmethod def Wrap(obj, i, N): - if i / N != 0: + if i // N != 0: obj.bounds_err = True return i % N @@ -384,7 +384,7 @@ class GenPoly(object): for i in range(0, len(lines)): tokens = lines[i].strip().split() if (len(tokens) == 3): - coords.append(map(float, tokens)) + coords.append(list(map(float, tokens))) self.N = len(coords) if self.N < 2: diff --git a/tools/moltemplate/moltemplate/ltemplify.py b/tools/moltemplate/moltemplate/ltemplify.py index 753d9b3ad0f0cc30438fb3d1405f3be04923dc90..2fa20b0d051fecc2d78cf505647944d3128b9b6c 100755 --- a/tools/moltemplate/moltemplate/ltemplify.py +++ b/tools/moltemplate/moltemplate/ltemplify.py @@ -2,7 +2,6 @@ # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California # All rights reserved. @@ -31,14 +30,14 @@ import sys try: from .ttree_lex import * from .lttree_styles import * -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * from lttree_styles import * g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' -g_version_str = '0.53.1' -g_date_str = '2017-6-08' +g_version_str = '0.54.0' +g_date_str = '2017-10-03' def Intify(s): if s.isdigit(): @@ -1279,7 +1278,7 @@ def main(): atomtype_i_str = tokens[0] if '*' in atomtype_i_str: raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' + ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ' character in the \"Pair Coeffs\" section.\n') else: i = int(atomtype_i_str) @@ -1308,7 +1307,7 @@ def main(): atomtype_j_str = tokens[1] if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2015-8, moltemplate forbids use of the "\*\" wildcard\n' + ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' ' character in the \"PairIJ Coeffs\" section.\n') else: i = int(atomtype_i_str) @@ -1828,8 +1827,11 @@ def main(): else: i_a = i_b = Intify(atomtype_i_str) + assert((type(i_a) is int) and (type(i_b) is int)) + i_a_final = None i_b_final = None + for i in range(i_a, i_b + 1): if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): i_a_final = i @@ -2615,7 +2617,7 @@ def main(): # ' --groups-- Attempting to parse \"group\" commands.\n' # ' This may cause '+g_program_name+' to crash.\n' # ' If so, comment out all group commands in your input script(s), and\n' - # ' try again. (And please report the error. -Andrew 2014-10-30)\n') + # ' try again. (And please report the error. -Andrew 2017-10)\n') i_line = 0 groups_needed = set(['all']) @@ -2885,9 +2887,9 @@ def main(): for i in range(atomids_lo, atomids_hi+1): if i in needed_atomids: l_new_set_commands.append((' ' * indent) + - tokens[0:2].join(' ')+' '+ + ' '.join(tokens[0:2])+' '+ str(i) + ' ' + - tokens[3:].join(' ')) + ' '.join(tokens[3:])) elif tokens[1] == 'mol': pattern = tokens[2].split('*') if pattern[0] == '': @@ -2903,9 +2905,9 @@ def main(): molids_hi = min(int(pattern[1]), max_needed_molid) for i in range(molids_lo, molids_hi+1): if i in needed_molids: - l_new_set_commands.append(tokens[0:2].join(' ')+' '+ + l_new_set_commands.append(' '.join(tokens[0:2])+' '+ str(i) + ' ' + - tokens[3:].join(' ')) + ' '.join(tokens[3:])) elif tokens[0] == 'group': group_name = tokens[2] if group_name in groups_needed: @@ -3480,7 +3482,7 @@ def main(): # sys.stderr.write('######################################################\n' # 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n' # ' Please check to make sure that the group(s) generated by\n' - # ' '+g_program_name+' contain the correct atoms. (-Andrew 2014-10-30)\n' + # ' '+g_program_name+' contain the correct atoms. (-Andrew 2017-10)\n' # '######################################################\n') assert(non_empty_output) @@ -3575,7 +3577,7 @@ def main(): ' Please look over the resulting LT file and check for errors.\n' ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' ' or type numbers to the corresponding $ or @-style counter variables.\n' - ' Feel free to report any bugs you find. (-Andrew Jewett 2015-8-02)\n') + ' Feel free to report any bugs you find. (-Andrew Jewett 2017-10)\n') except (ValueError, InputError) as err: diff --git a/tools/moltemplate/moltemplate/lttree.py b/tools/moltemplate/moltemplate/lttree.py index 168a60ecc33c6881bf4fa19955e094391c5fdfc3..9d5ee07ac2f969b1eef65c0fb6eeca00d216e475 100755 --- a/tools/moltemplate/moltemplate/lttree.py +++ b/tools/moltemplate/moltemplate/lttree.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2011, Regents of the University of California @@ -28,8 +29,8 @@ Additional LAMMPS-specific features may be added in the future. """ g_program_name = __file__.split('/')[-1] # ='lttree.py' -g_date_str = '2017-4-11' -g_version_str = '0.76.0' +g_date_str = '2018-3-15' +g_version_str = '0.77.0' import sys @@ -45,10 +46,22 @@ try: from .ttree_lex import InputError, TextBlock, DeleteLinesWithBadVars, \ TemplateLexer from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ - ColNames2Coords, ColNames2Vects, data_atoms, data_masses + ColNames2Coords, ColNames2Vects, \ + data_atoms, data_prefix, data_masses, \ + data_velocities, data_ellipsoids, data_triangles, data_lines, \ + data_pair_coeffs, data_bond_coeffs, data_angle_coeffs, \ + data_dihedral_coeffs, data_improper_coeffs, data_bondbond_coeffs, \ + data_bondangle_coeffs, data_middlebondtorsion_coeffs, \ + data_endbondtorsion_coeffs, data_angletorsion_coeffs, \ + data_angleangletorsion_coeffs, data_bondbond13_coeffs, \ + data_angleangle_coeffs, data_bonds_by_type, data_angles_by_type, \ + data_dihedrals_by_type, data_impropers_by_type, \ + data_bonds, data_bond_list, data_angles, data_dihedrals, data_impropers, \ + data_boundary, data_pbc, data_prefix_no_space, in_init, in_settings, \ + in_prefix from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from ttree_lex import * @@ -332,6 +345,60 @@ def TransformAtomText(text, matrix, settings): return '\n'.join(lines) + +def TransformEllipsoidText(text, matrix, settings): + """ Apply the transformation matrix to the quaternions represented + by the last four numbers on each line. + The \"matrix\" stores the aggregate sum of combined transformations + to be applied and the rotational part of this matrix + must be converted to a quaternion. + + """ + + #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') + + lines = text.split('\n') + + for i in range(0, len(lines)): + line_orig = lines[i] + ic = line_orig.find('#') + if ic != -1: + line = line_orig[:ic] + comment = ' ' + line_orig[ic:].rstrip('\n') + else: + line = line_orig.rstrip('\n') + comment = '' + + columns = line.split() + + if len(columns) != 0: + if len(columns) != 8: + raise InputError('Error (lttree.py): Expected 7 numbers' + + ' instead of ' + + str(len(columns)) + + '\nline:\n' + + line + + ' in each line of the ellipsoids\" section.\n"') + q_orig = [float(columns[-4]), + float(columns[-3]), + float(columns[-2]), + float(columns[-1])] + + qRot = [0.0, 0.0, 0.0, 0.0] + Matrix2Quaternion(matrix, qRot) + + q_new = [0.0, 0.0, 0.0, 0.0] + MultQuat(q_new, qRot, q_orig) + + columns[-4] = str(q_new[0]) + columns[-3] = str(q_new[1]) + columns[-2] = str(q_new[2]) + columns[-1] = str(q_new[3]) + lines[i] = ' '.join(columns) + comment + return '\n'.join(lines) + + + def CalcCM(text_Atoms, text_Masses=None, settings=None): @@ -487,8 +554,8 @@ def _ExecCommands(command_list, transform_block += '.' + transform transform = transform.split('(')[0] if ((transform == 'movecm') or - (transform == 'rotcm') or - (transform == 'scalecm')): + (transform == 'rotcm') or + (transform == 'scalecm')): break transform_blocks.append(transform_block) @@ -553,6 +620,8 @@ def _ExecCommands(command_list, # before passing them on to the caller. if command.filename == data_atoms: text = TransformAtomText(text, matrix_stack.M, settings) + if command.filename == data_ellipsoids: + text = TransformEllipsoidText(text, matrix_stack.M, settings) files_content[command.filename].append(text) @@ -599,6 +668,9 @@ def _ExecCommands(command_list, files_content[data_atoms] = \ TransformAtomText(files_content[data_atoms], matrix_stack.M, settings) + files_content[data_ellipsoids] = \ + TransformEllipsoidText(files_content[data_ellipsoids], + matrix_stack.M, settings) for ppcommand in postprocessing_commands: matrix_stack.Pop(which_stack=command.context_node) diff --git a/tools/moltemplate/moltemplate/lttree_check.py b/tools/moltemplate/moltemplate/lttree_check.py index 10daa89be2ec3164a798aab5c71cde148c16a764..5fb5b6f6ce1cea98539798283dd4daed864c18bf 100755 --- a/tools/moltemplate/moltemplate/lttree_check.py +++ b/tools/moltemplate/moltemplate/lttree_check.py @@ -1,6 +1,7 @@ #!/usr/bin/env python # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2011, Regents of the University of California @@ -45,7 +46,7 @@ the files generated by lttree.py or moltemplate.sh. import sys try: - from .ttree_lex import RemoveOuterQuotes, HasWildCard, InputError, \ + from .ttree_lex import RemoveOuterQuotes, HasWildcard, InputError, \ ErrorLeader, TextBlock, VarRef, TemplateLexer, \ ExtractCatName, TableFromTemplate from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ @@ -68,7 +69,7 @@ try: from .lttree import LttreeSettings, LttreeParseArgs from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ LinTransform -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * from ttree import * @@ -80,7 +81,7 @@ except (SystemError, ValueError): try: from .ttree import StaticObj, WriteFileCommand, DescrToCatLeafPtkns, \ AssignStaticVarPtrs, FindReplacementVarPairs, ReplaceVars -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import * from lttree import * @@ -93,8 +94,8 @@ if sys.version < '2.6': g_program_name = __file__.split('/')[-1] # = 'lttree_check.py' -g_version_str = '0.78.0' -g_date_str = '2017-4-11' +g_version_str = '0.80.1' +g_date_str = '2017-10-01' # g_no_check_msg = \ @@ -904,6 +905,7 @@ def CheckSyntaxCheap(lex): def CheckSyntaxStatic(context_node, root_node, atom_column_names, + allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -936,6 +938,7 @@ def CheckSyntaxStatic(context_node, elif (filename.find(in_prefix) == 0): # if filename begins with "In " CheckInFileSyntax(command.tmpl_list, root_node, + allow_wildcards, in_pair_coeffs_defined, in_bond_coeffs_defined, in_angle_coeffs_defined, @@ -1337,15 +1340,18 @@ def CheckSyntaxStatic(context_node, elif (isinstance(entry, VarRef) and ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('--- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, entry.srcloc.lineno) + '\n' 'The wildcard symbol, \"*\", is not recommended within \"' + filename + '\".\n' 'It is safer to specify the parameters for each type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @atom,@bond,@angle,@dihedral,@improper types are\n' + 'included in the a*b range of values, then MAKE SURE that these types are\n' + 'assigned to connsecutively increasing integer values by first defining them in\n' + 'that order, or if that fails, by using the \"-a\" to assign the values manually\n') if filename == 'Data Bond Coeffs': # Commenting the next line out. We did this already: @@ -1641,6 +1647,7 @@ def CheckSyntaxStatic(context_node, CheckSyntaxStatic(child, root_node, atom_column_names, + allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -1656,6 +1663,7 @@ def CheckSyntaxStatic(context_node, def CheckInFileSyntax(tmpl_list, root_node, + allow_wildcards, pair_coeffs_defined, bond_coeffs_defined, angle_coeffs_defined, @@ -1700,7 +1708,7 @@ def CheckInFileSyntax(tmpl_list, elif (isinstance(entry, VarRef) and ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('---- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, @@ -1708,8 +1716,11 @@ def CheckInFileSyntax(tmpl_list, 'The wildcard symbol, \"*\", is not recommended within a \"' + table[i][0].text + '\".\n' 'command. It is safer to specify the parameters for each bond type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @bond,@angle,@dihedral,@improper types are included\n' + 'in the range, then MAKE SURE these @bond,@angle,@dihedral,@improper types are\n' + 'assigned to connsecutively increasing integer values by first defining them in\n' + 'that order, or if that fails, by using the \"-a\" to assign the values manually\n') if ((isinstance(table[i][0], TextBlock)) and ((table[i][0].text.lower() == 'bondcoeff') or @@ -1857,9 +1868,9 @@ def CheckInFileSyntax(tmpl_list, if len(table[i]) > 2: # if not, deal with error later if ((isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*')) and - (isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*'))): + (table[i][1].text == '*')) and #'* *' <--BUG? + (isinstance(table[i][1], TextBlock) and # <--BUG? + (table[i][1].text == '*'))): # <--BUG? pair_coeffs_defined.add(('*', '*')) else: compound_wildcard = False @@ -1889,21 +1900,24 @@ def CheckInFileSyntax(tmpl_list, ('*' in entry.descr_str)): compound_wildcard = True - if compound_wildcard: + if compound_wildcard and (not allow_wildcards): raise InputError('---- Paranoid checking: ---\n' ' Possible error near ' + ErrorLeader(entry.srcloc.infile, entry.srcloc.lineno) + '\n' 'The wildcard symbol, \"*\", is not recommended within a \"pair_coeff\" command.\n' 'It is safer to specify the parameters for each bond type explicitly.\n' - 'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n' - 'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n') + 'To get past this error message, run moltemplate.sh with the \"-allow-wildcards\"\n' + 'argument. If not all of the @atom types are included in the range, then\n' + 'MAKE SURE the relevant @atom types in the * range are assigned to\n' + 'connsecutively increasing integer values by first defining them in that\n' + 'order, or if that fails, by using the \"-a\" to assign the values manually.\n') if ((len(table[i]) > 2) and - (isinstance(table[i][1], TextBlock) and - (table[i][1].text == '*')) and - (isinstance(table[i][2], TextBlock) and - (table[i][2].text == '*'))): + ((isinstance(table[i][1], TextBlock) and + (table[i][1].text == '*')) or + (isinstance(table[i][2], TextBlock) and + (table[i][2].text == '*')))): pass # we dealt with this case earlier elif (not ((len(table[i]) > 2) and @@ -1941,7 +1955,21 @@ def LttreeCheckParseArgs(argv, settings, main=False, show_warnings=True): if len(argv) == 1: raise InputError('Error: This program requires at least one argument\n' ' the name of a file containing ttree template commands\n') - elif len(argv) == 2: + settings.allow_wildcards = True + i = 1 + while i < len(argv): + if argv[i].lower() in ('-allow-wildcards', '-allowwildcards'): + settings.allow_wildcards = True + del argv[i:i+1] + elif argv[i].lower() in ('-forbid-wildcards', '-forbidwildcards'): + settings.allow_wildcards = False + del argv[i:i+1] + else: + i += 1 + #(perhaps later I'll add some additional argumets) + + # The only argument left should be the system.lt file we want to read: + if len(argv) == 2: try: # Parse text from the file named argv[1] settings.lex.infile = argv[1] @@ -1951,8 +1979,6 @@ def LttreeCheckParseArgs(argv, settings, main=False, show_warnings=True): ' \"' + argv[1] + '\"\n' ' for reading.\n') sys.exit(1) - del(argv[1:2]) - else: # if there are more than 2 remaining arguments, problem_args = ['\"' + arg + '\"' for arg in argv[1:]] @@ -2045,6 +2071,7 @@ def main(): CheckSyntaxStatic(static_tree_root, static_tree_root, settings.column_names, + settings.allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -2060,6 +2087,7 @@ def main(): CheckSyntaxStatic(static_tree_root, static_tree_root, settings.column_names, + settings.allow_wildcards, data_pair_coeffs_defined, data_bond_coeffs_defined, data_angle_coeffs_defined, @@ -2089,12 +2117,20 @@ def main(): else: bond_coeffs_defined = in_bond_coeffs_defined + bond_types_have_wildcards = False bond_bindings = static_tree_root.categories['bond'].bindings for nd, bond_binding in bond_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(bond_binding.full_name) + if has_wildcard: + bond_types_have_wildcards = True + for nd, bond_binding in bond_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(bond_binding.full_name) if ((not (bond_binding in bond_coeffs_defined)) and - (not HasWildCard(bond_binding.full_name)) and - (not ('*' in bond_coeffs_defined))): + #(not has_wildcard) and + (not bond_types_have_wildcards) and + (not ('*' in bond_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing bond coeff.\n\n' + ' No coeffs for the \"' + bond_binding.full_name + '\" bond type have been\n' + @@ -2108,7 +2144,7 @@ def main(): if 'angle' in static_tree_root.categories: if ((len(data_angle_coeffs_defined) > 0) and - (len(in_angle_coeffs_defined) > 0)): + (len(in_angle_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"angle_coeff\" commands\n' + ' OR you can have a \"Data Angle Coeffs\" section.\n' + @@ -2122,12 +2158,20 @@ def main(): else: angle_coeffs_defined = in_angle_coeffs_defined + angle_types_have_wildcards = False angle_bindings = static_tree_root.categories['angle'].bindings for nd, angle_binding in angle_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(angle_binding.full_name) + if has_wildcard: + angle_types_have_wildcards = True + for nd, angle_binding in angle_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(angle_binding.full_name) if ((not (angle_binding in angle_coeffs_defined)) and - #(not HasWildCard(angle_binding.full_name)) and - (not ('*' in angle_coeffs_defined))): + #(not has_wildcard)) and + (not angle_types_have_wildcards) and + (not ('*' in angle_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing angle coeff.\n\n' + ' No coeffs for the \"' + angle_binding.full_name + '\" angle type have been\n' + @@ -2142,7 +2186,7 @@ def main(): #sys.stderr.write('dihedral_bindings = '+str(dihedral_bindings)+'\n') if ((len(data_dihedral_coeffs_defined) > 0) and - (len(in_dihedral_coeffs_defined) > 0)): + (len(in_dihedral_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"dihedral_coeff\" commands\n' + ' OR you can have a \"Data Dihedral Coeffs\" section.\n' + @@ -2156,13 +2200,21 @@ def main(): else: dihedral_coeffs_defined = in_dihedral_coeffs_defined + dihedral_types_have_wildcards = False dihedral_bindings = static_tree_root.categories[ 'dihedral'].bindings for nd, dihedral_binding in dihedral_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(dihedral_binding.full_name) + if has_wildcard: + dihedral_types_have_wildcards = True + for nd, dihedral_binding in dihedral_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(dihedral_binding.full_name) if ((not (dihedral_binding in dihedral_coeffs_defined)) and - #(not HasWildCard(dihedral_binding.full_name)) and - (not ('*' in dihedral_coeffs_defined))): + #(not has_wildcard) and + (not dihedral_types_have_wildcards) and + (not ('*' in dihedral_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing dihedral coeff.\n\n' + ' No coeffs for the \"' + dihedral_binding.full_name + '\" dihedral type have been\n' + @@ -2190,13 +2242,21 @@ def main(): else: improper_coeffs_defined = in_improper_coeffs_defined + improper_types_have_wildcards = False improper_bindings = static_tree_root.categories[ 'improper'].bindings for nd, improper_binding in improper_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(improper_binding.full_name) + if has_wildcard: + improper_types_have_wildcards = True + for nd, improper_binding in improper_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(improper_binding.full_name) if ((not (improper_binding in improper_coeffs_defined)) and - #(not HasWildCard(improper_binding.full_name)) and - (not ('*' in improper_coeffs_defined))): + #(not has_wildcard) and + (not improper_types_have_wildcards) and + (not ('*' in improper_coeffs_defined))): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: Missing improper coeff.\n\n' + ' No coeffs for the \"' + improper_binding.full_name + '\" improper type have been\n' + @@ -2210,7 +2270,7 @@ def main(): if 'atom' in static_tree_root.categories: if ((len(data_pair_coeffs_defined) > 0) and - (len(in_pair_coeffs_defined) > 0)): + (len(in_pair_coeffs_defined) > 0)): raise InputError('---------------------------------------------------------------------\n' + ' Syntax error: You can EITHER use \"pair_coeff\" commands\n' + ' OR you can have a \"Data Pair Coeffs\" section.\n' + @@ -2225,13 +2285,21 @@ def main(): else: pair_coeffs_defined = in_pair_coeffs_defined + atom_types_have_wildcards = False atom_bindings = static_tree_root.categories['atom'].bindings for nd, atom_binding in atom_bindings.items(): if not nd.IsDeleted(): + has_wildcard = HasWildcard(atom_binding.full_name) + if has_wildcard: + atom_types_have_wildcards = True + for nd, atom_binding in atom_bindings.items(): + if not nd.IsDeleted(): + #has_wildcard = HasWildcard(atom_binding.full_name) if ((not ((atom_binding, atom_binding) in pair_coeffs_defined)) and - (not HasWildCard(atom_binding.full_name)) and + #(not has_wildcard) and + (not atom_types_have_wildcards) and (not (('*', '*') in pair_coeffs_defined)) and (not (atom_binding.nptr.cat_name, atom_binding.nptr.cat_node, diff --git a/tools/moltemplate/moltemplate/lttree_postprocess.py b/tools/moltemplate/moltemplate/lttree_postprocess.py index 1bb985361f4ea93c08f714f7f801d755bcc70748..41eb8ed85807356a8bc81df1bcfd3c4023a44e40 100755 --- a/tools/moltemplate/moltemplate/lttree_postprocess.py +++ b/tools/moltemplate/moltemplate/lttree_postprocess.py @@ -16,14 +16,14 @@ import sys try: from .lttree_styles import * from .ttree_lex import ExtractCatName -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from lttree_styles import * from ttree_lex import ExtractCatName g_program_name = __file__.split('/')[-1] # = 'lttree_postprocess.py' -g_version_str = '0.5.0' -g_date_str = '2016-12-21' +g_version_str = '0.5.1' +g_date_str = '2017-8-23' def main(): atom_style = 'full' diff --git a/tools/moltemplate/moltemplate/lttree_styles.py b/tools/moltemplate/moltemplate/lttree_styles.py index adeb1de749652ff9909a015d119a2858945593e3..5691aaddf6438a14e7a3f51fed566307c3078ced 100644 --- a/tools/moltemplate/moltemplate/lttree_styles.py +++ b/tools/moltemplate/moltemplate/lttree_styles.py @@ -2,6 +2,7 @@ # -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -9,7 +10,7 @@ try: from .ttree_lex import InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import InputError diff --git a/tools/moltemplate/moltemplate/nbody_Angles.py b/tools/moltemplate/moltemplate/nbody_Angles.py index e6b2fbff1fb4792ec87b5e0830c85e32ea769936..9cc5456b01a5116618e843d812801fd2119d3cb7 100644 --- a/tools/moltemplate/moltemplate/nbody_Angles.py +++ b/tools/moltemplate/moltemplate/nbody_Angles.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Bonds.py b/tools/moltemplate/moltemplate/nbody_Bonds.py index c11c3e60e29b5aa888abe33905038faee8ef7bd7..64c82700b71b81fbbd6213e28405aa3cd9e939df 100644 --- a/tools/moltemplate/moltemplate/nbody_Bonds.py +++ b/tools/moltemplate/moltemplate/nbody_Bonds.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Dihedrals.py b/tools/moltemplate/moltemplate/nbody_Dihedrals.py index 9197db914306744d43abb576685f65215ee7646b..86fbdd34147fdc57d4b83b41760046ef06512a6c 100644 --- a/tools/moltemplate/moltemplate/nbody_Dihedrals.py +++ b/tools/moltemplate/moltemplate/nbody_Dihedrals.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_Impropers.py b/tools/moltemplate/moltemplate/nbody_Impropers.py index 6b48d9aa19a533f2a1a28cc7741a14ce0fe5286a..bbb88bd37fb256d3642c3d9400d0758fd6401548 100644 --- a/tools/moltemplate/moltemplate/nbody_Impropers.py +++ b/tools/moltemplate/moltemplate/nbody_Impropers.py @@ -1,6 +1,6 @@ try: from .nbody_graph_search import Ugraph -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph diff --git a/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py new file mode 100644 index 0000000000000000000000000000000000000000..d4b7d22b2ea89fe98642e1f35dc29e23e0e792c1 --- /dev/null +++ b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenIflipJK.py @@ -0,0 +1,61 @@ +try: + from ..nbody_graph_search import Ugraph +except: + # not installed as a module + from nbody_graph_search import Ugraph + +# To find 4-body "improper" interactions, +# (by default, most of the time), we would use this subgraph: +# 3 +# * 1st bond connects atoms 0 and 1 +# | => 2nd bond connects atoms 0 and 2 +# _.*._ 3rd bond connects atoms 0 and 3 +# *' 0 `* +# 1 2 +# + +bond_pattern = Ugraph([(0,1), (0,2), (0,3)]) +# (Ugraph atom indices begin at 0, not 1) + + +def canonical_order(match): + """ + When searching for atoms with matching bond patterns GraphMatcher + often returns redundant results. We must define a "canonical_order" + function which sorts the atoms and bonds in a way which is consistent + with the type of N-body interaction being considered. + The atoms (and bonds) in a candidate match are rearranged by the + canonical_order(). Then the re-ordered list of atom and bond ids is + tested against the list of atom/bond ids in the matches-found-so-far, + before it is added to the list of interactions found so far. + (For example, it does not make sense to define a separate 4-body improper- + angle interaction between atoms 0, 1, 2, 3 AND 0, 2, 1, 3. + The "improper angle" is often defined as the angle between planes formed + by atoms 0,1,2 & 1,2,3. Alternately, it may instead be defined as the + angle between the 0,1,2 plane and atom 3. Either way, this angle does + not change when swapping the middle pair of atoms (1 and 2) + (except for a change of sign, which does not matter since the energy functions + used are typically sign invariant. Furthermore, neither of OUTER pair of atoms + are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.) + Consequently it does not make sense to define a separate 4-body improper- + interaction between atoms 0,1,2,3 AS WELL AS between 0,2,1,3. + So we sort the atoms and bonds so that the first atom has a always has + a lower atomID than the last atom. (Later we will check to see if we + have already defined an interaction between these 4 atoms. If not then + we create a new one.) + + """ + atom0 = match[0][0] + atom1 = match[0][1] + atom2 = match[0][2] + atom3 = match[0][3] + # match[1][0:2] contains the ID numbers for the 3 bonds + bond0 = match[1][0] + bond1 = match[1][1] + bond2 = match[1][2] + if atom1 <= atom2: + #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2)) + # But this is the same thing as: + return match + else: + return ((atom0,atom2,atom1,atom3), (bond1, bond0, bond2)) diff --git a/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py new file mode 100644 index 0000000000000000000000000000000000000000..b00a2afda89ffea41e1de6b5ad93a184ac087bd5 --- /dev/null +++ b/tools/moltemplate/moltemplate/nbody_alt_symmetry/cenJflipIL.py @@ -0,0 +1,68 @@ +try: + from ..nbody_graph_search import Ugraph +except: + # not installed as a module + from nbody_graph_search import Ugraph + +# To find 4-body "improper" interactions, +# (by default, most of the time), we would use this subgraph: +# 0 +# * 1st bond connects atoms 1 and 0 +# | => 2nd bond connects atoms 1 and 2 +# _.*._ 3rd bond connects atoms 1 and 3 +# *' 1 `* +# 2 3 +# +# In OPLS, the central atom is the second atom ("1"). +# This differs from other force-fields. +# We take this detail into account in the line below: + +bond_pattern = Ugraph([(1,0), (1,2), (1,3)]) + +# As with other force-fields, the improper-angle is the angle between the planes +# defined by the first three atoms (0,1,2) and last three atoms (1,2,3). +# (This is implemented in LAMMPS using an improper_style which requires +# that the atoms in the interaction will be listed in this order: 0,1,2,3.) + +def canonical_order(match): + """ + Before defining a new interaction, we must check to see if an + interaction between these same 4 atoms has already been created + (perhaps listed in a different, but equivalent order). + If we don't check for this this, we will create many unnecessary redundant + interactions (which can slow down he simulation). + To avoid this, I define a "canonical_order" function which sorts the atoms + and bonds in a way which is consistent with the symmetry of the interaction + being generated... Later the re-ordered list of atom and bond ids will be + tested against the list of atom/bond ids in the matches-found-so-far, + before it is added to the list of interactions found so far. Note that + the energy of an improper interactions is a function of the improper angle. + The "improper angle" is often defined as the angle between planes formed + by atoms 0,1,2 & 1,2,3. (Alternately, it is sometimes defined as the + angle between the 0,1,2 plane and atom 3.) + This angle does not change when swapping the OUTER pair of atoms (0 and 3) + (except for a change of sign, which does not matter since the energy functions + used are typically sign invariant. Furthermore, neither of OUTER pair of atoms + are the central atom. There are 3!=6 ways of ordering the remaining 3 atoms.) + Consequently it does not make sense to define a separate 4-body improper- + interaction between atoms 0,1,2,3 AS WELL AS between 3,1,2,0. + So we sort the atoms and bonds so that the first atom has a always has + a lower atomID than the last atom. (Later we will check to see if we + have already defined an interaction between these 4 atoms. If not then + we create a new one.) + + """ + atom0 = match[0][0] + atom1 = match[0][1] + atom2 = match[0][2] + atom3 = match[0][3] + # match[1][0:2] contains the ID numbers for the 3 bonds + bond0 = match[1][0] + bond1 = match[1][1] + bond2 = match[1][2] + if atom0 <= atom3: + #return ((atom0,atom1,atom2,atom3), (bond0, bond1, bond2)) + # But this is the same thing as: + return match + else: + return ((atom3,atom1,atom2,atom0), (bond2,bond1,bond0)) diff --git a/tools/moltemplate/moltemplate/nbody_by_type.py b/tools/moltemplate/moltemplate/nbody_by_type.py index 65b51064c8c057851069f14e471177ae1b5bfcad..1d73b23fb9c7f6134eb7876b996ff2498830fb19 100755 --- a/tools/moltemplate/moltemplate/nbody_by_type.py +++ b/tools/moltemplate/moltemplate/nbody_by_type.py @@ -169,7 +169,7 @@ try: from .nbody_by_type_lib import GenInteractions_str from .ttree_lex import * from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): from extract_lammps_data import * from nbody_by_type_lib import GenInteractions_str from ttree_lex import * @@ -373,7 +373,7 @@ def GenInteractions_files(lines_data, try: g = importlib.import_module(name, pkg) break - except (SystemError, ImportError): + except (ImportError, SystemError, ValueError): pass if g is None: @@ -513,7 +513,7 @@ def main(): ' (See nbody_Dihedrals.py for example.)\n') bond_pattern_module_name = argv[i + 1] # If the file name ends in ".py", then strip off this suffix. - # For some reason, the next line does not work: + # The next line does not work. Too lazy to care why. # bond_pattern_module_name=bond_pattern_module_name.rstrip('.py') # Do this instead pc = bond_pattern_module_name.rfind('.py') @@ -578,8 +578,8 @@ def main(): ' (The actual problem may be earlier in the argument list.)\n') if ((section_name == '') or - (section_name_bytype == '') or - (bond_pattern_module_name == '')): + (section_name_bytype == '') or + (bond_pattern_module_name == '')): raise InputError('Syntax Error(' + g_program_name + '):\n\n' ' You have not defined the following arguments:\n' ' -section name\n' diff --git a/tools/moltemplate/moltemplate/nbody_by_type_lib.py b/tools/moltemplate/moltemplate/nbody_by_type_lib.py index b8011a80d5a09d74d112c8e99f63a38cd9cea6dc..da5a3b045265612bb777988bf11bac1749b0a24e 100644 --- a/tools/moltemplate/moltemplate/nbody_by_type_lib.py +++ b/tools/moltemplate/moltemplate/nbody_by_type_lib.py @@ -30,7 +30,7 @@ from collections import defaultdict try: from .nbody_graph_search import Ugraph, GraphMatcher from .ttree_lex import MatchesPattern, MatchesAll, InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from nbody_graph_search import Ugraph, GraphMatcher from ttree_lex import MatchesPattern, MatchesAll, InputError diff --git a/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py b/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py index a975eb1b795e88d0acdb2bae0859897a67522a2a..d92cc87904c67a7b51db9854f3721387293aacdc 100755 --- a/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py +++ b/tools/moltemplate/moltemplate/nbody_fix_ttree_assignments.py @@ -46,7 +46,7 @@ import sys try: from .ttree_lex import SplitQuotedString, InputError -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * diff --git a/tools/moltemplate/moltemplate/nbody_reorder_atoms.py b/tools/moltemplate/moltemplate/nbody_reorder_atoms.py index 53a51a38c4fbdc6ca45398000a24000346135821..85b8b4e510571c800bb2d2c349f3f6144f72fadf 100755 --- a/tools/moltemplate/moltemplate/nbody_reorder_atoms.py +++ b/tools/moltemplate/moltemplate/nbody_reorder_atoms.py @@ -63,7 +63,7 @@ def main(): # defines g.bond_pattern, g.canonical_order g = importlib.import_module(name, pkg) break - except (SystemError, ImportError): + except (ImportError, SystemError, ValueError): pass if g is None: diff --git a/tools/moltemplate/moltemplate/postprocess_coeffs.py b/tools/moltemplate/moltemplate/postprocess_coeffs.py new file mode 100755 index 0000000000000000000000000000000000000000..439f6dc9c1bde241e749a6b2fd243091b2818344 --- /dev/null +++ b/tools/moltemplate/moltemplate/postprocess_coeffs.py @@ -0,0 +1,287 @@ +#!/usr/bin/env python + +man_page_text = """ +Usage (example): + +postprocess_coeffs.py ttree_assignments.txt < file.template > file_new.template + +Moltemplate users would like to be able to use commands with wildcards like: + bond_coeff @bond:*/A/* harmonic 533.7 120.0 + pair_coeff @atom:A* @atom:B* lj/cut 0.35 2.7 +as shorthand for specifying force field parameters for multiple atom&bond types: + bond_coeff @bond:a/A/c harmonic 533.7 120.0 + bond_coeff @bond:b/A/d harmonic 533.7 120.0 + pair_coeff @atom:A* @atom:B* lj/cut 0.35 2.7 + pair_coeff @atom:A @atom:B lj/cut 0.35 2.7 + pair_coeff @atom:A1 @atom:B1 lj/cut 0.35 2.7 + pair_coeff @atom:A1 @atom:B2 lj/cut 0.35 2.7 + pair_coeff @atom:A2 @atom:B1 lj/cut 0.35 2.7 + pair_coeff @atom:A2 @atom:B2 lj/cut 0.35 2.7 + : : : : : : +However LAMMPS does not interpret the * character this way. +Hence, this script will replace the line with the * wildcards above with the +lines text that follow above. This script also works for bond_coeff, +angle_coeff, dihedral_coeff, and improper_coeff commands (expanding wildcard +characters appearing in @bond, @angle, @dihedral, and @improper variables). + +This program expects an argument (ttree_assignments.txt) which has a list of all +of the atom types (and bond_types, and angle_types...) which have been defined +and it will substitute those variable names in place of the wildcard expressions +(The ttree_assignments.txt file is a 2-column file variables in the 1st column, + and their integer values in the 2nd column. The 2nd column is ignored.) + +The resulting list of commands with explicit variable names will be +printed to the standard-out. + +""" + + +import sys +import gc + +try: + from .ttree import ExtractFormattingCommands + from .ttree_lex import * + +except (ImportError, SystemError, ValueError): + # not installed as a package + from ttree import ExtractFormattingCommands + from ttree_lex import * + + +g_filename = __file__.split('/')[-1] +g_module_name = g_filename +if g_filename.rfind('.py') != -1: + g_module_name = g_filename[:g_filename.rfind('.py')] +g_date_str = '2018-6-09' +g_version_str = '0.2.0' +g_program_name = g_filename +#sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + + +def ExtractVarName(text): + """ Read a string like 'atom:A ' or '{/atom:A B/C/../D }ABC ' + and return ('','@atom:A',' ') or ('{','atom:A B/C/../D ','}ABC') + These are 3-tuples containing the portion of the text containing + only the variable's name (assumed to be within the text), + ...in addition to the text on either side of the variable name. + """ + i_begin = 0 + escape = '\'' + lparen = '{' + rparen = '}' + escaped = False + commenters = '#' + whitespace = ' \t\r\f\n' + terminators = whitespace + commenters + # Ideally, perhaps I should lookup these values from ttree_lex.TtreeLex to + # make sure I am being consistent, instead of re-defining them in this file. + #while ((i_begin < len(text)) and + # (text[i_begin] in whitespace)): + # i_begin += 1 + in_paren = text[i_begin:i_begin+1] == lparen + if in_paren: + terminators = rparen + i_begin += 1 + i_end = i_begin + while ((i_end < len(text)) and + (text[i_end] not in terminators)): + i_end += 1 + return (text[0: i_begin], + text[i_begin:i_end], + text[i_end:]) + + + +def main(): + try: + if (len(sys.argv) != 2): + raise InputError('Error running \"' + g_program_name + '\"\n' + ' Typical usage:\n' + ' postprocess_coeffs.py ttree_assignments.txt < file.template > file.rendered\n' + '\n' + ' Missing argument.\n' + ' Expected the name of a 2-column file containing\n' + ' variable names and their bindings (values).\n' + ' (This is likely a programmer error.\n' + ' This script was not intended to be run by end users.)\n') + + bindings_filename = sys.argv[1] + f = open(bindings_filename) + atom_types = set([]) + bond_types = set([]) + angle_types = set([]) + dihedral_types = set([]) + improper_types = set([]) + + #BasicUIReadBindingsStream(assignments, f, bindings_filename) + + # The line above is robust but it uses far too much memory. + # This for loop below works for most cases. + for line in f: + #tokens = lines.strip().split() + # like split but handles quotes + tokens = SplitQuotedString(line.strip()) + if len(tokens) < 2: + continue + if tokens[0].find('@') != 0: + continue + if tokens[0][2:].find('atom') == 0: + atom_types.add(tokens[0][1:]) + elif tokens[0][2:].find('bond') == 0: + bond_types.add(tokens[0][1:]) + elif tokens[0][2:].find('angle') == 0: + angle_types.add(tokens[0][1:]) + elif tokens[0][2:].find('dihedral') == 0: + dihedral_types.add(tokens[0][1:]) + elif tokens[0][2:].find('improper') == 0: + improper_types.add(tokens[0][1:]) + + f.close() + gc.collect() + + lex = LineLex(sys.stdin, '__standard_input_for_postprocess_coeffs__') + #lex = LineLex(open('deleteme.template', 'r'), '__standard_input_for_postprocess_coeffs_') + lex.commenters = '' #(don't attempt to skip over comments) + lex.line_extend_chars += '&' #(because LAMMPS interprets '&' as '\') + + while True: + line_orig = lex.ReadLine() + #sys.stderr.write('line_orig = \"'+str(line_orig)+'\"\n') + if (not line_orig) or (line_orig == ''): + break + tokens = line_orig.strip().split('@') + + if ((len(tokens) >= 2) and + (tokens[0].find('bond_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {})?' + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for btype in bond_types: + if MatchesPattern(btype, typepattern): + #assert(left_paren == '') + tokens[1] = btype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('angle_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for antype in angle_types: + if MatchesPattern(antype, typepattern): + #assert(left_paren == '') + tokens[1] = antype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('dihedral_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for dtype in dihedral_types: + if MatchesPattern(dtype, typepattern): + #assert(left_paren == '') + tokens[1] = dtype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + elif ((len(tokens) >= 2) and + (tokens[0].find('improper_coeff') == 0) and + #does this token contain '*' or '?' + HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + left_paren, typepattern, text_after = ExtractVarName(tokens[1]) + for itype in improper_types: + if MatchesPattern(itype, typepattern): + #assert(left_paren == '') + tokens[1] = itype + text_after + sys.stdout.write('@'.join(tokens) + '\n') + + #elif ((len(tokens) >= 3) and + # (tokens[0].find('pair_coeff') == 0) and + # (HasWildcard(tokens[1]) or HasWildcard(tokens[2]))): + elif ((len(tokens) >= 2) and + (tokens[0].find('pair_coeff') == 0)): + # First deal with cases with only one @variable, such as: + # pair_coeff @atom:A* * ... + # pair_coeff * @atom:A* ... + # (We don't deal with cases like "* *" because LAMMPS interprets + # these in a special way: manybody pair_styles use "* *") + if len(tokens) == 2: + if tokens[0].rstrip()[-1:] == '*': + tokens[0] = tokens[0].rstrip()[:-1] + tokens.insert(1, '/atom:* ') + else: + ic = tokens[1].find(' * ') + tokens.append('/atom:* '+tokens[1][ic+3:]) + tokens[1] = tokens[1][:ic]+' ' + + assert(len(tokens) >= 3) + left_paren1,typepattern1,text_after1=ExtractVarName(tokens[1]) + + # Then deal with cases like this: + # pair_coeff @{/atom:r1}*@{/atom:r3} @{/atom:r4}*@{/atom:r6} + # In this case we should be using ' ' as the delimeter, not '@' + # to separate the two arguments from eachother, since + # @{/atom:r1}*@{/atom:r3} is the first argument, and + # @{/atom:r4}*@{/atom:r6} is the second argument + + # Check: Were there any whitespace characters in the text + # separating token[1] from token[2]? + if ((left_paren1 == '{') and + (len(SplitQuotedString(text_after1)) == 1)): + # If not, then tokens[1] and tokens[2] are both part of + # the 1st argument. + tokens[1] = tokens[1]+'@'+tokens[2] + left_paren1 = '' + text_after1 = '' + typepattern1 = tokens[1] + del tokens[2] + + left_paren2,typepattern2,text_after2=ExtractVarName(tokens[2]) + # Check: Were there any whitespace characters in the text + # separating token[2] from what follows? + if ((len(tokens) > 3) and + (len(SplitQuotedString(text_after2)) == 1)): + # If not, then tokens[2] and tokens[3] are both part of + # the 2nd argument. + tokens[2] = tokens[2]+'@'+tokens[3] + left_paren2 = '' + text_after2 = '' + typepattern2 = tokens[2] + del tokens[3] + if (HasWildcard(tokens[1]) and + (tokens[1][0:1] != '{')): #(don't pattern match * in {}) + atom_types1 = atom_types + else: + atom_types1 = set([typepattern1]) + if (HasWildcard(tokens[2]) and + (tokens[2][0:1] != '{')): #(don't pattern match * in {}) + atom_types2 = atom_types + else: + atom_types2 = set([typepattern2]) + for atype1 in atom_types1: + #sys.stderr.write('atype1 = \"'+str(atype1)+'\"\n') + if MatchesPattern(atype1, typepattern1): + #assert(left_paren1 == '') + tokens[1] = left_paren1 + atype1 + text_after1 + for atype2 in atom_types2: + #sys.stderr.write(' atype2 = \"'+str(atype2)+'\"\n') + if MatchesPattern(atype2, typepattern2): + #assert(left_paren2 == '') + tokens[2] = left_paren2 + atype2 + text_after2 + sys.stdout.write('@'.join(tokens) + '\n') + else: + sys.stdout.write(line_orig) + + except (ValueError, InputError) as err: + sys.stderr.write('\n' + str(err) + '\n') + sys.exit(-1) + + return + +if __name__ == '__main__': + main() diff --git a/tools/moltemplate/moltemplate/postprocess_input_script.py b/tools/moltemplate/moltemplate/postprocess_input_script.py index b23f4e955f3129b1a7be9a0d788976e033052cd2..f237502e571f22dc98d8bde3f413b4f1566a59a2 100755 --- a/tools/moltemplate/moltemplate/postprocess_input_script.py +++ b/tools/moltemplate/moltemplate/postprocess_input_script.py @@ -1,4 +1,8 @@ #!/usr/bin/env python +# Author: Andrew Jewett (jewett.aij at g mail) +# License: 3-clause BSD License (See LICENSE.TXT) +# Copyright (c) 2017, California Institute of Technology +# All rights reserved. """ Reorder the integer arguments to the commands in a LAMMPS input diff --git a/tools/moltemplate/moltemplate/raw2data.py b/tools/moltemplate/moltemplate/raw2data.py index 8f029ee018df7a4ced7fe6a26f6b6366c2483e83..b39208a33f8e7806d69b8b3facd0036be21bf1d7 100755 --- a/tools/moltemplate/moltemplate/raw2data.py +++ b/tools/moltemplate/moltemplate/raw2data.py @@ -1,17 +1,21 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- +import sys, io + try: from .dump2data import * -except: + from .extract_lammps_data import lammps_data_sections +except (ImportError, SystemError, ValueError): # not installed as a package from dump2data import * + from extract_lammps_data import lammps_data_sections g_program_name = 'raw2data.py' g_date_str = '2016-12-21' g_version_str = 'v0.44.0' -####### Main Code Below: ####### + ####### Main Code Below: ####### def main(): sys.stderr.write(g_program_name + ' ' + g_version_str + ' ' + g_date_str) sys.stderr.write('\n') @@ -21,12 +25,64 @@ def main(): misc_settings = MiscSettings() misc_settings.multi = False + # First process any arguments which are specific to "raw2data.py" + # (and remove them before passing them to dump2data.ParseArgs()) + sort_data_file_by_atom_id = False + argv = [arg for arg in sys.argv] + i = 1 + while i < len(argv): + if argv[i].lower() == '-ignore-atom-id': + sort_data_file_by_atom_id = True + del argv[i:i+1] + if argv[i].lower() == '-sort': + sort_data_file_by_atom_id = False + del argv[i:i+1] + else: + i += 1 + #(perhaps later I'll add some additional argumets) + warning_strings = [] - ParseArgs(sys.argv, + ParseArgs(argv, misc_settings, data_settings, warning_strings) + frame_atom_order = [] + + # The atoms in the "Atoms" section of the data file might be out + # of order. Extract the text from that section, and figure out the + # atom-ID assigned to each atom (number in the first column). + # Then assign the these atom-ID numbers to entries in the + # coordinates list (frame_coords) in the same order. We want the + # lines of text in the coordinate file to pasted to the end of + # the lines of text in the "Atoms" section of the data file + # in the same order, regardless of the atom-ID numbers in that file. + # Counterintuitively, the only way to do that is to assign the same + # atom-ID numbers to the coordinate list in frame_coords". So we + # have to extract those numbers from the data file. + in_atoms_section = False + num_blank_lines = 0 + for line in data_settings.contents: + ic = line.find('#') + line = line[:ic] #(this also removes the newline character) + tokens = line.strip().split() + if line.strip() == 'Atoms': + in_atoms_section = True + elif line.strip() in lammps_data_sections: + in_atoms_section = False + elif in_atoms_section: + if len(tokens) > 0: + if sort_data_file_by_atom_id: + atomid = tokens[0] + frame_atom_order.append(atomid) + #sys.stderr.write('atomid=\"'+str(atomid)+'\"\n') + else: + frame_atom_order.append(str(len(frame_atom_order)+1)) + else: + num_blank_lines += 1 + if num_blank_lines > 1: + in_atoms_section = False + frame_coords = defaultdict(list) frame_coords_ixiyiz = defaultdict(list) frame_vects = defaultdict(list) @@ -48,8 +104,8 @@ def main(): finished_reading_frame = False read_last_frame = False - #in_coord_file = open('tmp_atom_coords.dat','r') in_coord_file = sys.stdin + #in_coord_file = open('tmp_atom_coords.dat','r') read_last_frame = False while True: @@ -61,11 +117,13 @@ def main(): if line == '': # if EOF break + #frame_vects = defaultdict(list) frame_coords = defaultdict(list) while line.strip() != '': n_crds = len(frame_coords) #sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n") - frame_coords[str(n_crds + 1)] = line.split() + frame_coords[frame_atom_order[n_crds]] = line.split() + #frame_vects[frame_atom_order[n_crds]] = ['0.0','0.0','0.0'] line = in_coord_file.readline() # Check to see if there are any blank lines at this location in the file @@ -91,6 +149,7 @@ def main(): None, misc_settings, data_settings, + None, frame_natoms, frame_coords, frame_coords_ixiyiz, diff --git a/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh b/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh index e5375674ae620a5c596ba020138d60de5ced3f67..5ffce307397941a2901f1e38c9d515b6f7a9e00a 100755 --- a/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/cleanup_moltemplate.sh @@ -1,3 +1,5 @@ +#!/usr/bin/env bash + # cleanup_moltemplate.sh # This script attempts to remove irrelevant information from LAMMPS # input scripts and data files (such as extra, unneeded atom types @@ -71,16 +73,29 @@ moltemplate.sh system.lt # This will create: "system.data" "system.in.init" "system.in.settings." - # That's it. The new "system.data" and system.in.* files should + # That's it. The new "system.data" and system.in.settings files should # be ready to run in LAMMPS. + # Special case: "set" commands + # Typically "set type" or "set atom" commands are used to assign atom charge + # If there is a "system.in.charges" file, then it contains these commands + # however the atom type numbers will be wrong, so we must rewrite it. + # Replace it with the corresponding commands from the system.in.settings + # (whose atom type numbers are correct) + if [ -f "../system.in.charges" ]; then + awk '{ if ((NF >= 5) && ($1 == "set") && ($4 == "charge")) print $0}' \ + < system.in.settings > system.in.charges + # There is no need to remove these lines from "system.in.settings", + # (because there's no harm to invoke the "set" command twice) + # ...but if you want to do that, try using a command similar to: + #sed '/set type/,+1 d' < system.in.settings > system.in.settings.tmp + #mv -f system.in.settings.tmp system.in.settings + fi + + # Now move the system.data and system.in.* files to their original location: mv -f system.data system.in.* ../ cd ../ - grep "set type" system.in.settings > system.in.charges - # now remove these lines from system.in.settings - sed '/set type/,+1 d' < system.in.settings > system.in.settings.tmp - mv -f system.in.settings.tmp system.in.settings # Finally, delete all of the temporary files we generated rm -rf new_lt_file_TMP diff --git a/tools/moltemplate/moltemplate/scripts/emoltemplate.sh b/tools/moltemplate/moltemplate/scripts/emoltemplate.sh index eaba9c4960200860ece7092c054533e19722aebc..e72d2d9e29c0dc5ede09eb52aef76eb7d965d522 100755 --- a/tools/moltemplate/moltemplate/scripts/emoltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/emoltemplate.sh @@ -10,8 +10,8 @@ # All rights reserved. G_PROGRAM_NAME="emoltemplate.sh" -G_VERSION="1.0.5" -G_DATE="2017-2-01" +G_VERSION="1.1.0" +G_DATE="2018-6-26" echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "" >&2 @@ -37,7 +37,6 @@ PY_SCR_DIR=`dirname "$0"` if [ ! -s "${PY_SCR_DIR}/ttree.py" ]; then PY_SCR_DIR="$PY_SCR_DIR/.." fi -MOLTEMPLATE_SCRIPT_DIR="$SCRIPT_DIR/../moltemplate/src" MSG_BAD_INSTALL=$(cat < "${data_atoms}.template.minimal"; then exit 4 @@ -599,7 +598,7 @@ if [ -s "${data_bond_list}.template" ]; then echo "Looking up bond types according to atom type" >&2 #-- Generate a file containing bondid bondtype atomid1 atomid2 -- - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/bonds_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/bonds_by_type.py" \ -atom-style "id type" \ -atoms "${data_atoms}.template.minimal" \ -bond-list "${data_bond_list}.template.minimal" \ @@ -641,7 +640,7 @@ if [ -s "${data_bond_list}.template" ]; then ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/bond' gen_bonds.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -659,7 +658,7 @@ if [ -s "${data_bond_list}.template" ]; then # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format.) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "${data_bonds}.template" \ > "$data_bonds"; then @@ -695,10 +694,10 @@ for FILE in "$data_angles_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Angles.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -708,7 +707,7 @@ for FILE in "$data_angles_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -721,7 +720,7 @@ for FILE in "$data_angles_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Angles" \ -sectionbytype "Angles By Type" \ @@ -767,7 +766,7 @@ for FILE in "$data_angles_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/angle' gen_angles.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -781,7 +780,7 @@ for FILE in "$data_angles_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_angles.template" \ > "$data_angles"; then @@ -815,10 +814,10 @@ for FILE in "$data_dihedrals_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Dihedrals.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -828,7 +827,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -841,7 +840,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Dihedrals" \ -sectionbytype "Dihedrals By Type" \ @@ -887,7 +886,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/dihedral' gen_dihedrals.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -901,7 +900,7 @@ for FILE in "$data_dihedrals_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_dihedrals.template" \ > "$data_dihedrals"; then @@ -938,10 +937,10 @@ for FILE in "$data_impropers_by_type"*.template; do SUBGRAPH_SCRIPT="nbody_Impropers.py" else echo "(using the rules in \"$SUBGRAPH_SCRIPT\")" >&2 - #if [ ! -s "${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then + #if [ ! -s "${PY_SCR_DIR}/nbody_alt_symmetry/$SUBGRAPH_SCRIPT" ]; then # echo "Error: File \"$SUBGRAPH_SCRIPT\" not found.\n" >&2 # echo " It should be located in this directory:\n" >&2 - # echo " ${MOLTEMPLATE_SCRIPT_DIR}/nbody_alt_symmetry/\n" >&2 + # echo " ${PY_SCR_DIR}/nbody_alt_symmetry/\n" >&2 # exit 4 #fi fi @@ -951,7 +950,7 @@ for FILE in "$data_impropers_by_type"*.template; do # The first step is to strip out the espresso-specific junk from each # section so we end up with a simple multi-column file containing only # the symbols we care about (which identify atom ids, atom and bond types) - if ! $PYTHON_COMMAND "${SCRIPT_DIR}/extract_espresso_atom_types.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/extract_espresso_atom_types.py" \ < "${data_atoms}.template" \ > "${data_atoms}.template.minimal"; then exit 4 @@ -964,7 +963,7 @@ for FILE in "$data_impropers_by_type"*.template; do < "${data_bonds}.template" \ > "${data_bonds}.template.minimal" - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_by_type.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ -section "Impropers" \ -sectionbytype "Impropers By Type" \ @@ -1012,7 +1011,7 @@ for FILE in "$data_impropers_by_type"*.template; do ## The next 2 lines extract the variable names from data_new.template.tmp ## and instert them into the appropriate place in ttree_assignments.txt ## (renumbering the relevant variable-assignments to avoid clashes). - #if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \ + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_fix_ttree_assignments.py" \ # '/improper' gen_impropers.template.tmp \ # < ttree_assignments.txt \ # > ttree_assignments.tmp; then @@ -1026,7 +1025,7 @@ for FILE in "$data_impropers_by_type"*.template; do # names present in the .template file. (We want to convert the file from # a .template format into an ordinary (numeric) LAMMPS data-section format) - if ! $PYTHON_COMMAND "${MOLTEMPLATE_SCRIPT_DIR}/ttree_render.py" \ + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ ttree_assignments.txt \ < "$data_impropers.template" \ > "$data_impropers"; then @@ -1216,7 +1215,6 @@ if [ -s "$data_atoms" ]; then cat "$data_atoms" >> "$OUT_FILE_TCL" fi - if [ -s "$tmp_atom_coords" ]; then rm -f "$OUT_FILE_COORDS" awk 'BEGIN{natom=0} {if (NF>=3) {print "part " natom " pos " $1 " " $2 " " $3; natom++}}' < "$tmp_atom_coords" >> "$OUT_FILE_TCL" diff --git a/tools/moltemplate/moltemplate/scripts/moltemplate.sh b/tools/moltemplate/moltemplate/scripts/moltemplate.sh index 870ab9c8cc8cfa41227faf52d57fbdadb2b22841..5e7fd2321c62f8fa8edd939917caa87d06e402bf 100755 --- a/tools/moltemplate/moltemplate/scripts/moltemplate.sh +++ b/tools/moltemplate/moltemplate/scripts/moltemplate.sh @@ -3,15 +3,14 @@ # # Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org -# http://jensenlab.caltech.edu # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.txt) # Copyright (c) 2012, Regents of the University of California # All rights reserved. G_PROGRAM_NAME="moltemplate.sh" -G_VERSION="2.3.7" -G_DATE="2017-8-22" +G_VERSION="2.8.6" +G_DATE="2018-6-27" echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2 echo "" >&2 @@ -223,6 +222,7 @@ $data_bonds_by_type* ${data_angles_by_type}* ${data_dihedrals_by_type}* ${data_impropers_by_type}* +$data_charge_by_bond $in_init $in_settings EOF @@ -395,6 +395,20 @@ while [ "$i" -lt "$ARGC" ]; do # Disable syntax checking by undefining LTTREE_CHECK_COMMAND unset LTTREE_CHECK_COMMAND unset LTTREE_POSTPROCESS_COMMAND + elif [ "$A" = "-allow-wildcards" ]; then + # Disable syntax checking by undefining LTTREE_CHECK_COMMAND + if [ -z "$LTTREE_CHECK_ARGS" ]; then + LTTREE_CHECK_ARGS="\"$A\"" + else + LTTREE_CHECK_ARGS="${LTTREE_CHECK_ARGS} \"$A\"" + fi + elif [ "$A" = "-forbid-wildcards" ]; then + # Disable syntax checking by undefining LTTREE_CHECK_COMMAND + if [ -z "$LTTREE_CHECK_ARGS" ]; then + LTTREE_CHECK_ARGS="\"$A\"" + else + LTTREE_CHECK_ARGS="${LTTREE_CHECK_ARGS} \"$A\"" + fi elif [ "$A" = "-checkff" ]; then # Disable syntax checking by undefining LTTREE_CHECK_COMMAND CHECKFF="$A" @@ -529,11 +543,23 @@ while [ "$i" -lt "$ARGC" ]; do fi #echo " (extracting coordinates from \"$PDB_FILE\")" >&2 if grep -q '^ATOM \|^HETATM' "$PDB_FILE"; then + # Extract the coordinates from the PDB file: + + # COMMENTING OUT ("pdbsort.py") + # I used to sort the PDB file by (ChainID,SeqNum,InsertCode) + # and then extract the coordinates from the file. + # This turned out to be inconvenient for users. Instead + # just read the coordinates in the order they appear in the file. + # OLD CODE: # Extract the coords from the "ATOM" records in the PDB file - if ! $PYTHON_COMMAND "${PY_SCR_DIR}/pdbsort.py" < "$PDB_FILE" \ - | awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then - ERR_INTERNAL - fi + #if ! $PYTHON_COMMAND "${PY_SCR_DIR}/pdbsort.py" < "$PDB_FILE" \ + # | awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then + # ERR_INTERNAL + #fi + # NEW CODE (USE THIS INSTEAD): + awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' \ + < "$PDB_FILE" \ + > "$tmp_atom_coords" else echo "$SYNTAX_MSG" >&2 echo "-----------------------" >&2 @@ -681,6 +707,7 @@ fi + OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in" OUT_FILE_INIT="${OUT_FILE_BASE}.in.init" OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings" @@ -701,16 +728,14 @@ rm -f "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_INIT" "$OUT_FILE_SETTINGS" "$OUT_FILE_ - # If checking is not disabled, then first check for common spelling errors. if [ -n "$LTTREE_CHECK_COMMAND" ]; then - if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS; then + if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS $LTTREE_CHECK_ARGS; then exit 1 fi fi - # --- Run ttree. --- # # 3, 2, 1, ... @@ -926,11 +951,12 @@ fi - +FILE_angles_by_type1="" +FILE_angles_by_type2="" #for FILE in "$data_angles_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_angles_by_type"*.template`; do +for FILE in `ls -v "$data_angles_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -964,6 +990,9 @@ for FILE in `ls -v "$data_angles_by_type"*.template`; do # fi fi + FILE_angles_by_type2="$FILE_angles_by_type1" + FILE_angles_by_type1="$FILE" + #-- Generate a file containing the list of interactions on separate lines -- if ! $PYTHON_COMMAND "${PY_SCR_DIR}/nbody_by_type.py" \ -subgraph "${SUBGRAPH_SCRIPT}" \ @@ -1033,7 +1062,7 @@ FILE_dihedrals_by_type2="" #for FILE in "$data_dihedrals_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_dihedrals_by_type"*.template`; do +for FILE in `ls -v "$data_dihedrals_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -1067,7 +1096,7 @@ for FILE in `ls -v "$data_dihedrals_by_type"*.template`; do # fi fi - FILE_dihedrals_by_type2="$FILE_impropers_by_type1" + FILE_dihedrals_by_type2="$FILE_dihedrals_by_type1" FILE_dihedrals_by_type1="$FILE" #-- Generate a file containing the list of interactions on separate lines -- @@ -1138,7 +1167,7 @@ FILE_impropers_by_type2="" #for FILE in "$data_impropers_by_type"*.template; do IFS_BACKUP="$IFS" IFS=$(echo -en "\n\b") -for FILE in `ls -v "$data_impropers_by_type"*.template`; do +for FILE in `ls -v "$data_impropers_by_type"*.template 2> /dev/null`; do if [ ! -s "$FILE" ] || [ ! -s "$data_bonds" ]; then break; # This handles with the special cases that occur when @@ -1238,6 +1267,39 @@ IFS="$IFS_BACKUP" +# Deal with wildcard characters ('*', '?') in "_coeff" commands +# appearing in any LAMMPS input scripts generated by moltemplate. +# Replace them with explicit variable names. Do this before rendering +#if [ -s "${in_settings}.template" ]; then +echo "expanding wildcards in \"_coeff\" commands" >&2 +#ls "${in_prefix}"*.template 2> /dev/null | while read file_name; do +for file_name in "${in_prefix}"*.template; do + + # invoking "postprocess_coeffs.py" can be very slow, so only do it if the + # file contains both _coeff commands and wildcards *,? on the same line: + if ! awk '{if (match($1,/'_coeff/') && match($0,/'[*,?]/')) exit 1}' < "$file_name"; then + + echo "expanding wildcards in \"_coeff\" commands in \"$file_name\"" >&2 + if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_coeffs.py" ttree_assignments.txt < "$file_name" > "${file_name}.tmp"; then + ERR_INTERNAL + fi + + mv -f "${file_name}.tmp" "$file_name" + # Now reassign integers to these variables + bn=`basename "$file_name" .template` + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/ttree_render.py" \ + ttree_assignments.txt \ + < "$file_name" \ + > "$bn"; then + exit 6 + fi + fi +done +#fi + + + + if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then echo "" >&2 @@ -1335,9 +1397,34 @@ if [ -s "${data_angles}" ]; then ERR_INTERNAL fi mv -f "${data_angles}.tmp" "${data_angles}" + + if [ ! -z $FILE_angles_by_type2 ]; then + MSG_MULTIPLE_ANGLE_RULES=$(cat <&2 + fi fi + + if [ -s "${data_dihedrals}" ]; then SUBGRAPH_SCRIPT="nbody_Dihedrals.py" if [ -n "$SUBGRAPH_SCRIPT_DIHEDRALS" ]; then @@ -1460,7 +1547,6 @@ fi - # ------------------ Charge By Bond ---------------------- # Assign atom partial charges according to who they are bonded to @@ -1508,7 +1594,6 @@ fi - # ------------------------------------------------------- rm -f "$OUT_FILE_DATA" @@ -1528,6 +1613,9 @@ NIMPROPERS="0" if [ -s "${data_atoms}" ]; then NATOMS=`awk 'END{print NR}' < "${data_atoms}"` fi +if [ -s "${data_ellipsoids}" ]; then + NELLIPSOIDS=`awk 'END{print NR}' < "${data_ellipsoids}"` +fi if [ -s "${data_bonds}" ]; then NBONDS=`awk 'END{print NR}' < "${data_bonds}"` fi @@ -1545,6 +1633,9 @@ fi echo "LAMMPS Description" > "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" echo " $NATOMS atoms" >> "$OUT_FILE_DATA" +if [ -n "$NELLIPSOIDS" ]; then + echo " $NATOMS ellipsoids" >> "$OUT_FILE_DATA" +fi if [ -n "$NBONDS" ]; then echo " $NBONDS bonds" >> "$OUT_FILE_DATA" fi @@ -1716,6 +1807,9 @@ fi echo "" >> "$OUT_FILE_DATA" + + + if [ -s "$data_masses" ]; then echo "Masses" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" @@ -1746,6 +1840,7 @@ if [ -n "$PAIR_COEFFS_IN_DATA" ]; then fi + if [ -s "$data_bond_coeffs" ]; then echo "Bond Coeffs" >> "$OUT_FILE_DATA" echo "" >> "$OUT_FILE_DATA" @@ -1992,7 +2087,7 @@ if [ -s "$tmp_atom_coords" ]; then # Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA rm -f "$OUT_FILE_COORDS" - if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/raw2data.py" $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then + if ! eval $PYTHON_COMMAND "${PY_SCR_DIR}/raw2data.py -ignore-atom-id " $ATOM_STYLE_ARG "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then ERR_INTERNAL fi mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA" @@ -2022,6 +2117,7 @@ fi + # ############## CLEAN UP ################ # A lot of files have been created along the way. @@ -2058,11 +2154,13 @@ IFS=$OIFS + # ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################ # N_data_prefix=`expr length "$data_prefix"` <-- not posix compliant. AVOID N_data_prefix=${#data_prefix} #<-- works even if $data_prefix contains spaces +#for file_name in "${data_prefix}"*; do ls "${data_prefix}"* 2> /dev/null | while read file_name; do #If using bash: #SECTION_NAME="${file_name:$N_data_prefix}" @@ -2080,6 +2178,7 @@ ls "${data_prefix}"* 2> /dev/null | while read file_name; do mv -f "$file_name" output_ttree/ done + if [ -e "$data_prefix_no_space" ]; then echo "" >> "$OUT_FILE_DATA" @@ -2098,33 +2197,37 @@ if [ -e "$OUT_FILE_DATA" ]; then fi + + + #N_in_prefix=`expr length "$in_prefix"` <-- not posix compliant. AVOID. N_in_prefix=${#in_prefix} #<-- works even if $in_prefix contains spaces +#for file_name in "${in_prefix}"*; do ls "${in_prefix}"* 2> /dev/null | while read file_name; do #If using bash: #SECTION_NAME="${file_name:$N_in_prefix}" #If using sh: #SECTION_NAME=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000` <-- not posix compliant. AVOID SECTION_NAME=`echo "" | awk "END{print substr(\"$file_name\",$((N_in_prefix+1)),1000000)}"` - FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'` + #FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'` + FILE_SUFFIX=`echo "$SECTION_NAME" | awk '{print tolower($0)}'|sed 's/ /./g'` # Create a new section in the lammps input script # matching the portion of the name of # the file after the in_prefix. - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" echo "# ----------------- $SECTION_NAME Section -----------------" >> $OUT_FILE_INPUT_SCRIPT - cp -f "$file_name" ${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX} + cp -f "$file_name" "${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}" - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" echo "include \"${OUT_FILE_INPUT_SCRIPT}.${FILE_SUFFIX}\"" >> $OUT_FILE_INPUT_SCRIPT - echo "" >> $OUT_FILE_INPUT_SCRIPT - + echo "" >> "$OUT_FILE_INPUT_SCRIPT" mv -f "$file_name" output_ttree/ done if [ -e "$in_prefix_no_space" ]; then - echo "" >> $OUT_FILE_INPUT_SCRIPT - cat "$in_prefix_no_space" >> $OUT_FILE_INPUT_SCRIPT - echo "" >> $OUT_FILE_INPUT_SCRIPT + echo "" >> "$OUT_FILE_INPUT_SCRIPT" + cat "$in_prefix_no_space" >> "$OUT_FILE_INPUT_SCRIPT" + echo "" >> "$OUT_FILE_INPUT_SCRIPT" mv -f "$in_prefix_no_space" output_ttree/ fi @@ -2145,6 +2248,7 @@ for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; ERR_INTERNAL fi echo "" >&2 + mv -f "$file_name.tmp" "$file_name" #cat "$file_name" >> input_scripts_so_far.tmp #dos2unix < "$file_name" >> input_scripts_so_far.tmp @@ -2174,13 +2278,24 @@ for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; done -ls "${in_prefix}"* 2> /dev/null | while read file_name; do +# Process any custom input script files created by the user afterwards +#ls "${OUT_FILE_INPUT_SCRIPT}"* 2> /dev/null | while read file_name; do +for file_name in "${OUT_FILE_INPUT_SCRIPT}."*; do + if [ "$file_name" = "$OUT_FILE_INIT" ] || [ $file_name = "$OUT_FILE_INPUT_SCRIPT" ] || [ $file_name = "$OUT_FILE_SETTINGS" ]; then + continue + fi + if [[ "$file_name" == *.tmp ]]; then + continue + fi + if [[ "$file_name" == *.template ]]; then + continue + fi echo "postprocessing file \"$file_name\"" >&2 - if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then + if ! $PYTHON_COMMAND "${PY_SCR_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name.tmp"; then ERR_INTERNAL fi echo "" >&2 - mv "$file_name".tmp "$file_name" + mv "$file_name.tmp" "$file_name" cat "$file_name" >> input_scripts_so_far.tmp done @@ -2188,6 +2303,7 @@ rm -f input_scripts_so_far.tmp + # ############ Optional: Add a fake run section as an example ############ diff --git a/tools/moltemplate/moltemplate/ttree.py b/tools/moltemplate/moltemplate/ttree.py index a68ada9f7539e62da4fd4fbcf5ccc99de44ce06e..89777f3bdc1153f036864c0c2269a82eb63855ea 100755 --- a/tools/moltemplate/moltemplate/ttree.py +++ b/tools/moltemplate/moltemplate/ttree.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -# Authors: Andrew Jewett (jewett.aij at g mail) +# Author: Andrew Jewett (jewett.aij at g mail) # http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) @@ -64,10 +64,10 @@ except NameError: # in words or tokens parsed by TtreeShlex. Otherwise it is identical to shlex. try: from .ttree_lex import TtreeShlex, SplitQuotedString, EscCharStrToChar, \ - SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildCard, \ + SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, HasWildcard, \ InputError, ErrorLeader, OSrcLoc, TextBlock, VarRef, VarBinding, \ TemplateLexer -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import * @@ -1519,7 +1519,7 @@ def DescrToCatLeafNodes(descr_str, elif (create_missing_nodes and ((i_last_ptkn == len(leaf_ptkns) - 1) or - HasWildCard('/'.join(leaf_ptkns)))): + HasWildcard('/'.join(leaf_ptkns)))): # elif (create_missing_nodes and # (i_last_ptkn == len(leaf_ptkns)-1)): @@ -1951,9 +1951,9 @@ class StaticObj(object): break if ((cmd_token == 'write') or - (cmd_token == 'write_once') or - (cmd_token == 'create_var') or - (cmd_token == 'replace')): + (cmd_token == 'write_once') or + (cmd_token == 'create_var') or + (cmd_token == 'replace')): open_paren = lex.get_token() #print('Parse(): open_paren=\"'+open_paren+'\"') @@ -1980,7 +1980,14 @@ class StaticObj(object): tmpl_filename = None # This means: define the template without attaching # a file name to it. (IE., don't write the contents - # of what's enclosed in the curly brackets { } to a file.) + # of what's enclosed in the curly brackets { } to a file. + # Why? + # "create_var" commands are implemented as "write() {...}" + # commands (containing one or more variables) which + # never get written to a file or the terminal. Parsing + # the contents of the curly brackets defines the variables + # inside in the same way as parsing the text inside an + # ordinary "write() {...}" command. if (cmd_token == 'replace'): tmpl_filename = "ttree_replacements.txt" @@ -4259,7 +4266,7 @@ def AutoAssignVals(cat_node, # category counter without incrementing it. var_binding.value = str(cat.counter.query()) - elif HasWildCard(var_binding.full_name): + elif HasWildcard(var_binding.full_name): # -- The wildcard hack --- # Variables containing * or ? characters in their names # are not allowed. These are not variables, but patterns @@ -4634,7 +4641,7 @@ def WriteVarBindingsFile(node): # Now omit variables whos names contain "*" or "?" # (these are actually not variables, but wildcard patterns) - if not HasWildCard(var_binding.full_name): + if not HasWildcard(var_binding.full_name): if len(var_binding.refs) > 0: usage_example = ' #' +\ ErrorLeader(var_binding.refs[0].srcloc.infile, diff --git a/tools/moltemplate/moltemplate/ttree_lex.py b/tools/moltemplate/moltemplate/ttree_lex.py index e29d4bc35b55d0bf70140cbdf2a65fbdf19a49e9..e93ca5bbd2d697c0757aa23298e848ddcf8fbf07 100644 --- a/tools/moltemplate/moltemplate/ttree_lex.py +++ b/tools/moltemplate/moltemplate/ttree_lex.py @@ -1,6 +1,7 @@ # -*- coding: iso-8859-1 -*- - +### -*- coding: utf-8 -*- # Author: Andrew Jewett (jewett.aij at g mail) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -43,7 +44,8 @@ __all__ = ["TtreeShlex", "SafelyEncodeString", "RemoveOuterQuotes", "MaxLenStr", - "HasWildCard", + "HasWildcard", + "MatchesPattern", #"IsRegex", "InputError", "ErrorLeader", @@ -93,6 +95,10 @@ class TtreeShlex(object): self.commenters = '#' self.wordchars = ('abcdfeghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_') + #if self.posix: + # self.wordchars += ('' + # '') + if self.posix: self.wordchars += ('��������������������������������' '������������������������������') @@ -650,7 +656,7 @@ def MaxLenStr(s1, s2): # """ # return (len(pat)>=2) and (pat[0]=='/') and (pat[-1] == '/') -def HasWildCard(pat): +def HasWildcard(pat): """ Returns true if a string (pat) contains a '*' or '?' character. @@ -658,7 +664,7 @@ def HasWildCard(pat): return (pat.find('*') != -1) or (pat.find('?') != -1) -# def HasWildCard(pat): +# def HasWildcard(pat): # """ # Returns true if a string (pat) contains a non-backslash-protected # * or ? character. @@ -693,7 +699,7 @@ def MatchesPattern(s, pattern): # return False # new code: # uses precompiled regular expressions (See "pattern.search" below) - if HasWildCard(pattern): + if HasWildcard(pattern): if not fnmatch.fnmatchcase(s, pattern): return False elif s != pattern: @@ -1194,7 +1200,10 @@ def SplitTemplate(ltmpl, delim, delete_blanks=False): token_ltmpl = [] i = 0 while i < len(ltmpl): + entry = ltmpl[i] + #sys.stderr.write('ltmpl['+str(i)+'] = '+str(entry)+'\n') + if isinstance(entry, TextBlock): # if hasattr(entry, 'text'): prev_src_loc = entry.srcloc diff --git a/tools/moltemplate/moltemplate/ttree_matrix_stack.py b/tools/moltemplate/moltemplate/ttree_matrix_stack.py index 9c45fdc48004df95079b345d888516a2b9c3158e..ba69cf7de7f1bf4b37ec37ee537df2f84795c3f3 100644 --- a/tools/moltemplate/moltemplate/ttree_matrix_stack.py +++ b/tools/moltemplate/moltemplate/ttree_matrix_stack.py @@ -1,4 +1,5 @@ # Author: Andrew Jewett (jewett.aij@gmail.com) +# http://www.moltemplate.org # http://www.chem.ucsb.edu/~sheagroup # License: 3-clause BSD License (See LICENSE.TXT) # Copyright (c) 2012, Regents of the University of California @@ -8,12 +9,19 @@ import random, math from collections import deque from array import array +#try: +# from StringIO import StringIO +#except ImportError: +# from io import StringIO + try: from .ttree_lex import InputError, ErrorLeader, OSrcLoc -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree_lex import InputError, ErrorLeader, OSrcLoc + + def MultMat(dest, A, B): """ Multiply two matrices together. Store result in "dest". @@ -27,6 +35,21 @@ def MultMat(dest, A, B): for k in range(0, K): dest[i][j] += A[i][k] * B[k][j] +def Transpose(M): + return [ [M[j][i] for j in range(0, len(M))] + for i in range(0, len(M[0])) ] + + +def TransposeInPlace(M): + N = len(M) + for i in range(0, N): + for j in range(0, i): + M_ij = M[i][j] + M_ji = M[j][i] + M[i][j] = M_ji + M[j][i] = M_ij + + def MatToStr(M): strs = [] @@ -381,6 +404,51 @@ class AffineStack(object): AffineCompose(Mtmp, moveCentBack, Mdest) CopyMat(Mdest, Mtmp) + elif ((transform_str.find('quat(') == 0) or + (transform_str.find('quatT(') == 0)): + i_paren_close = transform_str.find(')') + if i_paren_close == -1: + i_paren_close = len(transform_str) + args = transform_str[5:i_paren_close].split(',') + center_v = None + if (len(args) == 7): + center_v = [float(args[4]), float(args[5]), float(args[6])] + elif (len(args) != 4): + raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + ' Invalid command: \"' + transform_str + '\"\n' + ' This command requires either 4 or 7 numerical arguments. Either:\n' + ' rot(angle, axisX, axisY, axiZ) or \n' + ' rot(angle, axisX, axisY, axiZ, centerX, centerY, centerZ)') + M[0][3] = 0.0 # RotMatAXYZ() only modifies 3x3 submatrix of M + M[1][3] = 0.0 # The remaining final column must be zeroed by hand + M[2][3] = 0.0 + q = (float(args[0]), + float(args[1]), + float(args[2]), + float(args[3])) + Quaternion2Matrix(q, M) + if (transform_str.find('quatT(') == 0): + TransposeInPlace(M) + if (center_v == None): + AffineCompose(Mtmp, M, Mdest) + CopyMat(Mdest, Mtmp) + else: + # Move "center_v" to the origin + moveCentToOrig = [[1.0, 0.0, 0.0, -center_v[0]], + [0.0, 1.0, 0.0, -center_v[1]], + [0.0, 0.0, 1.0, -center_v[2]]] + AffineCompose(Mtmp, moveCentToOrig, Mdest) + CopyMat(Mdest, Mtmp) + # Rotate the coordinates (relative to the origin) + AffineCompose(Mtmp, M, Mdest) # M is the rotation matrix + CopyMat(Mdest, Mtmp) + # Move the origin back to center_v + moveCentBack = [[1.0, 0.0, 0.0, center_v[0]], + [0.0, 1.0, 0.0, center_v[1]], + [0.0, 0.0, 1.0, center_v[2]]] + AffineCompose(Mtmp, moveCentBack, Mdest) + CopyMat(Mdest, Mtmp) + # # elif transform_str.find('rotcm(') == 0: # # assert(xcm != None) # # i_paren_close = transform_str.find(')') @@ -585,6 +653,34 @@ class AffineStack(object): # # AffineCompose(Mtmp, moveCmBack, Mdest) # # CopyMat(Mdest, Mtmp) + #elif transform_str.find('read_xyz(') == 0: + # i_paren_close = transform_str.find(')') + # if i_paren_close == -1: + # i_paren_close = len(transform_str) + # args = transform_str[4:i_paren_close].split(',') + # if (len(args) != 1): + # raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + # ' Invalid command: \"' + transform_str + '\"\n' + # ' This command expects the name of a file in XYZ format.\n') + # file_name = args[0] + # if (not file_name in coord_files): + # f = open(file_name, 'r') + # f.close() + # f.readline() # skip the first 2 lines + # f.readline() # of an .xyz file (header) + # for line in f: + # tokens = line.split() + # if (len(tokens) != 3) and (len(tokens) != 0): + # raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' + # ' Invalid command: \"' + transform_str + '\"\n' + # ' This command expects the name of a file in XYZ format.\n') + # crds.append((float(tokens[0]), + # float(tokens[1]), + # float(tokens[2])) + # self.coord_files[file_name] = crds + # else: + # crds = self.coord_files[file_name] + else: raise InputError('Error near ' + ErrorLeader(src_loc.infile, src_loc.lineno) + ':\n' ' Unknown transformation command: \"' + transform_str + '\"\n') @@ -601,6 +697,7 @@ class MultiAffineStack(object): self.stacks = None self.M = None self.error_if_substack_empty = False + self.coord_files = {} self.Clear() def Clear(self): @@ -610,6 +707,7 @@ class MultiAffineStack(object): self.stacks = deque([]) self.M = self.tot_stack.M self.error_if_substack_empty = False + self.coord_files = {} def _Update(self): self.tot_stack.Clear() @@ -793,6 +891,70 @@ def RotMatAXYZ(dest, angle, axis_x, axis_y, axis_z): # RotMatAXYZ(r, 90.0, 0.0, 0.0, 1.0) +def Quaternion2Matrix(q, M): + "convert a quaternion (q) to a 3x3 rotation matrix (M)""" + + M[0][0] = (q[0]*q[0])-(q[1]*q[1])-(q[2]*q[2])+(q[3]*q[3]) + M[1][1] = -(q[0]*q[0])+(q[1]*q[1])-(q[2]*q[2])+(q[3]*q[3]) + M[2][2] = -(q[0]*q[0])-(q[1]*q[1])+(q[2]*q[2])+(q[3]*q[3]) + M[0][1] = 2*(q[0]*q[1] - q[2]*q[3]); + M[1][0] = 2*(q[0]*q[1] + q[2]*q[3]); + M[1][2] = 2*(q[1]*q[2] - q[0]*q[3]); + M[2][1] = 2*(q[1]*q[2] + q[0]*q[3]); + M[0][2] = 2*(q[0]*q[2] + q[1]*q[3]); + M[2][0] = 2*(q[0]*q[2] - q[1]*q[3]); + + + +def Matrix2Quaternion(M, q): + """convert a 3x3 rotation matrix (M) to a quaternion (q) + http://www.euclideanspace.com/maths/geometry/rotations/conversions/matrixToQuaternion/ + """ + tr = M[0][0] + M[1][1] + M[2][2] + if tr > 0: + S = math.sqrt(tr+1.0) * 2 # S=4*qw + qw = 0.25 * S + qx = (M[2][1] - M[1][2]) / S + qy = (M[0][2] - M[2][0]) / S + qz = (M[1][0] - M[0][1]) / S + elif (M[0][0] > M[1][1]) and (M[0][0] > M[2][2]): + S = math.sqrt(1.0 + M[0][0] - M[1][1] - M[2][2]) * 2 # S=4*qx + qw = (M[2][1] - M[1][2]) / S + qx = 0.25 * S + qy = (M[0][1] + M[1][0]) / S + qz = (M[0][2] + M[2][0]) / S + elif (M[1][1] > M[2][2]): + S = math.sqrt(1.0 + M[1][1] - M[0][0] - M[2][2]) * 2 # S=4*qy + qw = (M[0][2] - M[2][0]) / S + qx = (M[0][1] + M[1][0]) / S + qy = 0.25 * S + qz = (M[1][2] + M[2][1]) / S + else: + S = math.sqrt(1.0 + M[2][2] - M[0][0] - M[1][1]) * 2 # S=4*qz + qw = (M[1][0] - M[0][1]) / S + qx = (M[0][2] + M[2][0]) / S + qy = (M[1][2] + M[2][1]) / S + qz = 0.25 * S + q[0] = qw + q[1] = qx + q[2] = qy + q[3] = qz + + +def MultQuat(dest, q1, q2): + """ multiply 2 quaternions and store the result in "qdest" + (q1[0] + i*q1[1] + j*q1[2] + k*q1[3]) + * + (q2[0] + i*q2[1] + j*q3[2] + k*q3[3]) + https://en.wikipedia.org/wiki/Quaternion#Hamilton_product + """ + dest[0] = q1[0]*q2[0] - q1[1]*q2[1] - q1[2]*q2[2] - q1[3]*q2[3] + dest[1] = q1[0]*q2[1] + q1[1]*q2[0] + q1[2]*q2[3] - q1[3]*q2[2] + dest[2] = q1[0]*q2[2] - q1[1]*q2[3] + q1[2]*q2[0] + q1[3]*q2[1] + dest[3] = q1[0]*q2[3] + q1[1]*q2[2] - q1[2]*q2[1] + q1[3]*q2[0] + + + def CrossProd(dest, A, B): dest[0] = (A[1] * B[2] - B[1] * A[2]) dest[1] = (A[2] * B[0] - B[2] * A[0]) diff --git a/tools/moltemplate/moltemplate/ttree_render.py b/tools/moltemplate/moltemplate/ttree_render.py index f59a04aeb52fa2915f3a576ea42626aa6e61470a..15b26a2e70f53d6ccf6873e264613c0af75522ad 100755 --- a/tools/moltemplate/moltemplate/ttree_render.py +++ b/tools/moltemplate/moltemplate/ttree_render.py @@ -21,7 +21,7 @@ import gc try: from .ttree import ExtractFormattingCommands from .ttree_lex import SplitQuotedString, InputError, TemplateLexer -except (SystemError, ValueError): +except (ImportError, SystemError, ValueError): # not installed as a package from ttree import ExtractFormattingCommands from ttree_lex import SplitQuotedString, InputError, TemplateLexer @@ -31,11 +31,14 @@ g_filename = __file__.split('/')[-1] g_module_name = g_filename if g_filename.rfind('.py') != -1: g_module_name = g_filename[:g_filename.rfind('.py')] -g_date_str = '2016-12-21' -g_version_str = '0.2.0' +g_date_str = '2017-11-04' +g_version_str = '0.2.2' g_program_name = g_filename #sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') + + + def main(): try: if (len(sys.argv) != 2): @@ -79,21 +82,43 @@ def main(): assert(isinstance(entry, str)) if ((len(entry) > 1) and (entry[0] in lex.var_delim)): + + if ((len(entry) >= 3) and + (entry[1] == '{') and + (entry[-1] == '}')): + entry = entry[0] + entry[2:-1] + if '.' in entry: ic = entry.find('.') var_name = entry[:ic] var_suffix = entry[ic:] + if not var_suffix[0:7] in ('.ljust(', '.rjust('): + var_name = entry + var_suffix = '' else: var_name = entry var_suffix = '' - var_name = entry if var_name not in assignments: - raise(InputError('Error(' + g_program_name + ')' - #' at '+ErrorLeader(var_ref.src_loc.infile, - # var_ref.src_loc.lineno)+ - ' unknown variable:\n' - ' \"' + var_name + '\"\n')) + #COMMENTING OUT: + #raise(InputError('Error(' + g_program_name + ')' + # #' at '+ErrorLeader(var_ref.src_loc.infile, + # # var_ref.src_loc.lineno)+ + # ' unknown variable:\n' + # ' \"' + var_name + '\"\n')) + # ...actually don't raise an error message: + # Actually there are some legitimate reaons this could occur. + # Some users want to put LAMMPS-style variables in the + # write_once() {...} text blocks in their moltemplate files. + # Variables in both LAMMPS and moltemplate contain $ characters, + # and this script gets confused. Better to just ignore it + # when this happens instead of printing an error message. + # Just leave the text alone and print the variable name. + # + # Do this by substituting the variable's name as it's value: + + var_value = var_name + else: var_value = assignments[var_name] diff --git a/tools/moltemplate/setup.py b/tools/moltemplate/setup.py index 30e835de0c649e97c1e4df9d691364091db034bf..925850a49e158519c1f5bcfe5b748469cae27344 100644 --- a/tools/moltemplate/setup.py +++ b/tools/moltemplate/setup.py @@ -4,7 +4,12 @@ setup( name='moltemplate', - packages=['moltemplate', 'moltemplate/nbody_alt_symmetry'], + packages=['moltemplate', + 'moltemplate.nbody_alt_symmetry'], + + package_dir={'moltemplate': 'moltemplate'}, #.py files are in "moltemplate/" + + package_data={'moltemplate': ['force_fields/*.lt']}, #.lt files are in "moltemplate/force_fields/" description='A general cross-platform text-based molecule builder for LAMMPS', @@ -14,9 +19,9 @@ setup( url='https://github.com/jewettaij/moltemplate', - download_url='https://github.com/jewettaij/moltemplate/archive/v2.3.7.zip', + download_url='https://github.com/jewettaij/moltemplate/archive/v2.8.6.zip', - version='2.3.7', + version='2.8.6', keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder', 'ESPResSo'], @@ -32,7 +37,13 @@ setup( 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX :: Linux', - 'Operating System :: Microsoft :: Windows'], + 'Operating System :: Microsoft :: Windows', + 'Programming Language :: Python', + 'Programming Language :: Unix Shell', + 'Topic :: Scientific/Engineering :: Chemistry', + 'Topic :: Scientific/Engineering :: Physics', + 'Topic :: Multimedia :: Graphics :: 3D Modeling', + 'Intended Audience :: Science/Research'], scripts=['moltemplate/scripts/moltemplate.sh', 'moltemplate/scripts/cleanup_moltemplate.sh', @@ -58,13 +69,13 @@ setup( 'nbody_reorder_atoms.py=moltemplate.nbody_reorder_atoms:main', 'pdbsort.py=moltemplate.pdbsort:main', 'postprocess_input_script.py=moltemplate.postprocess_input_script:main', + 'postprocess_coeffs.py=moltemplate.postprocess_coeffs:main', 'raw2data.py=moltemplate.raw2data:main', 'remove_duplicate_atoms.py=moltemplate.remove_duplicate_atoms:main', 'remove_duplicates_nbody.py=moltemplate.remove_duplicates_nbody:main', 'renumber_DATA_first_column.py=moltemplate.renumber_DATA_first_column:main']}, - package_data={'moltemplate': ['force_fields/*.lt']}, - # install_requires=['numpy', 'scipy', 'biopython'], + # install_requires=['numpy', 'scipy'], setup_requires=['pytest-runner'], tests_require=['pytest'], zip_safe=True,